Starting phenix.real_space_refine on Thu Sep 18 05:36:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xen_38294/09_2025/8xen_38294_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xen_38294/09_2025/8xen_38294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xen_38294/09_2025/8xen_38294_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xen_38294/09_2025/8xen_38294_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xen_38294/09_2025/8xen_38294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xen_38294/09_2025/8xen_38294.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 94 5.16 5 C 7356 2.51 5 N 2003 2.21 5 O 2300 1.98 5 H 2606 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14359 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 8804 Classifications: {'peptide': 928} Link IDs: {'PCIS': 4, 'PTRANS': 42, 'TRANS': 881} Chain breaks: 1 Chain: "B" Number of atoms: 5555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 5555 Classifications: {'peptide': 593} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 564} Chain breaks: 2 Time building chain proxies: 3.07, per 1000 atoms: 0.21 Number of scatterers: 14359 At special positions: 0 Unit cell: (67.32, 102.3, 232.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 O 2300 8.00 N 2003 7.00 C 7356 6.00 H 2606 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 502 " distance=2.02 Simple disulfide: pdb=" SG CYS A 508 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 626 " - pdb=" SG CYS A 632 " distance=2.03 Simple disulfide: pdb=" SG CYS A 698 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A 852 " - pdb=" SG CYS A 914 " distance=2.03 Simple disulfide: pdb=" SG CYS A 904 " - pdb=" SG CYS A 909 " distance=2.03 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 39 " - pdb=" SG CYS B 461 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 64 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 459 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 497 " distance=2.03 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 521 " - pdb=" SG CYS B 532 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 547 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 554 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 562 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 575 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 586 " - pdb=" SG CYS B 609 " distance=2.03 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 607 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 612 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 624 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 575.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2802 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 27 sheets defined 14.3% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.697A pdb=" N PHE A 247 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 530 through 534 Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 798 through 802 Processing helix chain 'A' and resid 935 through 940 Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 39 through 46 removed outlier: 4.157A pdb=" N SER B 46 " --> pdb=" O CYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 73 Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.626A pdb=" N ILE B 80 " --> pdb=" O PRO B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 197 through 205 Proline residue: B 202 - end of helix removed outlier: 4.338A pdb=" N ASP B 205 " --> pdb=" O PRO B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 235 removed outlier: 3.934A pdb=" N PHE B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 258 removed outlier: 3.730A pdb=" N ALA B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.699A pdb=" N ARG B 287 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 removed outlier: 3.665A pdb=" N SER B 310 " --> pdb=" O TYR B 307 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR B 311 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 328 Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 365 through 378 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 474 through 478 Processing helix chain 'B' and resid 519 through 523 removed outlier: 3.519A pdb=" N SER B 522 " --> pdb=" O PRO B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 193 removed outlier: 3.880A pdb=" N SER A 190 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 255 through 259 removed outlier: 4.166A pdb=" N SER A 255 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 283 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN A 296 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A 285 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 310 through 313 Processing sheet with id=AA7, first strand: chain 'A' and resid 331 through 333 Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 378 removed outlier: 6.540A pdb=" N ILE A 374 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA A 391 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA A 389 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY A 378 " --> pdb=" O ASP A 387 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378 removed outlier: 6.540A pdb=" N ILE A 374 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA A 391 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA A 389 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY A 378 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A 419 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 489 through 492 removed outlier: 6.854A pdb=" N LYS A 489 " --> pdb=" O CYS A 502 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N CYS A 502 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 489 through 492 removed outlier: 6.854A pdb=" N LYS A 489 " --> pdb=" O CYS A 502 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N CYS A 502 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 483 through 484 removed outlier: 3.553A pdb=" N ILE A 585 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 636 through 642 removed outlier: 7.544A pdb=" N GLY A 726 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N VAL A 686 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARG A 728 " --> pdb=" O ILE A 684 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.256A pdb=" N ILE A 647 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG A 707 " --> pdb=" O ILE A 677 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 772 through 779 removed outlier: 6.847A pdb=" N ILE A 926 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE A 846 " --> pdb=" O ILE A 926 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR A 928 " --> pdb=" O TYR A 844 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR A 844 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS A 930 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 782 through 785 removed outlier: 4.162A pdb=" N ILE A 971 " --> pdb=" O VAL A 958 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN A 973 " --> pdb=" O PHE A 956 " (cutoff:3.500A) removed outlier: 13.510A pdb=" N SER A 949 " --> pdb=" O LYS A 832 " (cutoff:3.500A) removed outlier: 12.702A pdb=" N LYS A 832 " --> pdb=" O SER A 949 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LYS A 951 " --> pdb=" O PRO A 830 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 953 " --> pdb=" O GLN A 828 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS A 822 " --> pdb=" O ILE A 959 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN A 908 " --> pdb=" O TYR A 831 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 836 through 837 removed outlier: 6.567A pdb=" N LYS A 822 " --> pdb=" O ILE A 959 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 953 " --> pdb=" O GLN A 828 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LYS A 951 " --> pdb=" O PRO A 830 " (cutoff:3.500A) removed outlier: 12.702A pdb=" N LYS A 832 " --> pdb=" O SER A 949 " (cutoff:3.500A) removed outlier: 13.510A pdb=" N SER A 949 " --> pdb=" O LYS A 832 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N HIS A 900 " --> pdb=" O SER A 949 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LYS A 951 " --> pdb=" O HIS A 900 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 902 " --> pdb=" O LYS A 951 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N SER A 953 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AC1, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AC2, first strand: chain 'B' and resid 109 through 110 removed outlier: 3.866A pdb=" N SER B 422 " --> pdb=" O THR B 399 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 216 through 223 removed outlier: 6.636A pdb=" N PHE B 179 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N THR B 221 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE B 177 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR B 223 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU B 175 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP B 139 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 273 " --> pdb=" O ASP B 139 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR B 141 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR B 275 " --> pdb=" O TYR B 141 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU B 143 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS B 270 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE B 333 " --> pdb=" O HIS B 270 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 272 " --> pdb=" O ILE B 333 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA B 335 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N PHE B 274 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR B 337 " --> pdb=" O PHE B 274 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N THR B 276 " --> pdb=" O THR B 337 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 332 " --> pdb=" O THR B 355 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N GLY B 357 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE B 334 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU B 359 " --> pdb=" O PHE B 334 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL B 336 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 525 through 528 removed outlier: 3.675A pdb=" N GLU B 526 " --> pdb=" O VAL B 533 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 536 through 537 Processing sheet with id=AC6, first strand: chain 'B' and resid 556 through 557 Processing sheet with id=AC7, first strand: chain 'B' and resid 566 through 569 Processing sheet with id=AC8, first strand: chain 'B' and resid 579 through 580 Processing sheet with id=AC9, first strand: chain 'B' and resid 605 through 608 395 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 2606 1.02 - 1.22: 0 1.22 - 1.42: 5031 1.42 - 1.62: 6834 1.62 - 1.82: 125 Bond restraints: 14596 Sorted by residual: bond pdb=" NE ARG B 505 " pdb=" HE ARG B 505 " ideal model delta sigma weight residual 0.860 0.969 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" CB PRO B 490 " pdb=" CG PRO B 490 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.45e+00 bond pdb=" N ASN B 29 " pdb=" CA ASN B 29 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N PHE A 31 " pdb=" CA PHE A 31 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.60e+00 bond pdb=" CB PRO A 549 " pdb=" CG PRO A 549 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.33e+00 ... (remaining 14591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 20711 2.26 - 4.52: 181 4.52 - 6.77: 15 6.77 - 9.03: 0 9.03 - 11.29: 1 Bond angle restraints: 20908 Sorted by residual: angle pdb=" CA PRO B 490 " pdb=" N PRO B 490 " pdb=" CD PRO B 490 " ideal model delta sigma weight residual 112.00 106.63 5.37 1.40e+00 5.10e-01 1.47e+01 angle pdb=" N GLN B 508 " pdb=" CA GLN B 508 " pdb=" C GLN B 508 " ideal model delta sigma weight residual 113.18 108.57 4.61 1.21e+00 6.83e-01 1.45e+01 angle pdb=" CB MET B 594 " pdb=" CG MET B 594 " pdb=" SD MET B 594 " ideal model delta sigma weight residual 112.70 123.99 -11.29 3.00e+00 1.11e-01 1.42e+01 angle pdb=" N ALA A 907 " pdb=" CA ALA A 907 " pdb=" C ALA A 907 " ideal model delta sigma weight residual 109.24 114.47 -5.23 1.51e+00 4.39e-01 1.20e+01 angle pdb=" N ASP A 178 " pdb=" CA ASP A 178 " pdb=" C ASP A 178 " ideal model delta sigma weight residual 108.34 112.77 -4.43 1.31e+00 5.83e-01 1.14e+01 ... (remaining 20903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 8612 17.75 - 35.50: 568 35.50 - 53.26: 131 53.26 - 71.01: 40 71.01 - 88.76: 13 Dihedral angle restraints: 9364 sinusoidal: 4953 harmonic: 4411 Sorted by residual: dihedral pdb=" CB CYS B 400 " pdb=" SG CYS B 400 " pdb=" SG CYS B 412 " pdb=" CB CYS B 412 " ideal model delta sinusoidal sigma weight residual -86.00 -153.80 67.80 1 1.00e+01 1.00e-02 5.97e+01 dihedral pdb=" CA ASP A 176 " pdb=" C ASP A 176 " pdb=" N ILE A 177 " pdb=" CA ILE A 177 " ideal model delta harmonic sigma weight residual 180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA HIS A 143 " pdb=" C HIS A 143 " pdb=" N TRP A 144 " pdb=" CA TRP A 144 " ideal model delta harmonic sigma weight residual -180.00 -153.94 -26.06 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 9361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1142 0.034 - 0.069: 449 0.069 - 0.103: 106 0.103 - 0.138: 82 0.138 - 0.172: 5 Chirality restraints: 1784 Sorted by residual: chirality pdb=" CA PRO A 549 " pdb=" N PRO A 549 " pdb=" C PRO A 549 " pdb=" CB PRO A 549 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.42e-01 chirality pdb=" CB ILE B 417 " pdb=" CA ILE B 417 " pdb=" CG1 ILE B 417 " pdb=" CG2 ILE B 417 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA ILE B 291 " pdb=" N ILE B 291 " pdb=" C ILE B 291 " pdb=" CB ILE B 291 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1781 not shown) Planarity restraints: 3588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 509 " 0.238 2.00e-02 2.50e+03 3.50e-01 1.84e+03 pdb=" CD GLN B 509 " -0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN B 509 " -0.228 2.00e-02 2.50e+03 pdb=" NE2 GLN B 509 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN B 509 " -0.554 2.00e-02 2.50e+03 pdb="HE22 GLN B 509 " 0.566 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 548 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 549 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 549 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 549 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 508 " 0.033 2.00e-02 2.50e+03 3.66e-02 2.01e+01 pdb=" CD GLN B 508 " 0.002 2.00e-02 2.50e+03 pdb=" OE1 GLN B 508 " -0.034 2.00e-02 2.50e+03 pdb=" NE2 GLN B 508 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 508 " 0.053 2.00e-02 2.50e+03 pdb="HE22 GLN B 508 " -0.055 2.00e-02 2.50e+03 ... (remaining 3585 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 303 2.06 - 2.70: 7074 2.70 - 3.33: 24132 3.33 - 3.97: 33231 3.97 - 4.60: 48534 Nonbonded interactions: 113274 Sorted by model distance: nonbonded pdb=" O ARG A 579 " pdb=" HE ARG A 579 " model vdw 1.428 2.450 nonbonded pdb=" O ASP A 178 " pdb=" H GLY A 181 " model vdw 1.468 2.450 nonbonded pdb=" OE2 GLU B 435 " pdb=" H GLU B 437 " model vdw 1.496 2.450 nonbonded pdb=" OD2 ASP A 114 " pdb="HH21 ARG A 145 " model vdw 1.555 2.450 nonbonded pdb=" O VAL A 802 " pdb=" HG1 THR A 935 " model vdw 1.569 2.450 ... (remaining 113269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.930 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 12020 Z= 0.198 Angle : 0.632 11.288 16300 Z= 0.362 Chirality : 0.044 0.172 1784 Planarity : 0.005 0.114 2146 Dihedral : 13.686 88.759 4436 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.29 % Favored : 94.51 % Rotamer: Outliers : 0.31 % Allowed : 6.56 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.22), residues: 1511 helix: -1.40 (0.45), residues: 129 sheet: 0.17 (0.23), residues: 507 loop : -0.62 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 34 TYR 0.013 0.001 TYR B 142 PHE 0.013 0.001 PHE A 184 TRP 0.019 0.002 TRP A 144 HIS 0.004 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00444 (11990) covalent geometry : angle 0.63199 (16240) SS BOND : bond 0.00185 ( 30) SS BOND : angle 0.58993 ( 60) hydrogen bonds : bond 0.21713 ( 380) hydrogen bonds : angle 9.58151 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue LEU 624 is missing expected H atoms. Skipping. Residue VAL 631 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue VAL 638 is missing expected H atoms. Skipping. Residue VAL 640 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue ILE 649 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue THR 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue ALA 668 is missing expected H atoms. Skipping. Residue ALA 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue ILE 674 is missing expected H atoms. Skipping. Residue VAL 675 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ALA 681 is missing expected H atoms. Skipping. Residue ILE 684 is missing expected H atoms. Skipping. Residue VAL 686 is missing expected H atoms. Skipping. Residue VAL 687 is missing expected H atoms. Skipping. Residue ALA 692 is missing expected H atoms. Skipping. Residue LEU 693 is missing expected H atoms. Skipping. Residue ALA 694 is missing expected H atoms. Skipping. Residue LEU 696 is missing expected H atoms. Skipping. Residue ALA 699 is missing expected H atoms. Skipping. Residue THR 702 is missing expected H atoms. Skipping. Residue THR 706 is missing expected H atoms. Skipping. Residue VAL 709 is missing expected H atoms. Skipping. Residue VAL 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue ALA 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue ALA 725 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue VAL 731 is missing expected H atoms. Skipping. Residue MET 737 is missing expected H atoms. Skipping. Residue THR 739 is missing expected H atoms. Skipping. Residue VAL 741 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue ILE 747 is missing expected H atoms. Skipping. Residue LEU 752 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue VAL 759 is missing expected H atoms. Skipping. Residue VAL 760 is missing expected H atoms. Skipping. Residue VAL 764 is missing expected H atoms. Skipping. Residue LEU 766 is missing expected H atoms. Skipping. Residue ALA 767 is missing expected H atoms. Skipping. Residue VAL 768 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue ALA 770 is missing expected H atoms. Skipping. Residue ALA 771 is missing expected H atoms. Skipping. Residue VAL 772 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue VAL 777 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue THR 798 is missing expected H atoms. Skipping. Residue VAL 802 is missing expected H atoms. Skipping. Residue VAL 805 is missing expected H atoms. Skipping. Residue VAL 806 is missing expected H atoms. Skipping. Residue ILE 809 is missing expected H atoms. Skipping. Residue LEU 812 is missing expected H atoms. Skipping. Residue ALA 823 is missing expected H atoms. Skipping. Residue MET 824 is missing expected H atoms. Skipping. Residue LEU 825 is missing expected H atoms. Skipping. Residue LEU 827 is missing expected H atoms. Skipping. Residue THR 837 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue LEU 839 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue LEU 842 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue MET 850 is missing expected H atoms. Skipping. Residue THR 853 is missing expected H atoms. Skipping. Residue MET 856 is missing expected H atoms. Skipping. Residue ILE 858 is missing expected H atoms. Skipping. Residue LEU 861 is missing expected H atoms. Skipping. Residue ILE 863 is missing expected H atoms. Skipping. Residue ILE 865 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue THR 901 is missing expected H atoms. Skipping. Residue LEU 902 is missing expected H atoms. Skipping. Residue VAL 906 is missing expected H atoms. Skipping. Residue ALA 907 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue ILE 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue VAL 916 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue ALA 925 is missing expected H atoms. Skipping. Residue ILE 926 is missing expected H atoms. Skipping. Residue LEU 927 is missing expected H atoms. Skipping. Residue VAL 929 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue LEU 933 is missing expected H atoms. Skipping. Residue THR 935 is missing expected H atoms. Skipping. Residue THR 937 is missing expected H atoms. Skipping. Residue MET 939 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue ALA 954 is missing expected H atoms. Skipping. Residue VAL 958 is missing expected H atoms. Skipping. Residue ILE 959 is missing expected H atoms. Skipping. Residue LEU 966 is missing expected H atoms. Skipping. Residue ILE 968 is missing expected H atoms. Skipping. Residue ILE 971 is missing expected H atoms. Skipping. Residue THR 972 is missing expected H atoms. Skipping. Residue THR 975 is missing expected H atoms. Skipping. Residue LEU 976 is missing expected H atoms. Skipping. Residue VAL 977 is missing expected H atoms. Skipping. Residue THR 978 is missing expected H atoms. Skipping. Residue THR 979 is missing expected H atoms. Skipping. Residue VAL 981 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue ALA 988 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue VAL 520 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue VAL 533 is missing expected H atoms. Skipping. Residue ILE 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue VAL 555 is missing expected H atoms. Skipping. Residue MET 561 is missing expected H atoms. Skipping. Residue LEU 574 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 587 is missing expected H atoms. Skipping. Residue THR 588 is missing expected H atoms. Skipping. Residue THR 590 is missing expected H atoms. Skipping. Residue THR 592 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue ILE 615 is missing expected H atoms. Skipping. Residue THR 623 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.6092 (mtp) cc_final: 0.5713 (mtt) REVERT: A 762 HIS cc_start: 0.4069 (t70) cc_final: 0.3061 (t-90) REVERT: B 505 ARG cc_start: 0.6178 (OUTLIER) cc_final: 0.5143 (ptm160) REVERT: B 594 MET cc_start: 0.4902 (ppp) cc_final: 0.4665 (ppp) outliers start: 4 outliers final: 2 residues processed: 57 average time/residue: 0.1684 time to fit residues: 13.6328 Evaluate side-chains 52 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain B residue 505 ARG Chi-restraints excluded: chain B residue 546 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 40.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 GLN ** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.129369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.085060 restraints weight = 46967.775| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.39 r_work: 0.3154 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 12020 Z= 0.166 Angle : 0.529 6.838 16300 Z= 0.284 Chirality : 0.044 0.212 1784 Planarity : 0.005 0.114 2146 Dihedral : 5.171 38.664 1644 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.63 % Favored : 95.23 % Rotamer: Outliers : 0.84 % Allowed : 7.10 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.22), residues: 1511 helix: -0.63 (0.47), residues: 111 sheet: -0.05 (0.23), residues: 532 loop : -0.54 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 145 TYR 0.011 0.001 TYR B 136 PHE 0.013 0.001 PHE A 49 TRP 0.020 0.001 TRP A 144 HIS 0.005 0.001 HIS B 270 Details of bonding type rmsd covalent geometry : bond 0.00387 (11990) covalent geometry : angle 0.52826 (16240) SS BOND : bond 0.00178 ( 30) SS BOND : angle 0.62188 ( 60) hydrogen bonds : bond 0.03710 ( 380) hydrogen bonds : angle 6.44912 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue LEU 624 is missing expected H atoms. Skipping. Residue VAL 631 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue VAL 638 is missing expected H atoms. Skipping. Residue VAL 640 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue ILE 649 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue THR 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue ALA 668 is missing expected H atoms. Skipping. Residue ALA 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue ILE 674 is missing expected H atoms. Skipping. Residue VAL 675 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ALA 681 is missing expected H atoms. Skipping. Residue ILE 684 is missing expected H atoms. Skipping. Residue VAL 686 is missing expected H atoms. Skipping. Residue VAL 687 is missing expected H atoms. Skipping. Residue ALA 692 is missing expected H atoms. Skipping. Residue LEU 693 is missing expected H atoms. Skipping. Residue ALA 694 is missing expected H atoms. Skipping. Residue LEU 696 is missing expected H atoms. Skipping. Residue ALA 699 is missing expected H atoms. Skipping. Residue THR 702 is missing expected H atoms. Skipping. Residue THR 706 is missing expected H atoms. Skipping. Residue VAL 709 is missing expected H atoms. Skipping. Residue VAL 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue ALA 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue ALA 725 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue VAL 731 is missing expected H atoms. Skipping. Residue MET 737 is missing expected H atoms. Skipping. Residue THR 739 is missing expected H atoms. Skipping. Residue VAL 741 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue ILE 747 is missing expected H atoms. Skipping. Residue LEU 752 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue VAL 759 is missing expected H atoms. Skipping. Residue VAL 760 is missing expected H atoms. Skipping. Residue VAL 764 is missing expected H atoms. Skipping. Residue LEU 766 is missing expected H atoms. Skipping. Residue ALA 767 is missing expected H atoms. Skipping. Residue VAL 768 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue ALA 770 is missing expected H atoms. Skipping. Residue ALA 771 is missing expected H atoms. Skipping. Residue VAL 772 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue VAL 777 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue THR 798 is missing expected H atoms. Skipping. Residue VAL 802 is missing expected H atoms. Skipping. Residue VAL 805 is missing expected H atoms. Skipping. Residue VAL 806 is missing expected H atoms. Skipping. Residue ILE 809 is missing expected H atoms. Skipping. Residue LEU 812 is missing expected H atoms. Skipping. Residue ALA 823 is missing expected H atoms. Skipping. Residue MET 824 is missing expected H atoms. Skipping. Residue LEU 825 is missing expected H atoms. Skipping. Residue LEU 827 is missing expected H atoms. Skipping. Residue THR 837 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue LEU 839 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue LEU 842 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue MET 850 is missing expected H atoms. Skipping. Residue THR 853 is missing expected H atoms. Skipping. Residue MET 856 is missing expected H atoms. Skipping. Residue ILE 858 is missing expected H atoms. Skipping. Residue LEU 861 is missing expected H atoms. Skipping. Residue ILE 863 is missing expected H atoms. Skipping. Residue ILE 865 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue THR 901 is missing expected H atoms. Skipping. Residue LEU 902 is missing expected H atoms. Skipping. Residue VAL 906 is missing expected H atoms. Skipping. Residue ALA 907 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue ILE 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue VAL 916 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue ALA 925 is missing expected H atoms. Skipping. Residue ILE 926 is missing expected H atoms. Skipping. Residue LEU 927 is missing expected H atoms. Skipping. Residue VAL 929 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue LEU 933 is missing expected H atoms. Skipping. Residue THR 935 is missing expected H atoms. Skipping. Residue THR 937 is missing expected H atoms. Skipping. Residue MET 939 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue ALA 954 is missing expected H atoms. Skipping. Residue VAL 958 is missing expected H atoms. Skipping. Residue ILE 959 is missing expected H atoms. Skipping. Residue LEU 966 is missing expected H atoms. Skipping. Residue ILE 968 is missing expected H atoms. Skipping. Residue ILE 971 is missing expected H atoms. Skipping. Residue THR 972 is missing expected H atoms. Skipping. Residue THR 975 is missing expected H atoms. Skipping. Residue LEU 976 is missing expected H atoms. Skipping. Residue VAL 977 is missing expected H atoms. Skipping. Residue THR 978 is missing expected H atoms. Skipping. Residue THR 979 is missing expected H atoms. Skipping. Residue VAL 981 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue ALA 988 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue VAL 520 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue VAL 533 is missing expected H atoms. Skipping. Residue ILE 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue VAL 555 is missing expected H atoms. Skipping. Residue MET 561 is missing expected H atoms. Skipping. Residue LEU 574 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 587 is missing expected H atoms. Skipping. Residue THR 588 is missing expected H atoms. Skipping. Residue THR 590 is missing expected H atoms. Skipping. Residue THR 592 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue ILE 615 is missing expected H atoms. Skipping. Residue THR 623 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 ARG cc_start: 0.7918 (mpp-170) cc_final: 0.6337 (mtp85) REVERT: A 762 HIS cc_start: 0.2856 (t70) cc_final: 0.2249 (t-90) outliers start: 11 outliers final: 5 residues processed: 59 average time/residue: 0.1561 time to fit residues: 13.2709 Evaluate side-chains 56 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 826 HIS Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 546 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 22 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.129310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.083344 restraints weight = 47492.227| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.61 r_work: 0.3167 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 12020 Z= 0.139 Angle : 0.472 6.529 16300 Z= 0.254 Chirality : 0.043 0.199 1784 Planarity : 0.004 0.115 2146 Dihedral : 4.663 38.400 1640 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.83 % Favored : 95.04 % Rotamer: Outliers : 1.22 % Allowed : 8.32 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.22), residues: 1511 helix: -0.37 (0.48), residues: 117 sheet: 0.05 (0.23), residues: 532 loop : -0.56 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 119 TYR 0.009 0.001 TYR A 142 PHE 0.010 0.001 PHE A 49 TRP 0.016 0.001 TRP A 144 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00323 (11990) covalent geometry : angle 0.47155 (16240) SS BOND : bond 0.00151 ( 30) SS BOND : angle 0.47643 ( 60) hydrogen bonds : bond 0.03294 ( 380) hydrogen bonds : angle 5.85054 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue LEU 624 is missing expected H atoms. Skipping. Residue VAL 631 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue VAL 638 is missing expected H atoms. Skipping. Residue VAL 640 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue ILE 649 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue THR 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue ALA 668 is missing expected H atoms. Skipping. Residue ALA 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue ILE 674 is missing expected H atoms. Skipping. Residue VAL 675 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ALA 681 is missing expected H atoms. Skipping. Residue ILE 684 is missing expected H atoms. Skipping. Residue VAL 686 is missing expected H atoms. Skipping. Residue VAL 687 is missing expected H atoms. Skipping. Residue ALA 692 is missing expected H atoms. Skipping. Residue LEU 693 is missing expected H atoms. Skipping. Residue ALA 694 is missing expected H atoms. Skipping. Residue LEU 696 is missing expected H atoms. Skipping. Residue ALA 699 is missing expected H atoms. Skipping. Residue THR 702 is missing expected H atoms. Skipping. Residue THR 706 is missing expected H atoms. Skipping. Residue VAL 709 is missing expected H atoms. Skipping. Residue VAL 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue ALA 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue ALA 725 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue VAL 731 is missing expected H atoms. Skipping. Residue MET 737 is missing expected H atoms. Skipping. Residue THR 739 is missing expected H atoms. Skipping. Residue VAL 741 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue ILE 747 is missing expected H atoms. Skipping. Residue LEU 752 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue VAL 759 is missing expected H atoms. Skipping. Residue VAL 760 is missing expected H atoms. Skipping. Residue VAL 764 is missing expected H atoms. Skipping. Residue LEU 766 is missing expected H atoms. Skipping. Residue ALA 767 is missing expected H atoms. Skipping. Residue VAL 768 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue ALA 770 is missing expected H atoms. Skipping. Residue ALA 771 is missing expected H atoms. Skipping. Residue VAL 772 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue VAL 777 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue THR 798 is missing expected H atoms. Skipping. Residue VAL 802 is missing expected H atoms. Skipping. Residue VAL 805 is missing expected H atoms. Skipping. Residue VAL 806 is missing expected H atoms. Skipping. Residue ILE 809 is missing expected H atoms. Skipping. Residue LEU 812 is missing expected H atoms. Skipping. Residue ALA 823 is missing expected H atoms. Skipping. Residue MET 824 is missing expected H atoms. Skipping. Residue LEU 825 is missing expected H atoms. Skipping. Residue LEU 827 is missing expected H atoms. Skipping. Residue THR 837 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue LEU 839 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue LEU 842 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue MET 850 is missing expected H atoms. Skipping. Residue THR 853 is missing expected H atoms. Skipping. Residue MET 856 is missing expected H atoms. Skipping. Residue ILE 858 is missing expected H atoms. Skipping. Residue LEU 861 is missing expected H atoms. Skipping. Residue ILE 863 is missing expected H atoms. Skipping. Residue ILE 865 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue THR 901 is missing expected H atoms. Skipping. Residue LEU 902 is missing expected H atoms. Skipping. Residue VAL 906 is missing expected H atoms. Skipping. Residue ALA 907 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue ILE 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue VAL 916 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue ALA 925 is missing expected H atoms. Skipping. Residue ILE 926 is missing expected H atoms. Skipping. Residue LEU 927 is missing expected H atoms. Skipping. Residue VAL 929 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue LEU 933 is missing expected H atoms. Skipping. Residue THR 935 is missing expected H atoms. Skipping. Residue THR 937 is missing expected H atoms. Skipping. Residue MET 939 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue ALA 954 is missing expected H atoms. Skipping. Residue VAL 958 is missing expected H atoms. Skipping. Residue ILE 959 is missing expected H atoms. Skipping. Residue LEU 966 is missing expected H atoms. Skipping. Residue ILE 968 is missing expected H atoms. Skipping. Residue ILE 971 is missing expected H atoms. Skipping. Residue THR 972 is missing expected H atoms. Skipping. Residue THR 975 is missing expected H atoms. Skipping. Residue LEU 976 is missing expected H atoms. Skipping. Residue VAL 977 is missing expected H atoms. Skipping. Residue THR 978 is missing expected H atoms. Skipping. Residue THR 979 is missing expected H atoms. Skipping. Residue VAL 981 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue ALA 988 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue VAL 520 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue VAL 533 is missing expected H atoms. Skipping. Residue ILE 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue VAL 555 is missing expected H atoms. Skipping. Residue MET 561 is missing expected H atoms. Skipping. Residue LEU 574 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 587 is missing expected H atoms. Skipping. Residue THR 588 is missing expected H atoms. Skipping. Residue THR 590 is missing expected H atoms. Skipping. Residue THR 592 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue ILE 615 is missing expected H atoms. Skipping. Residue THR 623 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 ARG cc_start: 0.7928 (mpp-170) cc_final: 0.6248 (mtp85) REVERT: B 487 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7941 (mmt180) outliers start: 16 outliers final: 8 residues processed: 67 average time/residue: 0.1725 time to fit residues: 16.2577 Evaluate side-chains 59 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 826 HIS Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 546 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 30.0000 chunk 118 optimal weight: 0.0770 chunk 64 optimal weight: 30.0000 chunk 70 optimal weight: 30.0000 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 GLN ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.125868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.078445 restraints weight = 47000.781| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.15 r_work: 0.3091 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 12020 Z= 0.361 Angle : 0.677 10.669 16300 Z= 0.355 Chirality : 0.048 0.172 1784 Planarity : 0.005 0.120 2146 Dihedral : 5.460 38.633 1639 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 26.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.68 % Favored : 92.19 % Rotamer: Outliers : 1.68 % Allowed : 9.39 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.22), residues: 1511 helix: -1.11 (0.45), residues: 116 sheet: -0.25 (0.23), residues: 525 loop : -0.89 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 93 TYR 0.021 0.002 TYR A 142 PHE 0.025 0.002 PHE A 49 TRP 0.018 0.002 TRP A 144 HIS 0.008 0.001 HIS A 762 Details of bonding type rmsd covalent geometry : bond 0.00844 (11990) covalent geometry : angle 0.67639 (16240) SS BOND : bond 0.00333 ( 30) SS BOND : angle 0.83122 ( 60) hydrogen bonds : bond 0.04097 ( 380) hydrogen bonds : angle 6.45726 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue LEU 624 is missing expected H atoms. Skipping. Residue VAL 631 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue VAL 638 is missing expected H atoms. Skipping. Residue VAL 640 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue ILE 649 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue THR 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue ALA 668 is missing expected H atoms. Skipping. Residue ALA 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue ILE 674 is missing expected H atoms. Skipping. Residue VAL 675 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ALA 681 is missing expected H atoms. Skipping. Residue ILE 684 is missing expected H atoms. Skipping. Residue VAL 686 is missing expected H atoms. Skipping. Residue VAL 687 is missing expected H atoms. Skipping. Residue ALA 692 is missing expected H atoms. Skipping. Residue LEU 693 is missing expected H atoms. Skipping. Residue ALA 694 is missing expected H atoms. Skipping. Residue LEU 696 is missing expected H atoms. Skipping. Residue ALA 699 is missing expected H atoms. Skipping. Residue THR 702 is missing expected H atoms. Skipping. Residue THR 706 is missing expected H atoms. Skipping. Residue VAL 709 is missing expected H atoms. Skipping. Residue VAL 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue ALA 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue ALA 725 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue VAL 731 is missing expected H atoms. Skipping. Residue MET 737 is missing expected H atoms. Skipping. Residue THR 739 is missing expected H atoms. Skipping. Residue VAL 741 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue ILE 747 is missing expected H atoms. Skipping. Residue LEU 752 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue VAL 759 is missing expected H atoms. Skipping. Residue VAL 760 is missing expected H atoms. Skipping. Residue VAL 764 is missing expected H atoms. Skipping. Residue LEU 766 is missing expected H atoms. Skipping. Residue ALA 767 is missing expected H atoms. Skipping. Residue VAL 768 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue ALA 770 is missing expected H atoms. Skipping. Residue ALA 771 is missing expected H atoms. Skipping. Residue VAL 772 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue VAL 777 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue THR 798 is missing expected H atoms. Skipping. Residue VAL 802 is missing expected H atoms. Skipping. Residue VAL 805 is missing expected H atoms. Skipping. Residue VAL 806 is missing expected H atoms. Skipping. Residue ILE 809 is missing expected H atoms. Skipping. Residue LEU 812 is missing expected H atoms. Skipping. Residue ALA 823 is missing expected H atoms. Skipping. Residue MET 824 is missing expected H atoms. Skipping. Residue LEU 825 is missing expected H atoms. Skipping. Residue LEU 827 is missing expected H atoms. Skipping. Residue THR 837 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue LEU 839 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue LEU 842 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue MET 850 is missing expected H atoms. Skipping. Residue THR 853 is missing expected H atoms. Skipping. Residue MET 856 is missing expected H atoms. Skipping. Residue ILE 858 is missing expected H atoms. Skipping. Residue LEU 861 is missing expected H atoms. Skipping. Residue ILE 863 is missing expected H atoms. Skipping. Residue ILE 865 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue THR 901 is missing expected H atoms. Skipping. Residue LEU 902 is missing expected H atoms. Skipping. Residue VAL 906 is missing expected H atoms. Skipping. Residue ALA 907 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue ILE 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue VAL 916 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue ALA 925 is missing expected H atoms. Skipping. Residue ILE 926 is missing expected H atoms. Skipping. Residue LEU 927 is missing expected H atoms. Skipping. Residue VAL 929 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue LEU 933 is missing expected H atoms. Skipping. Residue THR 935 is missing expected H atoms. Skipping. Residue THR 937 is missing expected H atoms. Skipping. Residue MET 939 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue ALA 954 is missing expected H atoms. Skipping. Residue VAL 958 is missing expected H atoms. Skipping. Residue ILE 959 is missing expected H atoms. Skipping. Residue LEU 966 is missing expected H atoms. Skipping. Residue ILE 968 is missing expected H atoms. Skipping. Residue ILE 971 is missing expected H atoms. Skipping. Residue THR 972 is missing expected H atoms. Skipping. Residue THR 975 is missing expected H atoms. Skipping. Residue LEU 976 is missing expected H atoms. Skipping. Residue VAL 977 is missing expected H atoms. Skipping. Residue THR 978 is missing expected H atoms. Skipping. Residue THR 979 is missing expected H atoms. Skipping. Residue VAL 981 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue ALA 988 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue VAL 520 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue VAL 533 is missing expected H atoms. Skipping. Residue ILE 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue VAL 555 is missing expected H atoms. Skipping. Residue MET 561 is missing expected H atoms. Skipping. Residue LEU 574 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 587 is missing expected H atoms. Skipping. Residue THR 588 is missing expected H atoms. Skipping. Residue THR 590 is missing expected H atoms. Skipping. Residue THR 592 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue ILE 615 is missing expected H atoms. Skipping. Residue THR 623 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 445 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.7494 (m-30) REVERT: A 539 ARG cc_start: 0.7892 (mpp-170) cc_final: 0.6411 (mtp85) outliers start: 22 outliers final: 14 residues processed: 70 average time/residue: 0.1540 time to fit residues: 15.6123 Evaluate side-chains 64 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 546 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 46 optimal weight: 0.0980 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 110 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.129061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.080734 restraints weight = 46522.328| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.24 r_work: 0.3093 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 12020 Z= 0.093 Angle : 0.453 6.322 16300 Z= 0.243 Chirality : 0.042 0.185 1784 Planarity : 0.004 0.114 2146 Dihedral : 4.529 38.506 1639 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.37 % Favored : 95.50 % Rotamer: Outliers : 0.53 % Allowed : 10.99 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.22), residues: 1511 helix: -0.43 (0.46), residues: 122 sheet: 0.02 (0.23), residues: 527 loop : -0.62 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 524 TYR 0.008 0.001 TYR B 344 PHE 0.008 0.001 PHE B 274 TRP 0.019 0.001 TRP A 144 HIS 0.003 0.000 HIS A 762 Details of bonding type rmsd covalent geometry : bond 0.00221 (11990) covalent geometry : angle 0.45069 (16240) SS BOND : bond 0.00314 ( 30) SS BOND : angle 0.92310 ( 60) hydrogen bonds : bond 0.02740 ( 380) hydrogen bonds : angle 5.57764 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue LEU 624 is missing expected H atoms. Skipping. Residue VAL 631 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue VAL 638 is missing expected H atoms. Skipping. Residue VAL 640 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue ILE 649 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue THR 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue ALA 668 is missing expected H atoms. Skipping. Residue ALA 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue ILE 674 is missing expected H atoms. Skipping. Residue VAL 675 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ALA 681 is missing expected H atoms. Skipping. Residue ILE 684 is missing expected H atoms. Skipping. Residue VAL 686 is missing expected H atoms. Skipping. Residue VAL 687 is missing expected H atoms. Skipping. Residue ALA 692 is missing expected H atoms. Skipping. Residue LEU 693 is missing expected H atoms. Skipping. Residue ALA 694 is missing expected H atoms. Skipping. Residue LEU 696 is missing expected H atoms. Skipping. Residue ALA 699 is missing expected H atoms. Skipping. Residue THR 702 is missing expected H atoms. Skipping. Residue THR 706 is missing expected H atoms. Skipping. Residue VAL 709 is missing expected H atoms. Skipping. Residue VAL 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue ALA 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue ALA 725 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue VAL 731 is missing expected H atoms. Skipping. Residue MET 737 is missing expected H atoms. Skipping. Residue THR 739 is missing expected H atoms. Skipping. Residue VAL 741 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue ILE 747 is missing expected H atoms. Skipping. Residue LEU 752 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue VAL 759 is missing expected H atoms. Skipping. Residue VAL 760 is missing expected H atoms. Skipping. Residue VAL 764 is missing expected H atoms. Skipping. Residue LEU 766 is missing expected H atoms. Skipping. Residue ALA 767 is missing expected H atoms. Skipping. Residue VAL 768 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue ALA 770 is missing expected H atoms. Skipping. Residue ALA 771 is missing expected H atoms. Skipping. Residue VAL 772 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue VAL 777 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue THR 798 is missing expected H atoms. Skipping. Residue VAL 802 is missing expected H atoms. Skipping. Residue VAL 805 is missing expected H atoms. Skipping. Residue VAL 806 is missing expected H atoms. Skipping. Residue ILE 809 is missing expected H atoms. Skipping. Residue LEU 812 is missing expected H atoms. Skipping. Residue ALA 823 is missing expected H atoms. Skipping. Residue MET 824 is missing expected H atoms. Skipping. Residue LEU 825 is missing expected H atoms. Skipping. Residue LEU 827 is missing expected H atoms. Skipping. Residue THR 837 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue LEU 839 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue LEU 842 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue MET 850 is missing expected H atoms. Skipping. Residue THR 853 is missing expected H atoms. Skipping. Residue MET 856 is missing expected H atoms. Skipping. Residue ILE 858 is missing expected H atoms. Skipping. Residue LEU 861 is missing expected H atoms. Skipping. Residue ILE 863 is missing expected H atoms. Skipping. Residue ILE 865 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue THR 901 is missing expected H atoms. Skipping. Residue LEU 902 is missing expected H atoms. Skipping. Residue VAL 906 is missing expected H atoms. Skipping. Residue ALA 907 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue ILE 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue VAL 916 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue ALA 925 is missing expected H atoms. Skipping. Residue ILE 926 is missing expected H atoms. Skipping. Residue LEU 927 is missing expected H atoms. Skipping. Residue VAL 929 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue LEU 933 is missing expected H atoms. Skipping. Residue THR 935 is missing expected H atoms. Skipping. Residue THR 937 is missing expected H atoms. Skipping. Residue MET 939 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue ALA 954 is missing expected H atoms. Skipping. Residue VAL 958 is missing expected H atoms. Skipping. Residue ILE 959 is missing expected H atoms. Skipping. Residue LEU 966 is missing expected H atoms. Skipping. Residue ILE 968 is missing expected H atoms. Skipping. Residue ILE 971 is missing expected H atoms. Skipping. Residue THR 972 is missing expected H atoms. Skipping. Residue THR 975 is missing expected H atoms. Skipping. Residue LEU 976 is missing expected H atoms. Skipping. Residue VAL 977 is missing expected H atoms. Skipping. Residue THR 978 is missing expected H atoms. Skipping. Residue THR 979 is missing expected H atoms. Skipping. Residue VAL 981 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue ALA 988 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue VAL 520 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue VAL 533 is missing expected H atoms. Skipping. Residue ILE 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue VAL 555 is missing expected H atoms. Skipping. Residue MET 561 is missing expected H atoms. Skipping. Residue LEU 574 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 587 is missing expected H atoms. Skipping. Residue THR 588 is missing expected H atoms. Skipping. Residue THR 590 is missing expected H atoms. Skipping. Residue THR 592 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue ILE 615 is missing expected H atoms. Skipping. Residue THR 623 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 539 ARG cc_start: 0.7786 (mpp-170) cc_final: 0.6127 (mtp85) REVERT: A 555 MET cc_start: 0.6447 (mtp) cc_final: 0.6011 (mtt) REVERT: B 487 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7734 (mmt180) outliers start: 7 outliers final: 5 residues processed: 53 average time/residue: 0.1620 time to fit residues: 12.4519 Evaluate side-chains 55 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 546 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 78 optimal weight: 20.0000 chunk 124 optimal weight: 0.0050 chunk 93 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 chunk 75 optimal weight: 50.0000 chunk 53 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.128168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079308 restraints weight = 46415.050| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.56 r_work: 0.3065 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12020 Z= 0.147 Angle : 0.468 6.152 16300 Z= 0.249 Chirality : 0.043 0.178 1784 Planarity : 0.004 0.112 2146 Dihedral : 4.471 39.062 1639 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 24.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.35 % Favored : 93.51 % Rotamer: Outliers : 0.99 % Allowed : 10.84 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.22), residues: 1511 helix: -0.39 (0.47), residues: 122 sheet: 0.02 (0.23), residues: 522 loop : -0.64 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 524 TYR 0.011 0.001 TYR A 142 PHE 0.012 0.001 PHE A 49 TRP 0.013 0.001 TRP A 144 HIS 0.002 0.001 HIS B 472 Details of bonding type rmsd covalent geometry : bond 0.00345 (11990) covalent geometry : angle 0.46678 (16240) SS BOND : bond 0.00211 ( 30) SS BOND : angle 0.68704 ( 60) hydrogen bonds : bond 0.02895 ( 380) hydrogen bonds : angle 5.51194 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue LEU 624 is missing expected H atoms. Skipping. Residue VAL 631 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue VAL 638 is missing expected H atoms. Skipping. Residue VAL 640 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue ILE 649 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue THR 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue ALA 668 is missing expected H atoms. Skipping. Residue ALA 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue ILE 674 is missing expected H atoms. Skipping. Residue VAL 675 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ALA 681 is missing expected H atoms. Skipping. Residue ILE 684 is missing expected H atoms. Skipping. Residue VAL 686 is missing expected H atoms. Skipping. Residue VAL 687 is missing expected H atoms. Skipping. Residue ALA 692 is missing expected H atoms. Skipping. Residue LEU 693 is missing expected H atoms. Skipping. Residue ALA 694 is missing expected H atoms. Skipping. Residue LEU 696 is missing expected H atoms. Skipping. Residue ALA 699 is missing expected H atoms. Skipping. Residue THR 702 is missing expected H atoms. Skipping. Residue THR 706 is missing expected H atoms. Skipping. Residue VAL 709 is missing expected H atoms. Skipping. Residue VAL 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue ALA 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue ALA 725 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue VAL 731 is missing expected H atoms. Skipping. Residue MET 737 is missing expected H atoms. Skipping. Residue THR 739 is missing expected H atoms. Skipping. Residue VAL 741 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue ILE 747 is missing expected H atoms. Skipping. Residue LEU 752 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue VAL 759 is missing expected H atoms. Skipping. Residue VAL 760 is missing expected H atoms. Skipping. Residue VAL 764 is missing expected H atoms. Skipping. Residue LEU 766 is missing expected H atoms. Skipping. Residue ALA 767 is missing expected H atoms. Skipping. Residue VAL 768 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue ALA 770 is missing expected H atoms. Skipping. Residue ALA 771 is missing expected H atoms. Skipping. Residue VAL 772 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue VAL 777 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue THR 798 is missing expected H atoms. Skipping. Residue VAL 802 is missing expected H atoms. Skipping. Residue VAL 805 is missing expected H atoms. Skipping. Residue VAL 806 is missing expected H atoms. Skipping. Residue ILE 809 is missing expected H atoms. Skipping. Residue LEU 812 is missing expected H atoms. Skipping. Residue ALA 823 is missing expected H atoms. Skipping. Residue MET 824 is missing expected H atoms. Skipping. Residue LEU 825 is missing expected H atoms. Skipping. Residue LEU 827 is missing expected H atoms. Skipping. Residue THR 837 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue LEU 839 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue LEU 842 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue MET 850 is missing expected H atoms. Skipping. Residue THR 853 is missing expected H atoms. Skipping. Residue MET 856 is missing expected H atoms. Skipping. Residue ILE 858 is missing expected H atoms. Skipping. Residue LEU 861 is missing expected H atoms. Skipping. Residue ILE 863 is missing expected H atoms. Skipping. Residue ILE 865 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue THR 901 is missing expected H atoms. Skipping. Residue LEU 902 is missing expected H atoms. Skipping. Residue VAL 906 is missing expected H atoms. Skipping. Residue ALA 907 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue ILE 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue VAL 916 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue ALA 925 is missing expected H atoms. Skipping. Residue ILE 926 is missing expected H atoms. Skipping. Residue LEU 927 is missing expected H atoms. Skipping. Residue VAL 929 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue LEU 933 is missing expected H atoms. Skipping. Residue THR 935 is missing expected H atoms. Skipping. Residue THR 937 is missing expected H atoms. Skipping. Residue MET 939 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue ALA 954 is missing expected H atoms. Skipping. Residue VAL 958 is missing expected H atoms. Skipping. Residue ILE 959 is missing expected H atoms. Skipping. Residue LEU 966 is missing expected H atoms. Skipping. Residue ILE 968 is missing expected H atoms. Skipping. Residue ILE 971 is missing expected H atoms. Skipping. Residue THR 972 is missing expected H atoms. Skipping. Residue THR 975 is missing expected H atoms. Skipping. Residue LEU 976 is missing expected H atoms. Skipping. Residue VAL 977 is missing expected H atoms. Skipping. Residue THR 978 is missing expected H atoms. Skipping. Residue THR 979 is missing expected H atoms. Skipping. Residue VAL 981 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue ALA 988 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue VAL 520 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue VAL 533 is missing expected H atoms. Skipping. Residue ILE 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue VAL 555 is missing expected H atoms. Skipping. Residue MET 561 is missing expected H atoms. Skipping. Residue LEU 574 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 587 is missing expected H atoms. Skipping. Residue THR 588 is missing expected H atoms. Skipping. Residue THR 590 is missing expected H atoms. Skipping. Residue THR 592 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue ILE 615 is missing expected H atoms. Skipping. Residue THR 623 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 539 ARG cc_start: 0.7783 (mpp-170) cc_final: 0.6224 (mtp85) REVERT: A 555 MET cc_start: 0.6483 (mtp) cc_final: 0.6048 (mtt) REVERT: B 487 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7748 (mmt180) outliers start: 13 outliers final: 7 residues processed: 60 average time/residue: 0.1653 time to fit residues: 14.1585 Evaluate side-chains 57 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 546 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 95 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 ASN B 454 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.126112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.079055 restraints weight = 46506.575| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.86 r_work: 0.3113 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 12020 Z= 0.293 Angle : 0.603 11.406 16300 Z= 0.316 Chirality : 0.046 0.169 1784 Planarity : 0.005 0.114 2146 Dihedral : 5.092 39.214 1639 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 29.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.60 % Favored : 91.26 % Rotamer: Outliers : 1.60 % Allowed : 11.45 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.22), residues: 1511 helix: -0.85 (0.44), residues: 122 sheet: -0.21 (0.23), residues: 526 loop : -0.81 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 117 TYR 0.018 0.002 TYR A 142 PHE 0.019 0.002 PHE A 49 TRP 0.015 0.002 TRP A 144 HIS 0.006 0.001 HIS B 472 Details of bonding type rmsd covalent geometry : bond 0.00682 (11990) covalent geometry : angle 0.60213 (16240) SS BOND : bond 0.00303 ( 30) SS BOND : angle 0.88834 ( 60) hydrogen bonds : bond 0.03569 ( 380) hydrogen bonds : angle 6.03708 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue LEU 624 is missing expected H atoms. Skipping. Residue VAL 631 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue VAL 638 is missing expected H atoms. Skipping. Residue VAL 640 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue ILE 649 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue THR 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue ALA 668 is missing expected H atoms. Skipping. Residue ALA 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue ILE 674 is missing expected H atoms. Skipping. Residue VAL 675 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ALA 681 is missing expected H atoms. Skipping. Residue ILE 684 is missing expected H atoms. Skipping. Residue VAL 686 is missing expected H atoms. Skipping. Residue VAL 687 is missing expected H atoms. Skipping. Residue ALA 692 is missing expected H atoms. Skipping. Residue LEU 693 is missing expected H atoms. Skipping. Residue ALA 694 is missing expected H atoms. Skipping. Residue LEU 696 is missing expected H atoms. Skipping. Residue ALA 699 is missing expected H atoms. Skipping. Residue THR 702 is missing expected H atoms. Skipping. Residue THR 706 is missing expected H atoms. Skipping. Residue VAL 709 is missing expected H atoms. Skipping. Residue VAL 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue ALA 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue ALA 725 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue VAL 731 is missing expected H atoms. Skipping. Residue MET 737 is missing expected H atoms. Skipping. Residue THR 739 is missing expected H atoms. Skipping. Residue VAL 741 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue ILE 747 is missing expected H atoms. Skipping. Residue LEU 752 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue VAL 759 is missing expected H atoms. Skipping. Residue VAL 760 is missing expected H atoms. Skipping. Residue VAL 764 is missing expected H atoms. Skipping. Residue LEU 766 is missing expected H atoms. Skipping. Residue ALA 767 is missing expected H atoms. Skipping. Residue VAL 768 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue ALA 770 is missing expected H atoms. Skipping. Residue ALA 771 is missing expected H atoms. Skipping. Residue VAL 772 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue VAL 777 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue THR 798 is missing expected H atoms. Skipping. Residue VAL 802 is missing expected H atoms. Skipping. Residue VAL 805 is missing expected H atoms. Skipping. Residue VAL 806 is missing expected H atoms. Skipping. Residue ILE 809 is missing expected H atoms. Skipping. Residue LEU 812 is missing expected H atoms. Skipping. Residue ALA 823 is missing expected H atoms. Skipping. Residue MET 824 is missing expected H atoms. Skipping. Residue LEU 825 is missing expected H atoms. Skipping. Residue LEU 827 is missing expected H atoms. Skipping. Residue THR 837 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue LEU 839 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue LEU 842 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue MET 850 is missing expected H atoms. Skipping. Residue THR 853 is missing expected H atoms. Skipping. Residue MET 856 is missing expected H atoms. Skipping. Residue ILE 858 is missing expected H atoms. Skipping. Residue LEU 861 is missing expected H atoms. Skipping. Residue ILE 863 is missing expected H atoms. Skipping. Residue ILE 865 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue THR 901 is missing expected H atoms. Skipping. Residue LEU 902 is missing expected H atoms. Skipping. Residue VAL 906 is missing expected H atoms. Skipping. Residue ALA 907 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue ILE 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue VAL 916 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue ALA 925 is missing expected H atoms. Skipping. Residue ILE 926 is missing expected H atoms. Skipping. Residue LEU 927 is missing expected H atoms. Skipping. Residue VAL 929 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue LEU 933 is missing expected H atoms. Skipping. Residue THR 935 is missing expected H atoms. Skipping. Residue THR 937 is missing expected H atoms. Skipping. Residue MET 939 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue ALA 954 is missing expected H atoms. Skipping. Residue VAL 958 is missing expected H atoms. Skipping. Residue ILE 959 is missing expected H atoms. Skipping. Residue LEU 966 is missing expected H atoms. Skipping. Residue ILE 968 is missing expected H atoms. Skipping. Residue ILE 971 is missing expected H atoms. Skipping. Residue THR 972 is missing expected H atoms. Skipping. Residue THR 975 is missing expected H atoms. Skipping. Residue LEU 976 is missing expected H atoms. Skipping. Residue VAL 977 is missing expected H atoms. Skipping. Residue THR 978 is missing expected H atoms. Skipping. Residue THR 979 is missing expected H atoms. Skipping. Residue VAL 981 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue ALA 988 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue VAL 520 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue VAL 533 is missing expected H atoms. Skipping. Residue ILE 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue VAL 555 is missing expected H atoms. Skipping. Residue MET 561 is missing expected H atoms. Skipping. Residue LEU 574 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 587 is missing expected H atoms. Skipping. Residue THR 588 is missing expected H atoms. Skipping. Residue THR 590 is missing expected H atoms. Skipping. Residue THR 592 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue ILE 615 is missing expected H atoms. Skipping. Residue THR 623 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 445 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: A 555 MET cc_start: 0.6842 (mtp) cc_final: 0.6412 (mtt) REVERT: B 487 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7630 (mmt180) outliers start: 21 outliers final: 13 residues processed: 65 average time/residue: 0.1275 time to fit residues: 12.3886 Evaluate side-chains 62 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 546 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 121 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 100 optimal weight: 0.0870 chunk 71 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.128823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.080910 restraints weight = 46141.520| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.29 r_work: 0.3097 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 12020 Z= 0.082 Angle : 0.434 5.588 16300 Z= 0.232 Chirality : 0.042 0.179 1784 Planarity : 0.004 0.109 2146 Dihedral : 4.295 40.616 1639 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 25.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.90 % Favored : 94.97 % Rotamer: Outliers : 0.99 % Allowed : 11.98 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.22), residues: 1511 helix: -0.24 (0.47), residues: 123 sheet: 0.06 (0.24), residues: 523 loop : -0.56 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 524 TYR 0.007 0.001 TYR B 583 PHE 0.009 0.001 PHE B 274 TRP 0.019 0.001 TRP A 144 HIS 0.002 0.000 HIS B 270 Details of bonding type rmsd covalent geometry : bond 0.00193 (11990) covalent geometry : angle 0.43396 (16240) SS BOND : bond 0.00170 ( 30) SS BOND : angle 0.53197 ( 60) hydrogen bonds : bond 0.02519 ( 380) hydrogen bonds : angle 5.26773 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue LEU 624 is missing expected H atoms. Skipping. Residue VAL 631 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue VAL 638 is missing expected H atoms. Skipping. Residue VAL 640 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue ILE 649 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue THR 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue ALA 668 is missing expected H atoms. Skipping. Residue ALA 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue ILE 674 is missing expected H atoms. Skipping. Residue VAL 675 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ALA 681 is missing expected H atoms. Skipping. Residue ILE 684 is missing expected H atoms. Skipping. Residue VAL 686 is missing expected H atoms. Skipping. Residue VAL 687 is missing expected H atoms. Skipping. Residue ALA 692 is missing expected H atoms. Skipping. Residue LEU 693 is missing expected H atoms. Skipping. Residue ALA 694 is missing expected H atoms. Skipping. Residue LEU 696 is missing expected H atoms. Skipping. Residue ALA 699 is missing expected H atoms. Skipping. Residue THR 702 is missing expected H atoms. Skipping. Residue THR 706 is missing expected H atoms. Skipping. Residue VAL 709 is missing expected H atoms. Skipping. Residue VAL 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue ALA 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue ALA 725 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue VAL 731 is missing expected H atoms. Skipping. Residue MET 737 is missing expected H atoms. Skipping. Residue THR 739 is missing expected H atoms. Skipping. Residue VAL 741 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue ILE 747 is missing expected H atoms. Skipping. Residue LEU 752 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue VAL 759 is missing expected H atoms. Skipping. Residue VAL 760 is missing expected H atoms. Skipping. Residue VAL 764 is missing expected H atoms. Skipping. Residue LEU 766 is missing expected H atoms. Skipping. Residue ALA 767 is missing expected H atoms. Skipping. Residue VAL 768 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue ALA 770 is missing expected H atoms. Skipping. Residue ALA 771 is missing expected H atoms. Skipping. Residue VAL 772 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue VAL 777 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue THR 798 is missing expected H atoms. Skipping. Residue VAL 802 is missing expected H atoms. Skipping. Residue VAL 805 is missing expected H atoms. Skipping. Residue VAL 806 is missing expected H atoms. Skipping. Residue ILE 809 is missing expected H atoms. Skipping. Residue LEU 812 is missing expected H atoms. Skipping. Residue ALA 823 is missing expected H atoms. Skipping. Residue MET 824 is missing expected H atoms. Skipping. Residue LEU 825 is missing expected H atoms. Skipping. Residue LEU 827 is missing expected H atoms. Skipping. Residue THR 837 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue LEU 839 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue LEU 842 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue MET 850 is missing expected H atoms. Skipping. Residue THR 853 is missing expected H atoms. Skipping. Residue MET 856 is missing expected H atoms. Skipping. Residue ILE 858 is missing expected H atoms. Skipping. Residue LEU 861 is missing expected H atoms. Skipping. Residue ILE 863 is missing expected H atoms. Skipping. Residue ILE 865 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue THR 901 is missing expected H atoms. Skipping. Residue LEU 902 is missing expected H atoms. Skipping. Residue VAL 906 is missing expected H atoms. Skipping. Residue ALA 907 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue ILE 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue VAL 916 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue ALA 925 is missing expected H atoms. Skipping. Residue ILE 926 is missing expected H atoms. Skipping. Residue LEU 927 is missing expected H atoms. Skipping. Residue VAL 929 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue LEU 933 is missing expected H atoms. Skipping. Residue THR 935 is missing expected H atoms. Skipping. Residue THR 937 is missing expected H atoms. Skipping. Residue MET 939 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue ALA 954 is missing expected H atoms. Skipping. Residue VAL 958 is missing expected H atoms. Skipping. Residue ILE 959 is missing expected H atoms. Skipping. Residue LEU 966 is missing expected H atoms. Skipping. Residue ILE 968 is missing expected H atoms. Skipping. Residue ILE 971 is missing expected H atoms. Skipping. Residue THR 972 is missing expected H atoms. Skipping. Residue THR 975 is missing expected H atoms. Skipping. Residue LEU 976 is missing expected H atoms. Skipping. Residue VAL 977 is missing expected H atoms. Skipping. Residue THR 978 is missing expected H atoms. Skipping. Residue THR 979 is missing expected H atoms. Skipping. Residue VAL 981 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue ALA 988 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue VAL 520 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue VAL 533 is missing expected H atoms. Skipping. Residue ILE 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue VAL 555 is missing expected H atoms. Skipping. Residue MET 561 is missing expected H atoms. Skipping. Residue LEU 574 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 587 is missing expected H atoms. Skipping. Residue THR 588 is missing expected H atoms. Skipping. Residue THR 590 is missing expected H atoms. Skipping. Residue THR 592 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue ILE 615 is missing expected H atoms. Skipping. Residue THR 623 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.6922 (m-30) REVERT: A 555 MET cc_start: 0.6513 (mtp) cc_final: 0.6106 (mtt) REVERT: A 737 MET cc_start: 0.5660 (mmp) cc_final: 0.5398 (mmp) REVERT: B 487 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7688 (mmt180) REVERT: B 516 GLU cc_start: 0.7741 (pm20) cc_final: 0.7501 (mp0) outliers start: 13 outliers final: 8 residues processed: 60 average time/residue: 0.1522 time to fit residues: 13.3673 Evaluate side-chains 58 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 546 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 64 optimal weight: 30.0000 chunk 65 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 chunk 108 optimal weight: 0.7980 chunk 142 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.126717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.078202 restraints weight = 46372.688| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.17 r_work: 0.3037 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12020 Z= 0.222 Angle : 0.521 5.708 16300 Z= 0.275 Chirality : 0.044 0.163 1784 Planarity : 0.004 0.109 2146 Dihedral : 4.657 39.667 1639 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 27.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.41 % Favored : 92.46 % Rotamer: Outliers : 1.30 % Allowed : 11.53 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.22), residues: 1511 helix: -0.50 (0.46), residues: 122 sheet: -0.06 (0.23), residues: 524 loop : -0.71 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 119 TYR 0.015 0.001 TYR A 142 PHE 0.015 0.001 PHE A 49 TRP 0.013 0.001 TRP A 144 HIS 0.003 0.001 HIS B 472 Details of bonding type rmsd covalent geometry : bond 0.00517 (11990) covalent geometry : angle 0.52042 (16240) SS BOND : bond 0.00239 ( 30) SS BOND : angle 0.68375 ( 60) hydrogen bonds : bond 0.03075 ( 380) hydrogen bonds : angle 5.61839 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue LEU 624 is missing expected H atoms. Skipping. Residue VAL 631 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue VAL 638 is missing expected H atoms. Skipping. Residue VAL 640 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue ILE 649 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue THR 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue ALA 668 is missing expected H atoms. Skipping. Residue ALA 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue ILE 674 is missing expected H atoms. Skipping. Residue VAL 675 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ALA 681 is missing expected H atoms. Skipping. Residue ILE 684 is missing expected H atoms. Skipping. Residue VAL 686 is missing expected H atoms. Skipping. Residue VAL 687 is missing expected H atoms. Skipping. Residue ALA 692 is missing expected H atoms. Skipping. Residue LEU 693 is missing expected H atoms. Skipping. Residue ALA 694 is missing expected H atoms. Skipping. Residue LEU 696 is missing expected H atoms. Skipping. Residue ALA 699 is missing expected H atoms. Skipping. Residue THR 702 is missing expected H atoms. Skipping. Residue THR 706 is missing expected H atoms. Skipping. Residue VAL 709 is missing expected H atoms. Skipping. Residue VAL 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue ALA 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue ALA 725 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue VAL 731 is missing expected H atoms. Skipping. Residue MET 737 is missing expected H atoms. Skipping. Residue THR 739 is missing expected H atoms. Skipping. Residue VAL 741 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue ILE 747 is missing expected H atoms. Skipping. Residue LEU 752 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue VAL 759 is missing expected H atoms. Skipping. Residue VAL 760 is missing expected H atoms. Skipping. Residue VAL 764 is missing expected H atoms. Skipping. Residue LEU 766 is missing expected H atoms. Skipping. Residue ALA 767 is missing expected H atoms. Skipping. Residue VAL 768 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue ALA 770 is missing expected H atoms. Skipping. Residue ALA 771 is missing expected H atoms. Skipping. Residue VAL 772 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue VAL 777 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue THR 798 is missing expected H atoms. Skipping. Residue VAL 802 is missing expected H atoms. Skipping. Residue VAL 805 is missing expected H atoms. Skipping. Residue VAL 806 is missing expected H atoms. Skipping. Residue ILE 809 is missing expected H atoms. Skipping. Residue LEU 812 is missing expected H atoms. Skipping. Residue ALA 823 is missing expected H atoms. Skipping. Residue MET 824 is missing expected H atoms. Skipping. Residue LEU 825 is missing expected H atoms. Skipping. Residue LEU 827 is missing expected H atoms. Skipping. Residue THR 837 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue LEU 839 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue LEU 842 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue MET 850 is missing expected H atoms. Skipping. Residue THR 853 is missing expected H atoms. Skipping. Residue MET 856 is missing expected H atoms. Skipping. Residue ILE 858 is missing expected H atoms. Skipping. Residue LEU 861 is missing expected H atoms. Skipping. Residue ILE 863 is missing expected H atoms. Skipping. Residue ILE 865 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue THR 901 is missing expected H atoms. Skipping. Residue LEU 902 is missing expected H atoms. Skipping. Residue VAL 906 is missing expected H atoms. Skipping. Residue ALA 907 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue ILE 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue VAL 916 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue ALA 925 is missing expected H atoms. Skipping. Residue ILE 926 is missing expected H atoms. Skipping. Residue LEU 927 is missing expected H atoms. Skipping. Residue VAL 929 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue LEU 933 is missing expected H atoms. Skipping. Residue THR 935 is missing expected H atoms. Skipping. Residue THR 937 is missing expected H atoms. Skipping. Residue MET 939 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue ALA 954 is missing expected H atoms. Skipping. Residue VAL 958 is missing expected H atoms. Skipping. Residue ILE 959 is missing expected H atoms. Skipping. Residue LEU 966 is missing expected H atoms. Skipping. Residue ILE 968 is missing expected H atoms. Skipping. Residue ILE 971 is missing expected H atoms. Skipping. Residue THR 972 is missing expected H atoms. Skipping. Residue THR 975 is missing expected H atoms. Skipping. Residue LEU 976 is missing expected H atoms. Skipping. Residue VAL 977 is missing expected H atoms. Skipping. Residue THR 978 is missing expected H atoms. Skipping. Residue THR 979 is missing expected H atoms. Skipping. Residue VAL 981 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue ALA 988 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue VAL 520 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue VAL 533 is missing expected H atoms. Skipping. Residue ILE 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue VAL 555 is missing expected H atoms. Skipping. Residue MET 561 is missing expected H atoms. Skipping. Residue LEU 574 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 587 is missing expected H atoms. Skipping. Residue THR 588 is missing expected H atoms. Skipping. Residue THR 590 is missing expected H atoms. Skipping. Residue THR 592 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue ILE 615 is missing expected H atoms. Skipping. Residue THR 623 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 MET cc_start: 0.8628 (mtt) cc_final: 0.8396 (mtt) REVERT: A 445 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7374 (m-30) REVERT: A 555 MET cc_start: 0.6735 (mtp) cc_final: 0.6326 (mtt) REVERT: B 487 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7734 (mmt180) outliers start: 17 outliers final: 11 residues processed: 60 average time/residue: 0.1556 time to fit residues: 13.7217 Evaluate side-chains 59 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 546 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 134 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 148 optimal weight: 30.0000 chunk 139 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 147 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.127823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.079760 restraints weight = 45795.992| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.31 r_work: 0.3068 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12020 Z= 0.121 Angle : 0.452 5.305 16300 Z= 0.241 Chirality : 0.042 0.166 1784 Planarity : 0.004 0.107 2146 Dihedral : 4.375 39.749 1639 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 26.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.96 % Favored : 93.91 % Rotamer: Outliers : 0.99 % Allowed : 11.68 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.22), residues: 1511 helix: -0.27 (0.47), residues: 123 sheet: -0.02 (0.23), residues: 525 loop : -0.62 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 119 TYR 0.008 0.001 TYR A 142 PHE 0.008 0.001 PHE B 274 TRP 0.015 0.001 TRP A 144 HIS 0.002 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00283 (11990) covalent geometry : angle 0.45148 (16240) SS BOND : bond 0.00189 ( 30) SS BOND : angle 0.52308 ( 60) hydrogen bonds : bond 0.02672 ( 380) hydrogen bonds : angle 5.34572 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue MET 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue ALA 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue ALA 111 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ALA 126 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ALA 137 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue MET 148 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 179 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue ALA 196 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue VAL 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue ALA 239 is missing expected H atoms. Skipping. Residue THR 240 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ALA 243 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue VAL 256 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 258 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue ALA 276 is missing expected H atoms. Skipping. Residue ALA 277 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue MET 282 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue MET 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue ALA 304 is missing expected H atoms. Skipping. Residue VAL 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue ILE 315 is missing expected H atoms. Skipping. Residue ALA 321 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue ALA 327 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue MET 331 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue VAL 342 is missing expected H atoms. Skipping. Residue VAL 345 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue THR 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ALA 389 is missing expected H atoms. Skipping. Residue ILE 390 is missing expected H atoms. Skipping. Residue ALA 391 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue ILE 405 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue ALA 415 is missing expected H atoms. Skipping. Residue VAL 416 is missing expected H atoms. Skipping. Residue ILE 420 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue ALA 426 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue MET 438 is missing expected H atoms. Skipping. Residue ALA 441 is missing expected H atoms. Skipping. Residue THR 442 is missing expected H atoms. Skipping. Residue ILE 444 is missing expected H atoms. Skipping. Residue LEU 452 is missing expected H atoms. Skipping. Residue ILE 453 is missing expected H atoms. Skipping. Residue VAL 454 is missing expected H atoms. Skipping. Residue ALA 456 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue ILE 471 is missing expected H atoms. Skipping. Residue THR 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue ALA 475 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue VAL 479 is missing expected H atoms. Skipping. Residue ILE 483 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 500 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue LEU 517 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue LEU 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue ALA 541 is missing expected H atoms. Skipping. Residue LEU 542 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue MET 555 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue ILE 557 is missing expected H atoms. Skipping. Residue LEU 562 is missing expected H atoms. Skipping. Residue MET 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 569 is missing expected H atoms. Skipping. Residue ALA 570 is missing expected H atoms. Skipping. Residue LEU 572 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue THR 583 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue THR 586 is missing expected H atoms. Skipping. Residue ILE 587 is missing expected H atoms. Skipping. Residue MET 589 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ALA 598 is missing expected H atoms. Skipping. Residue ALA 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue THR 602 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue LEU 608 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue ALA 614 is missing expected H atoms. Skipping. Residue ILE 616 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue LEU 624 is missing expected H atoms. Skipping. Residue VAL 631 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue VAL 638 is missing expected H atoms. Skipping. Residue VAL 640 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue ILE 649 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue THR 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue ILE 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue ALA 668 is missing expected H atoms. Skipping. Residue ALA 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue ILE 674 is missing expected H atoms. Skipping. Residue VAL 675 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ALA 681 is missing expected H atoms. Skipping. Residue ILE 684 is missing expected H atoms. Skipping. Residue VAL 686 is missing expected H atoms. Skipping. Residue VAL 687 is missing expected H atoms. Skipping. Residue ALA 692 is missing expected H atoms. Skipping. Residue LEU 693 is missing expected H atoms. Skipping. Residue ALA 694 is missing expected H atoms. Skipping. Residue LEU 696 is missing expected H atoms. Skipping. Residue ALA 699 is missing expected H atoms. Skipping. Residue THR 702 is missing expected H atoms. Skipping. Residue THR 706 is missing expected H atoms. Skipping. Residue VAL 709 is missing expected H atoms. Skipping. Residue VAL 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue ALA 719 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue ALA 725 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue VAL 731 is missing expected H atoms. Skipping. Residue MET 737 is missing expected H atoms. Skipping. Residue THR 739 is missing expected H atoms. Skipping. Residue VAL 741 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue ILE 747 is missing expected H atoms. Skipping. Residue LEU 752 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue VAL 759 is missing expected H atoms. Skipping. Residue VAL 760 is missing expected H atoms. Skipping. Residue VAL 764 is missing expected H atoms. Skipping. Residue LEU 766 is missing expected H atoms. Skipping. Residue ALA 767 is missing expected H atoms. Skipping. Residue VAL 768 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue ALA 770 is missing expected H atoms. Skipping. Residue ALA 771 is missing expected H atoms. Skipping. Residue VAL 772 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue VAL 777 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue THR 798 is missing expected H atoms. Skipping. Residue VAL 802 is missing expected H atoms. Skipping. Residue VAL 805 is missing expected H atoms. Skipping. Residue VAL 806 is missing expected H atoms. Skipping. Residue ILE 809 is missing expected H atoms. Skipping. Residue LEU 812 is missing expected H atoms. Skipping. Residue ALA 823 is missing expected H atoms. Skipping. Residue MET 824 is missing expected H atoms. Skipping. Residue LEU 825 is missing expected H atoms. Skipping. Residue LEU 827 is missing expected H atoms. Skipping. Residue THR 837 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue LEU 839 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue LEU 842 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue MET 850 is missing expected H atoms. Skipping. Residue THR 853 is missing expected H atoms. Skipping. Residue MET 856 is missing expected H atoms. Skipping. Residue ILE 858 is missing expected H atoms. Skipping. Residue LEU 861 is missing expected H atoms. Skipping. Residue ILE 863 is missing expected H atoms. Skipping. Residue ILE 865 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue THR 901 is missing expected H atoms. Skipping. Residue LEU 902 is missing expected H atoms. Skipping. Residue VAL 906 is missing expected H atoms. Skipping. Residue ALA 907 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue ILE 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue VAL 916 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue ALA 925 is missing expected H atoms. Skipping. Residue ILE 926 is missing expected H atoms. Skipping. Residue LEU 927 is missing expected H atoms. Skipping. Residue VAL 929 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue LEU 933 is missing expected H atoms. Skipping. Residue THR 935 is missing expected H atoms. Skipping. Residue THR 937 is missing expected H atoms. Skipping. Residue MET 939 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue ALA 954 is missing expected H atoms. Skipping. Residue VAL 958 is missing expected H atoms. Skipping. Residue ILE 959 is missing expected H atoms. Skipping. Residue LEU 966 is missing expected H atoms. Skipping. Residue ILE 968 is missing expected H atoms. Skipping. Residue ILE 971 is missing expected H atoms. Skipping. Residue THR 972 is missing expected H atoms. Skipping. Residue THR 975 is missing expected H atoms. Skipping. Residue LEU 976 is missing expected H atoms. Skipping. Residue VAL 977 is missing expected H atoms. Skipping. Residue THR 978 is missing expected H atoms. Skipping. Residue THR 979 is missing expected H atoms. Skipping. Residue VAL 981 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue ALA 988 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue VAL 84 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue ILE 140 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue MET 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue THR 162 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue ALA 181 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue MET 191 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue MET 213 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue THR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 244 is missing expected H atoms. Skipping. Residue ALA 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue MET 253 is missing expected H atoms. Skipping. Residue ALA 255 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue ILE 262 is missing expected H atoms. Skipping. Residue ALA 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue ALA 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue ILE 282 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ALA 289 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue VAL 292 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue MET 313 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue MET 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ILE 333 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue VAL 341 is missing expected H atoms. Skipping. Residue LEU 343 is missing expected H atoms. Skipping. Residue LEU 350 is missing expected H atoms. Skipping. Residue ILE 351 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue VAL 356 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 361 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue VAL 371 is missing expected H atoms. Skipping. Residue ALA 373 is missing expected H atoms. Skipping. Residue ILE 377 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue VAL 385 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue ALA 398 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue ILE 406 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue MET 413 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue THR 420 is missing expected H atoms. Skipping. Residue VAL 421 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue ALA 427 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 441 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue ILE 452 is missing expected H atoms. Skipping. Residue VAL 453 is missing expected H atoms. Skipping. Residue VAL 455 is missing expected H atoms. Skipping. Residue THR 456 is missing expected H atoms. Skipping. Residue ALA 462 is missing expected H atoms. Skipping. Residue ALA 465 is missing expected H atoms. Skipping. Residue ALA 467 is missing expected H atoms. Skipping. Residue THR 480 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue VAL 520 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue VAL 533 is missing expected H atoms. Skipping. Residue ILE 542 is missing expected H atoms. Skipping. Residue THR 543 is missing expected H atoms. Skipping. Residue VAL 555 is missing expected H atoms. Skipping. Residue MET 561 is missing expected H atoms. Skipping. Residue LEU 574 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 587 is missing expected H atoms. Skipping. Residue THR 588 is missing expected H atoms. Skipping. Residue THR 590 is missing expected H atoms. Skipping. Residue THR 592 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue ILE 615 is missing expected H atoms. Skipping. Residue THR 623 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 MET cc_start: 0.8593 (mtt) cc_final: 0.8389 (mtt) REVERT: A 445 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.6940 (m-30) REVERT: A 555 MET cc_start: 0.6562 (mtp) cc_final: 0.6142 (mtt) REVERT: B 487 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7665 (mmt180) outliers start: 13 outliers final: 11 residues processed: 55 average time/residue: 0.1543 time to fit residues: 12.4158 Evaluate side-chains 58 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 546 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 101 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 115 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.128336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.080452 restraints weight = 46075.524| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.26 r_work: 0.3084 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 12020 Z= 0.104 Angle : 0.435 5.140 16300 Z= 0.231 Chirality : 0.042 0.169 1784 Planarity : 0.004 0.104 2146 Dihedral : 4.163 39.616 1639 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 26.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.62 % Favored : 93.25 % Rotamer: Outliers : 1.07 % Allowed : 11.60 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.22), residues: 1511 helix: -0.09 (0.47), residues: 123 sheet: 0.05 (0.24), residues: 522 loop : -0.56 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 63 TYR 0.007 0.001 TYR B 344 PHE 0.008 0.001 PHE B 274 TRP 0.015 0.001 TRP A 144 HIS 0.002 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00247 (11990) covalent geometry : angle 0.43492 (16240) SS BOND : bond 0.00164 ( 30) SS BOND : angle 0.46665 ( 60) hydrogen bonds : bond 0.02530 ( 380) hydrogen bonds : angle 5.17128 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5782.42 seconds wall clock time: 98 minutes 58.02 seconds (5938.02 seconds total)