Starting phenix.real_space_refine on Sun Oct 12 13:35:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sob_40652/10_2025/8sob_40652_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sob_40652/10_2025/8sob_40652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sob_40652/10_2025/8sob_40652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sob_40652/10_2025/8sob_40652.map" model { file = "/net/cci-nas-00/data/ceres_data/8sob_40652/10_2025/8sob_40652_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sob_40652/10_2025/8sob_40652_trim.cif" } resolution = 3.9 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= 0.022 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 62 5.16 5 C 7804 2.51 5 N 2075 2.21 5 O 2218 1.98 5 H 12255 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24416 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 16374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 16374 Classifications: {'peptide': 1005} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 959} Chain breaks: 6 Chain: "B" Number of atoms: 8015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 8015 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 476} Chain breaks: 8 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.21, per 1000 atoms: 0.17 Number of scatterers: 24416 At special positions: 0 Unit cell: (101.52, 116.64, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 2 15.00 O 2218 8.00 N 2075 7.00 C 7804 6.00 H 12255 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.30 Conformation dependent library (CDL) restraints added in 721.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2880 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 15 sheets defined 51.8% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.608A pdb=" N GLU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 91 removed outlier: 4.002A pdb=" N TYR A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 115 through 118 Processing helix chain 'A' and resid 119 through 129 removed outlier: 4.017A pdb=" N ARG A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 159 Processing helix chain 'A' and resid 171 through 180 Processing helix chain 'A' and resid 180 through 190 removed outlier: 3.699A pdb=" N ARG A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.543A pdb=" N LYS A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 255 through 260 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 286 through 289 Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 568 through 578 Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 584 through 587 removed outlier: 7.152A pdb=" N LYS A 587 " --> pdb=" O LYS A 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 584 through 587' Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.771A pdb=" N SER A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 595 " --> pdb=" O LYS A 591 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 613 removed outlier: 3.888A pdb=" N LYS A 613 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 623 through 632 removed outlier: 3.611A pdb=" N GLN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 649 removed outlier: 3.810A pdb=" N ARG A 641 " --> pdb=" O ASP A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 667 removed outlier: 3.538A pdb=" N VAL A 656 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LEU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLN A 662 " --> pdb=" O HIS A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 670 No H-bonds generated for 'chain 'A' and resid 668 through 670' Processing helix chain 'A' and resid 675 through 688 removed outlier: 3.952A pdb=" N ARG A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 688 " --> pdb=" O ARG A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 706 removed outlier: 3.503A pdb=" N GLN A 705 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 726 through 751 Processing helix chain 'A' and resid 761 through 777 Processing helix chain 'A' and resid 838 through 858 Processing helix chain 'A' and resid 888 through 896 removed outlier: 3.805A pdb=" N THR A 895 " --> pdb=" O ILE A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 915 removed outlier: 4.199A pdb=" N SER A 908 " --> pdb=" O ASP A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 943 Processing helix chain 'A' and resid 988 through 996 removed outlier: 3.579A pdb=" N LEU A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 Processing helix chain 'A' and resid 1023 through 1038 Processing helix chain 'A' and resid 1044 through 1056 removed outlier: 4.398A pdb=" N ILE A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A1056 " --> pdb=" O ARG A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1079 removed outlier: 3.967A pdb=" N GLY A1079 " --> pdb=" O CYS A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1092 Processing helix chain 'B' and resid 8 through 22 Processing helix chain 'B' and resid 39 through 49 Processing helix chain 'B' and resid 51 through 73 removed outlier: 4.047A pdb=" N PHE B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.579A pdb=" N LEU B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 90 " --> pdb=" O TYR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 110 Processing helix chain 'B' and resid 118 through 136 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 172 through 184 Processing helix chain 'B' and resid 188 through 206 Processing helix chain 'B' and resid 210 through 220 removed outlier: 3.671A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.734A pdb=" N GLN B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.655A pdb=" N VAL B 269 " --> pdb=" O PHE B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 307 removed outlier: 3.664A pdb=" N LEU B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 543 removed outlier: 3.847A pdb=" N LYS B 528 " --> pdb=" O ARG B 524 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 532 " --> pdb=" O LYS B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 550 removed outlier: 3.593A pdb=" N PHE B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 613 removed outlier: 3.693A pdb=" N LEU B 609 " --> pdb=" O ILE B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 620 Processing helix chain 'B' and resid 650 through 663 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 139 Processing sheet with id=AA3, first strand: chain 'A' and resid 229 through 236 removed outlier: 4.564A pdb=" N ILE A 303 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A 307 " --> pdb=" O HIS A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.345A pdb=" N VAL A 352 " --> pdb=" O ALA A 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 407 through 419 removed outlier: 6.511A pdb=" N ARG A 366 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL A 412 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS A 364 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 414 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG A 362 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N PHE A 416 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LYS A 360 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER A 517 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE A 368 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER A 515 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 398 removed outlier: 6.547A pdb=" N ILE A 387 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLN A 396 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA A 385 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG A 398 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL A 383 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 398 removed outlier: 6.547A pdb=" N ILE A 387 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLN A 396 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA A 385 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG A 398 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL A 383 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 431 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR A 463 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE A 433 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 463 " --> pdb=" O TRP A 485 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 783 through 784 Processing sheet with id=AA9, first strand: chain 'A' and resid 802 through 803 removed outlier: 6.509A pdb=" N ILE A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AB2, first strand: chain 'B' and resid 289 through 292 removed outlier: 6.372A pdb=" N THR B 162 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N TYR B 291 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU B 164 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL B 161 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL B 518 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL B 163 " --> pdb=" O VAL B 518 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE B 520 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU B 165 " --> pdb=" O PHE B 520 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 665 through 667 removed outlier: 3.792A pdb=" N ILE B 869 " --> pdb=" O VAL B 667 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 683 through 688 removed outlier: 7.042A pdb=" N GLN B 673 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 832 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU B 675 " --> pdb=" O CYS B 830 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS B 830 " --> pdb=" O GLU B 675 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR B 677 " --> pdb=" O ILE B 828 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 683 through 688 removed outlier: 7.042A pdb=" N GLN B 673 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 832 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU B 675 " --> pdb=" O CYS B 830 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS B 830 " --> pdb=" O GLU B 675 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR B 677 " --> pdb=" O ILE B 828 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS B 822 " --> pdb=" O LEU B 816 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 816 " --> pdb=" O LYS B 822 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER B 826 " --> pdb=" O PHE B 812 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N PHE B 812 " --> pdb=" O SER B 826 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 692 through 694 removed outlier: 3.832A pdb=" N LEU B 774 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER B 795 " --> pdb=" O LEU B 774 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1776 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: 5.97 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 12218 1.03 - 1.22: 38 1.22 - 1.42: 5109 1.42 - 1.61: 7231 1.61 - 1.81: 87 Bond restraints: 24683 Sorted by residual: bond pdb=" CB ILE A1051 " pdb=" CG2 ILE A1051 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.36e+00 bond pdb=" CB TRP B 115 " pdb=" CG TRP B 115 " ideal model delta sigma weight residual 1.498 1.451 0.047 3.10e-02 1.04e+03 2.26e+00 bond pdb=" C4 ADP A1201 " pdb=" C5 ADP A1201 " ideal model delta sigma weight residual 1.490 1.460 0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" CB PHE A 832 " pdb=" CG PHE A 832 " ideal model delta sigma weight residual 1.502 1.469 0.033 2.30e-02 1.89e+03 2.07e+00 bond pdb=" CB PHE A 696 " pdb=" CG PHE A 696 " ideal model delta sigma weight residual 1.502 1.469 0.033 2.30e-02 1.89e+03 2.02e+00 ... (remaining 24678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 43032 1.28 - 2.56: 1515 2.56 - 3.85: 132 3.85 - 5.13: 23 5.13 - 6.41: 7 Bond angle restraints: 44709 Sorted by residual: angle pdb=" N GLY A 133 " pdb=" CA GLY A 133 " pdb=" C GLY A 133 " ideal model delta sigma weight residual 111.93 115.59 -3.66 1.15e+00 7.56e-01 1.01e+01 angle pdb=" N ILE A1048 " pdb=" CA ILE A1048 " pdb=" C ILE A1048 " ideal model delta sigma weight residual 111.09 107.92 3.17 1.25e+00 6.40e-01 6.42e+00 angle pdb=" CA CYS B 123 " pdb=" CB CYS B 123 " pdb=" SG CYS B 123 " ideal model delta sigma weight residual 114.40 108.66 5.74 2.30e+00 1.89e-01 6.24e+00 angle pdb=" N ILE B 525 " pdb=" CA ILE B 525 " pdb=" C ILE B 525 " ideal model delta sigma weight residual 113.16 109.57 3.59 1.49e+00 4.50e-01 5.81e+00 angle pdb=" O1B ADP A1201 " pdb=" PB ADP A1201 " pdb=" O2B ADP A1201 " ideal model delta sigma weight residual 119.90 113.49 6.41 3.00e+00 1.11e-01 4.56e+00 ... (remaining 44704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.97: 11135 22.97 - 45.95: 323 45.95 - 68.92: 91 68.92 - 91.89: 5 91.89 - 114.87: 1 Dihedral angle restraints: 11555 sinusoidal: 6323 harmonic: 5232 Sorted by residual: dihedral pdb=" CD ARG A 641 " pdb=" NE ARG A 641 " pdb=" CZ ARG A 641 " pdb=" NH1 ARG A 641 " ideal model delta sinusoidal sigma weight residual 0.00 -73.39 73.39 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" C5' ADP A1201 " pdb=" O5' ADP A1201 " pdb=" PA ADP A1201 " pdb=" O2A ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 -174.86 114.87 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" CD ARG A 579 " pdb=" NE ARG A 579 " pdb=" CZ ARG A 579 " pdb=" NH1 ARG A 579 " ideal model delta sinusoidal sigma weight residual 0.00 35.40 -35.40 1 1.00e+01 1.00e-02 1.77e+01 ... (remaining 11552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1301 0.034 - 0.069: 430 0.069 - 0.103: 133 0.103 - 0.137: 54 0.137 - 0.171: 3 Chirality restraints: 1921 Sorted by residual: chirality pdb=" CA PHE B 662 " pdb=" N PHE B 662 " pdb=" C PHE B 662 " pdb=" CB PHE B 662 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CA ILE A 387 " pdb=" N ILE A 387 " pdb=" C ILE A 387 " pdb=" CB ILE A 387 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA PRO A 789 " pdb=" N PRO A 789 " pdb=" C PRO A 789 " pdb=" CB PRO A 789 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 1918 not shown) Planarity restraints: 3543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 641 " 0.951 9.50e-02 1.11e+02 3.18e-01 1.15e+02 pdb=" NE ARG A 641 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG A 641 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 641 " -0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG A 641 " -0.021 2.00e-02 2.50e+03 pdb="HH11 ARG A 641 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 641 " 0.017 2.00e-02 2.50e+03 pdb="HH21 ARG A 641 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 641 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 579 " 0.541 9.50e-02 1.11e+02 1.81e-01 4.02e+01 pdb=" NE ARG A 579 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 579 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG A 579 " -0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG A 579 " -0.015 2.00e-02 2.50e+03 pdb="HH11 ARG A 579 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 579 " 0.009 2.00e-02 2.50e+03 pdb="HH21 ARG A 579 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 579 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 302 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C GLN B 302 " 0.040 2.00e-02 2.50e+03 pdb=" O GLN B 302 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU B 303 " -0.014 2.00e-02 2.50e+03 ... (remaining 3540 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 431 2.08 - 2.71: 42579 2.71 - 3.34: 69060 3.34 - 3.97: 84048 3.97 - 4.60: 137292 Nonbonded interactions: 333410 Sorted by model distance: nonbonded pdb=" OD2 ASP A 637 " pdb=" H VAL A 640 " model vdw 1.452 2.450 nonbonded pdb=" O GLY B 521 " pdb=" H VAL B 559 " model vdw 1.487 2.450 nonbonded pdb=" OD2 ASP A 192 " pdb=" H LEU A 195 " model vdw 1.502 2.450 nonbonded pdb=" OD2 ASP A 674 " pdb="HH21 ARG A 679 " model vdw 1.550 2.450 nonbonded pdb="HD22 ASN A 465 " pdb=" O LYS A 501 " model vdw 1.560 2.450 ... (remaining 333405 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 group one per residue 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.200 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 : 0.006 0.069 12428 Z= 0.302 Angle : 0.629 6.409 16845 Z= 0.338 Chirality : 0.041 0.171 1921 Planarity : 0.011 0.409 2122 Dihedral : 11.264 114.866 4615 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.19 % Favored : 92.75 % Rotamer: Outliers : 2.74 % Allowed : 4.07 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.07 (0.23), residues: 1475 helix: 1.48 (0.21), residues: 660 sheet: -1.47 (0.35), residues: 218 loop : -0.95 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.001 ARG A 641 TYR 0.031 0.002 TYR B 658 PHE 0.016 0.002 PHE B 554 TRP 0.014 0.001 TRP A 812 HIS 0.005 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00630 (12428) covalent geometry : angle 0.62913 (16845) hydrogen bonds : bond 0.17152 ( 620) hydrogen bonds : angle 7.05036 ( 1776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.6438 (ptp90) REVERT: A 684 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7506 (mmt180) REVERT: A 731 ASP cc_start: 0.8581 (m-30) cc_final: 0.8283 (m-30) REVERT: A 878 MET cc_start: 0.7554 (ttm) cc_final: 0.7340 (ttm) REVERT: A 953 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8323 (mtp) outliers start: 37 outliers final: 21 residues processed: 196 average time/residue: 0.3333 time to fit residues: 88.6281 Evaluate side-chains 114 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 684 ARG Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 22 HIS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 TYR Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 771 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 GLN A 619 GLN A 639 ASN A 967 HIS B 302 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.074529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.056289 restraints weight = 160847.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.058901 restraints weight = 73447.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.060445 restraints weight = 45777.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.061080 restraints weight = 34513.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.061798 restraints weight = 30349.516| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12428 Z= 0.168 Angle : 0.554 6.417 16845 Z= 0.287 Chirality : 0.039 0.162 1921 Planarity : 0.004 0.046 2122 Dihedral : 6.683 71.572 1676 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.86 % Favored : 96.07 % Rotamer: Outliers : 1.63 % Allowed : 7.85 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.23 (0.23), residues: 1475 helix: 1.56 (0.20), residues: 688 sheet: -1.68 (0.32), residues: 236 loop : -0.71 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 641 TYR 0.015 0.001 TYR A1050 PHE 0.012 0.001 PHE A 635 TRP 0.009 0.001 TRP A 812 HIS 0.005 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00352 (12428) covalent geometry : angle 0.55435 (16845) hydrogen bonds : bond 0.04695 ( 620) hydrogen bonds : angle 5.52412 ( 1776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.6231 (ptp90) REVERT: A 953 MET cc_start: 0.8843 (mtp) cc_final: 0.8591 (mtp) REVERT: B 515 LEU cc_start: 0.9599 (tp) cc_final: 0.9333 (tp) REVERT: B 619 ASN cc_start: 0.4456 (m-40) cc_final: 0.3513 (t0) outliers start: 22 outliers final: 17 residues processed: 122 average time/residue: 0.3114 time to fit residues: 53.1700 Evaluate side-chains 106 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 683 LYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain B residue 22 HIS Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 TYR Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain B residue 552 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 18 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN B 808 ASN ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.073074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.054707 restraints weight = 161932.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.057321 restraints weight = 75092.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.058859 restraints weight = 46464.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.059794 restraints weight = 34875.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.060277 restraints weight = 29328.513| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12428 Z= 0.246 Angle : 0.580 6.001 16845 Z= 0.302 Chirality : 0.039 0.154 1921 Planarity : 0.005 0.057 2122 Dihedral : 5.991 56.791 1653 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.02 % Favored : 94.92 % Rotamer: Outliers : 2.30 % Allowed : 8.30 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.08 (0.22), residues: 1475 helix: 1.29 (0.19), residues: 688 sheet: -1.82 (0.32), residues: 237 loop : -0.87 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 268 TYR 0.017 0.001 TYR A1050 PHE 0.013 0.001 PHE A 416 TRP 0.010 0.001 TRP B 115 HIS 0.006 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00519 (12428) covalent geometry : angle 0.57955 (16845) hydrogen bonds : bond 0.04602 ( 620) hydrogen bonds : angle 5.39483 ( 1776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.6346 (ptp90) REVERT: A 706 SER cc_start: 0.8383 (t) cc_final: 0.8167 (p) REVERT: B 515 LEU cc_start: 0.9572 (tp) cc_final: 0.9353 (tp) REVERT: B 535 ASN cc_start: 0.9439 (OUTLIER) cc_final: 0.9159 (m-40) REVERT: B 619 ASN cc_start: 0.4563 (m-40) cc_final: 0.3639 (t0) outliers start: 31 outliers final: 18 residues processed: 116 average time/residue: 0.3267 time to fit residues: 52.5324 Evaluate side-chains 100 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 683 LYS Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 TYR Chi-restraints excluded: chain B residue 535 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 HIS B 808 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.073858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.055503 restraints weight = 161533.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.058189 restraints weight = 74606.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.059650 restraints weight = 46046.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.060667 restraints weight = 34927.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.061180 restraints weight = 29145.612| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12428 Z= 0.138 Angle : 0.508 5.893 16845 Z= 0.257 Chirality : 0.038 0.155 1921 Planarity : 0.004 0.051 2122 Dihedral : 5.278 58.409 1646 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.85 % Allowed : 9.70 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.40 (0.23), residues: 1475 helix: 1.78 (0.20), residues: 682 sheet: -1.74 (0.32), residues: 236 loop : -0.66 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 268 TYR 0.015 0.001 TYR A1050 PHE 0.013 0.001 PHE A 416 TRP 0.008 0.001 TRP B 293 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00293 (12428) covalent geometry : angle 0.50848 (16845) hydrogen bonds : bond 0.03811 ( 620) hydrogen bonds : angle 4.87773 ( 1776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.6261 (ptp90) REVERT: A 706 SER cc_start: 0.8448 (t) cc_final: 0.8198 (p) REVERT: B 515 LEU cc_start: 0.9587 (tp) cc_final: 0.9369 (tp) REVERT: B 535 ASN cc_start: 0.9427 (OUTLIER) cc_final: 0.9119 (m-40) REVERT: B 619 ASN cc_start: 0.4568 (m-40) cc_final: 0.3691 (t0) outliers start: 25 outliers final: 21 residues processed: 111 average time/residue: 0.3095 time to fit residues: 48.2615 Evaluate side-chains 109 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 683 LYS Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 533 TYR Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 808 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 18 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.074492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.056243 restraints weight = 159967.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.058919 restraints weight = 72850.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.060521 restraints weight = 45044.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.061474 restraints weight = 33601.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.061974 restraints weight = 28163.110| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12428 Z= 0.097 Angle : 0.485 6.306 16845 Z= 0.241 Chirality : 0.038 0.155 1921 Planarity : 0.004 0.055 2122 Dihedral : 4.947 59.363 1644 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.56 % Allowed : 9.56 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.71 (0.23), residues: 1475 helix: 2.07 (0.20), residues: 690 sheet: -1.60 (0.32), residues: 230 loop : -0.59 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 268 TYR 0.013 0.001 TYR A1050 PHE 0.009 0.001 PHE A 270 TRP 0.008 0.001 TRP A1080 HIS 0.009 0.001 HIS B 607 Details of bonding type rmsd covalent geometry : bond 0.00211 (12428) covalent geometry : angle 0.48546 (16845) hydrogen bonds : bond 0.03446 ( 620) hydrogen bonds : angle 4.56536 ( 1776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ASP cc_start: 0.7494 (p0) cc_final: 0.7003 (t0) REVERT: A 191 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.6206 (ptp90) REVERT: A 706 SER cc_start: 0.8377 (t) cc_final: 0.8087 (p) REVERT: B 196 LEU cc_start: 0.9186 (mt) cc_final: 0.8933 (mt) REVERT: B 515 LEU cc_start: 0.9594 (tp) cc_final: 0.9368 (tp) REVERT: B 535 ASN cc_start: 0.9385 (OUTLIER) cc_final: 0.9080 (m-40) REVERT: B 619 ASN cc_start: 0.4531 (m-40) cc_final: 0.3674 (t0) outliers start: 21 outliers final: 16 residues processed: 107 average time/residue: 0.3097 time to fit residues: 46.7131 Evaluate side-chains 103 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain B residue 533 TYR Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain B residue 773 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 52 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN B 727 GLN B 808 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.072609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.054324 restraints weight = 164113.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.056893 restraints weight = 76311.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.058428 restraints weight = 47547.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.059367 restraints weight = 35629.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.059928 restraints weight = 29982.677| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12428 Z= 0.267 Angle : 0.580 5.847 16845 Z= 0.304 Chirality : 0.040 0.165 1921 Planarity : 0.004 0.056 2122 Dihedral : 5.233 58.346 1644 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.22 % Allowed : 10.52 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.15 (0.22), residues: 1475 helix: 1.55 (0.19), residues: 683 sheet: -1.88 (0.31), residues: 237 loop : -0.72 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 268 TYR 0.017 0.002 TYR A1050 PHE 0.014 0.001 PHE A 497 TRP 0.011 0.001 TRP B 293 HIS 0.005 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00562 (12428) covalent geometry : angle 0.58007 (16845) hydrogen bonds : bond 0.04108 ( 620) hydrogen bonds : angle 5.03421 ( 1776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.6493 (ptp90) REVERT: A 706 SER cc_start: 0.8438 (t) cc_final: 0.8236 (p) REVERT: B 515 LEU cc_start: 0.9594 (tp) cc_final: 0.9370 (tp) REVERT: B 535 ASN cc_start: 0.9411 (OUTLIER) cc_final: 0.9080 (m-40) REVERT: B 619 ASN cc_start: 0.4520 (m-40) cc_final: 0.3608 (t0) outliers start: 30 outliers final: 20 residues processed: 108 average time/residue: 0.3146 time to fit residues: 47.6790 Evaluate side-chains 101 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 683 LYS Chi-restraints excluded: chain A residue 743 GLN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 533 TYR Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain B residue 773 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.073102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.054879 restraints weight = 162763.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.057473 restraints weight = 75859.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.058877 restraints weight = 47153.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.059847 restraints weight = 36061.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.060347 restraints weight = 30235.636| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12428 Z= 0.174 Angle : 0.524 7.330 16845 Z= 0.267 Chirality : 0.039 0.155 1921 Planarity : 0.004 0.067 2122 Dihedral : 5.097 59.830 1642 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.00 % Allowed : 10.59 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.27 (0.22), residues: 1475 helix: 1.68 (0.20), residues: 683 sheet: -1.83 (0.31), residues: 236 loop : -0.71 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 268 TYR 0.013 0.001 TYR A1050 PHE 0.015 0.001 PHE A 497 TRP 0.010 0.001 TRP B 293 HIS 0.003 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00365 (12428) covalent geometry : angle 0.52379 (16845) hydrogen bonds : bond 0.03735 ( 620) hydrogen bonds : angle 4.79956 ( 1776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.6331 (ptp90) REVERT: B 196 LEU cc_start: 0.9269 (mt) cc_final: 0.9029 (mt) REVERT: B 515 LEU cc_start: 0.9609 (tp) cc_final: 0.9371 (tp) REVERT: B 535 ASN cc_start: 0.9369 (OUTLIER) cc_final: 0.9043 (m-40) REVERT: B 619 ASN cc_start: 0.4460 (m-40) cc_final: 0.3554 (t0) outliers start: 27 outliers final: 18 residues processed: 105 average time/residue: 0.3019 time to fit residues: 45.0527 Evaluate side-chains 99 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 533 TYR Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain B residue 773 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 53 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.073135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.055026 restraints weight = 163319.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.057572 restraints weight = 75913.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.058976 restraints weight = 47391.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.059946 restraints weight = 36263.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.060449 restraints weight = 30434.433| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12428 Z= 0.176 Angle : 0.525 7.852 16845 Z= 0.268 Chirality : 0.038 0.152 1921 Planarity : 0.004 0.071 2122 Dihedral : 4.968 59.989 1640 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.63 % Allowed : 11.26 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.29 (0.22), residues: 1475 helix: 1.68 (0.19), residues: 684 sheet: -1.80 (0.32), residues: 234 loop : -0.70 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 268 TYR 0.014 0.001 TYR A1050 PHE 0.013 0.001 PHE A 497 TRP 0.010 0.001 TRP B 293 HIS 0.003 0.001 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00370 (12428) covalent geometry : angle 0.52518 (16845) hydrogen bonds : bond 0.03676 ( 620) hydrogen bonds : angle 4.75424 ( 1776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.6485 (ptp90) REVERT: B 196 LEU cc_start: 0.9267 (mt) cc_final: 0.9028 (mt) REVERT: B 515 LEU cc_start: 0.9613 (tp) cc_final: 0.9376 (tp) REVERT: B 619 ASN cc_start: 0.4452 (m-40) cc_final: 0.3558 (t0) outliers start: 22 outliers final: 20 residues processed: 100 average time/residue: 0.3062 time to fit residues: 43.3223 Evaluate side-chains 99 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 533 TYR Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain B residue 773 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 GLN B 808 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.073549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.055430 restraints weight = 163222.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.057949 restraints weight = 74962.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.059479 restraints weight = 46955.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.060391 restraints weight = 35342.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.060932 restraints weight = 29946.289| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12428 Z= 0.135 Angle : 0.503 7.933 16845 Z= 0.253 Chirality : 0.038 0.153 1921 Planarity : 0.004 0.075 2122 Dihedral : 4.784 59.049 1639 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.56 % Allowed : 11.33 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.48 (0.23), residues: 1475 helix: 1.85 (0.19), residues: 691 sheet: -1.74 (0.32), residues: 237 loop : -0.64 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 268 TYR 0.012 0.001 TYR A1050 PHE 0.016 0.001 PHE B 298 TRP 0.011 0.001 TRP B 293 HIS 0.003 0.001 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00288 (12428) covalent geometry : angle 0.50306 (16845) hydrogen bonds : bond 0.03413 ( 620) hydrogen bonds : angle 4.55628 ( 1776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.6197 (ptp90) REVERT: B 196 LEU cc_start: 0.9267 (mt) cc_final: 0.9024 (mt) REVERT: B 515 LEU cc_start: 0.9621 (tp) cc_final: 0.9377 (tp) REVERT: B 535 ASN cc_start: 0.9311 (OUTLIER) cc_final: 0.9028 (m-40) REVERT: B 619 ASN cc_start: 0.4195 (m-40) cc_final: 0.3439 (t0) outliers start: 21 outliers final: 17 residues processed: 98 average time/residue: 0.2860 time to fit residues: 39.7217 Evaluate side-chains 97 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 533 TYR Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain B residue 773 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 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 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.073955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.056010 restraints weight = 161017.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.058561 restraints weight = 73581.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.060102 restraints weight = 46034.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.061045 restraints weight = 34541.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.061551 restraints weight = 29034.904| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12428 Z= 0.111 Angle : 0.491 8.290 16845 Z= 0.244 Chirality : 0.038 0.154 1921 Planarity : 0.004 0.075 2122 Dihedral : 4.617 58.432 1639 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.33 % Allowed : 11.33 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.66 (0.23), residues: 1475 helix: 2.08 (0.20), residues: 691 sheet: -1.72 (0.31), residues: 240 loop : -0.64 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 268 TYR 0.012 0.001 TYR A1050 PHE 0.016 0.001 PHE A1084 TRP 0.011 0.001 TRP B 293 HIS 0.004 0.000 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00240 (12428) covalent geometry : angle 0.49139 (16845) hydrogen bonds : bond 0.03204 ( 620) hydrogen bonds : angle 4.37720 ( 1776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.6107 (ptp90) REVERT: B 196 LEU cc_start: 0.9225 (mt) cc_final: 0.8997 (mt) REVERT: B 515 LEU cc_start: 0.9609 (tp) cc_final: 0.9372 (tp) REVERT: B 535 ASN cc_start: 0.9264 (OUTLIER) cc_final: 0.8935 (m-40) REVERT: B 615 TRP cc_start: 0.5036 (t-100) cc_final: 0.4064 (t-100) REVERT: B 619 ASN cc_start: 0.4189 (m-40) cc_final: 0.2925 (t0) outliers start: 18 outliers final: 13 residues processed: 97 average time/residue: 0.3033 time to fit residues: 41.1704 Evaluate side-chains 94 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain B residue 773 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 122 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 55 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.074096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.055975 restraints weight = 161173.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.058631 restraints weight = 74809.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.060206 restraints weight = 46294.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.061191 restraints weight = 34533.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.061714 restraints weight = 28904.651| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12428 Z= 0.116 Angle : 0.488 8.321 16845 Z= 0.241 Chirality : 0.038 0.153 1921 Planarity : 0.004 0.074 2122 Dihedral : 4.443 58.132 1637 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.19 % Allowed : 11.70 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.70 (0.23), residues: 1475 helix: 2.10 (0.19), residues: 698 sheet: -1.68 (0.32), residues: 240 loop : -0.65 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 268 TYR 0.011 0.001 TYR A1050 PHE 0.019 0.001 PHE B 298 TRP 0.014 0.001 TRP B 293 HIS 0.004 0.000 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00250 (12428) covalent geometry : angle 0.48800 (16845) hydrogen bonds : bond 0.03160 ( 620) hydrogen bonds : angle 4.31479 ( 1776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3929.59 seconds wall clock time: 67 minutes 53.06 seconds (4073.06 seconds total)