Starting phenix.real_space_refine on Sat Jun 21 09:36:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sob_40652/06_2025/8sob_40652_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sob_40652/06_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_40652/06_2025/8sob_40652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sob_40652/06_2025/8sob_40652.map" model { file = "/net/cci-nas-00/data/ceres_data/8sob_40652/06_2025/8sob_40652_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sob_40652/06_2025/8sob_40652_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.31, per 1000 atoms: 0.46 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: 6.50 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.56 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: 9.22 Time building geometry restraints manager: 7.89 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.400 Extract box with map and model: 0.980 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 52.070 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.070 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP A 812 HIS 0.005 0.001 HIS A 129 PHE 0.016 0.002 PHE B 554 TYR 0.031 0.002 TYR B 658 ARG 0.048 0.001 ARG A 641 Details of bonding type rmsd hydrogen bonds : bond 0.17152 ( 620) hydrogen bonds : angle 7.05036 ( 1776) covalent geometry : bond 0.00630 (12428) covalent geometry : angle 0.62913 (16845) *********************** 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 : 1.808 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: 0.8284 (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: 0.6553 time to fit residues: 175.3056 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 : 1.990 ------------------------------------------------------------------------------- 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 126 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 GLN A 639 ASN A 846 GLN A 967 HIS B 302 GLN B 670 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.074262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.055934 restraints weight = 160536.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.058610 restraints weight = 73775.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.060066 restraints weight = 45480.034| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12428 Z= 0.192 Angle : 0.568 6.366 16845 Z= 0.296 Chirality : 0.040 0.163 1921 Planarity : 0.005 0.047 2122 Dihedral : 6.755 76.153 1676 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.14 % Favored : 95.80 % Rotamer: Outliers : 1.70 % Allowed : 8.00 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.23), residues: 1475 helix: 1.42 (0.20), residues: 690 sheet: -1.71 (0.32), residues: 235 loop : -0.78 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 812 HIS 0.006 0.001 HIS A 129 PHE 0.012 0.001 PHE A 635 TYR 0.015 0.001 TYR A1050 ARG 0.006 0.000 ARG A 947 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 620) hydrogen bonds : angle 5.61057 ( 1776) covalent geometry : bond 0.00404 (12428) covalent geometry : angle 0.56807 (16845) *********************** 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: 23 poor density : 101 time to evaluate : 2.041 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: A 191 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.6359 (ptp90) REVERT: A 778 ASN cc_start: 0.8068 (m-40) cc_final: 0.7818 (p0) REVERT: A 953 MET cc_start: 0.8846 (mtp) cc_final: 0.8570 (mtp) REVERT: B 515 LEU cc_start: 0.9582 (tp) cc_final: 0.9347 (tp) REVERT: B 535 ASN cc_start: 0.9471 (OUTLIER) cc_final: 0.9191 (m-40) outliers start: 23 outliers final: 17 residues processed: 122 average time/residue: 0.6197 time to fit residues: 106.0948 Evaluate side-chains 108 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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 1047 ASP 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 33 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 ASN B 808 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.073335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.054963 restraints weight = 161348.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.057585 restraints weight = 74673.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.059119 restraints weight = 46224.391| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12428 Z= 0.230 Angle : 0.566 5.958 16845 Z= 0.294 Chirality : 0.039 0.160 1921 Planarity : 0.004 0.061 2122 Dihedral : 6.009 57.202 1655 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.81 % Favored : 95.12 % Rotamer: Outliers : 2.37 % Allowed : 8.00 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1475 helix: 1.35 (0.19), residues: 688 sheet: -1.82 (0.32), residues: 237 loop : -0.85 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.005 0.001 HIS A 129 PHE 0.014 0.001 PHE A 416 TYR 0.017 0.001 TYR A1050 ARG 0.007 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 620) hydrogen bonds : angle 5.36457 ( 1776) covalent geometry : bond 0.00484 (12428) covalent geometry : angle 0.56550 (16845) *********************** 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 128 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 2.099 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: A 191 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.6485 (ptp90) REVERT: A 706 SER cc_start: 0.8372 (t) cc_final: 0.8145 (p) REVERT: A 1047 ASP cc_start: 0.7976 (m-30) cc_final: 0.7756 (t0) REVERT: B 515 LEU cc_start: 0.9566 (tp) cc_final: 0.9359 (tp) REVERT: B 535 ASN cc_start: 0.9481 (OUTLIER) cc_final: 0.9171 (m-40) REVERT: B 619 ASN cc_start: 0.4594 (m-40) cc_final: 0.3690 (t0) outliers start: 32 outliers final: 19 residues processed: 123 average time/residue: 0.6356 time to fit residues: 110.2083 Evaluate side-chains 106 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 1.942 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain B residue 552 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 131 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 126 optimal weight: 0.0970 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 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 = 0.3704 r_free = 0.3704 target = 0.073978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.055537 restraints weight = 162060.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.058259 restraints weight = 74710.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.059717 restraints weight = 45991.727| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12428 Z= 0.138 Angle : 0.506 5.888 16845 Z= 0.256 Chirality : 0.038 0.152 1921 Planarity : 0.004 0.045 2122 Dihedral : 5.435 58.306 1648 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.78 % Allowed : 9.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1475 helix: 1.75 (0.20), residues: 683 sheet: -1.77 (0.32), residues: 236 loop : -0.69 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 293 HIS 0.003 0.001 HIS A 199 PHE 0.015 0.001 PHE A 497 TYR 0.015 0.001 TYR A1050 ARG 0.005 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 620) hydrogen bonds : angle 4.88800 ( 1776) covalent geometry : bond 0.00292 (12428) covalent geometry : angle 0.50572 (16845) *********************** 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 120 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.900 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: A 191 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.6289 (ptp90) REVERT: A 706 SER cc_start: 0.8328 (t) cc_final: 0.8112 (p) REVERT: B 515 LEU cc_start: 0.9601 (tp) cc_final: 0.9370 (tp) REVERT: B 535 ASN cc_start: 0.9440 (OUTLIER) cc_final: 0.9110 (m-40) REVERT: B 619 ASN cc_start: 0.4582 (m-40) cc_final: 0.3711 (t0) outliers start: 24 outliers final: 19 residues processed: 115 average time/residue: 0.5955 time to fit residues: 97.8040 Evaluate side-chains 110 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 2.203 ------------------------------------------------------------------------------- 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 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 165 LEU 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 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 142 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 147 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 43 optimal weight: 0.0010 overall best weight: 0.8788 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.074323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.056070 restraints weight = 160212.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.058747 restraints weight = 74328.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.060282 restraints weight = 45938.806| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12428 Z= 0.109 Angle : 0.485 6.179 16845 Z= 0.243 Chirality : 0.038 0.158 1921 Planarity : 0.004 0.050 2122 Dihedral : 5.153 59.201 1646 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.63 % Allowed : 10.07 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1475 helix: 1.95 (0.20), residues: 691 sheet: -1.63 (0.32), residues: 237 loop : -0.59 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 293 HIS 0.010 0.001 HIS B 607 PHE 0.012 0.001 PHE A 497 TYR 0.013 0.001 TYR A1050 ARG 0.008 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 620) hydrogen bonds : angle 4.64190 ( 1776) covalent geometry : bond 0.00233 (12428) covalent geometry : angle 0.48535 (16845) *********************** 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 114 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 2.182 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 171 ASP cc_start: 0.7396 (p0) cc_final: 0.6929 (t0) REVERT: A 191 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.6170 (ptp90) REVERT: A 706 SER cc_start: 0.8191 (t) cc_final: 0.7970 (p) REVERT: B 196 LEU cc_start: 0.9245 (mt) cc_final: 0.8982 (mt) REVERT: B 515 LEU cc_start: 0.9605 (tp) cc_final: 0.9367 (tp) REVERT: B 619 ASN cc_start: 0.4545 (m-40) cc_final: 0.3687 (t0) outliers start: 22 outliers final: 17 residues processed: 110 average time/residue: 0.6276 time to fit residues: 97.3190 Evaluate side-chains 107 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.883 ------------------------------------------------------------------------------- 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 1048 ILE 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 773 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.073795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.055423 restraints weight = 161792.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.058065 restraints weight = 74851.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.059608 restraints weight = 46343.643| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12428 Z= 0.162 Angle : 0.511 6.260 16845 Z= 0.259 Chirality : 0.038 0.170 1921 Planarity : 0.004 0.059 2122 Dihedral : 4.984 59.226 1644 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.00 % Allowed : 10.07 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.23), residues: 1475 helix: 1.84 (0.20), residues: 690 sheet: -1.61 (0.32), residues: 230 loop : -0.65 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 293 HIS 0.004 0.001 HIS A 693 PHE 0.014 0.001 PHE A1084 TYR 0.015 0.001 TYR A1050 ARG 0.010 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 620) hydrogen bonds : angle 4.70033 ( 1776) covalent geometry : bond 0.00343 (12428) covalent geometry : angle 0.51118 (16845) *********************** 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 116 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 2.103 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: 0.8450 (OUTLIER) cc_final: 0.6241 (ptp90) REVERT: A 706 SER cc_start: 0.8288 (t) cc_final: 0.8085 (p) REVERT: B 196 LEU cc_start: 0.9245 (mt) cc_final: 0.9004 (mt) REVERT: B 515 LEU cc_start: 0.9609 (tp) cc_final: 0.9380 (tp) REVERT: B 619 ASN cc_start: 0.4481 (m-40) cc_final: 0.3600 (t0) outliers start: 27 outliers final: 20 residues processed: 111 average time/residue: 0.6360 time to fit residues: 101.4683 Evaluate side-chains 107 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 2.029 ------------------------------------------------------------------------------- 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 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 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 7 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 143 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.072934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.054633 restraints weight = 164371.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.057249 restraints weight = 76087.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.058788 restraints weight = 47124.627| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12428 Z= 0.213 Angle : 0.549 6.925 16845 Z= 0.284 Chirality : 0.039 0.152 1921 Planarity : 0.004 0.065 2122 Dihedral : 5.023 59.204 1640 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.15 % Allowed : 10.30 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1475 helix: 1.59 (0.19), residues: 684 sheet: -1.76 (0.32), residues: 229 loop : -0.72 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 293 HIS 0.004 0.001 HIS A 129 PHE 0.012 0.001 PHE A 270 TYR 0.015 0.001 TYR A1050 ARG 0.011 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 620) hydrogen bonds : angle 4.85998 ( 1776) covalent geometry : bond 0.00447 (12428) covalent geometry : angle 0.54914 (16845) *********************** 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 117 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 4.910 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: A 191 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.6506 (ptp90) REVERT: B 515 LEU cc_start: 0.9614 (tp) cc_final: 0.9387 (tp) REVERT: B 619 ASN cc_start: 0.4347 (m-40) cc_final: 0.3535 (t0) outliers start: 29 outliers final: 22 residues processed: 110 average time/residue: 0.8707 time to fit residues: 140.2475 Evaluate side-chains 106 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 3.370 ------------------------------------------------------------------------------- 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 571 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 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 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 552 LEU 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 13 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 149 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.074495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056211 restraints weight = 162032.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.058865 restraints weight = 75929.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.060432 restraints weight = 47329.952| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12428 Z= 0.110 Angle : 0.488 7.835 16845 Z= 0.243 Chirality : 0.038 0.153 1921 Planarity : 0.004 0.067 2122 Dihedral : 4.758 59.224 1640 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.48 % Allowed : 10.96 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1475 helix: 1.95 (0.20), residues: 691 sheet: -1.69 (0.32), residues: 236 loop : -0.54 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 293 HIS 0.004 0.001 HIS A 693 PHE 0.010 0.001 PHE A 497 TYR 0.011 0.001 TYR A1050 ARG 0.011 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 620) hydrogen bonds : angle 4.46845 ( 1776) covalent geometry : bond 0.00238 (12428) covalent geometry : angle 0.48760 (16845) *********************** 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 109 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 2.142 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 171 ASP cc_start: 0.7382 (p0) cc_final: 0.6968 (t0) REVERT: A 191 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.6112 (ptp90) REVERT: B 196 LEU cc_start: 0.9232 (mt) cc_final: 0.8997 (mt) REVERT: B 515 LEU cc_start: 0.9624 (tp) cc_final: 0.9389 (tp) REVERT: B 619 ASN cc_start: 0.4454 (m-40) cc_final: 0.3581 (t0) outliers start: 20 outliers final: 18 residues processed: 104 average time/residue: 0.6080 time to fit residues: 89.8961 Evaluate side-chains 104 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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 429 LEU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 667 VAL 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 1036 MET 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 Chi-restraints excluded: chain B residue 808 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.073580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.055176 restraints weight = 162321.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.057818 restraints weight = 75224.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.059265 restraints weight = 46758.978| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12428 Z= 0.171 Angle : 0.514 8.284 16845 Z= 0.260 Chirality : 0.038 0.148 1921 Planarity : 0.004 0.073 2122 Dihedral : 4.774 59.795 1639 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.33 % Allowed : 11.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.23), residues: 1475 helix: 1.86 (0.20), residues: 689 sheet: -1.73 (0.31), residues: 236 loop : -0.58 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 293 HIS 0.003 0.001 HIS A 693 PHE 0.010 0.001 PHE A 270 TYR 0.013 0.001 TYR A1050 ARG 0.012 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 620) hydrogen bonds : angle 4.57062 ( 1776) covalent geometry : bond 0.00360 (12428) covalent geometry : angle 0.51445 (16845) *********************** 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: 18 poor density : 84 time to evaluate : 1.883 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: A 191 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.6195 (ptp90) REVERT: B 196 LEU cc_start: 0.9252 (mt) cc_final: 0.9002 (mt) REVERT: B 515 LEU cc_start: 0.9617 (tp) cc_final: 0.9395 (tp) REVERT: B 619 ASN cc_start: 0.4303 (m-40) cc_final: 0.3540 (t0) outliers start: 18 outliers final: 16 residues processed: 98 average time/residue: 0.6481 time to fit residues: 89.6703 Evaluate side-chains 100 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 2.190 ------------------------------------------------------------------------------- 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 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 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 14 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 114 optimal weight: 0.0070 chunk 10 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.074814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.056632 restraints weight = 160887.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.059288 restraints weight = 72755.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.060890 restraints weight = 44862.591| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12428 Z= 0.091 Angle : 0.483 8.536 16845 Z= 0.237 Chirality : 0.038 0.153 1921 Planarity : 0.004 0.073 2122 Dihedral : 4.515 58.354 1639 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.11 % Allowed : 11.70 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1475 helix: 2.20 (0.20), residues: 697 sheet: -1.53 (0.32), residues: 233 loop : -0.54 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 293 HIS 0.005 0.000 HIS A 693 PHE 0.010 0.001 PHE A 497 TYR 0.010 0.001 TYR B 658 ARG 0.015 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 620) hydrogen bonds : angle 4.22931 ( 1776) covalent geometry : bond 0.00201 (12428) covalent geometry : angle 0.48296 (16845) ********************** 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 104 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 2.155 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: A 171 ASP cc_start: 0.7491 (p0) cc_final: 0.6954 (t0) REVERT: A 191 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.6012 (ptp90) REVERT: B 196 LEU cc_start: 0.9206 (mt) cc_final: 0.8973 (mt) REVERT: B 515 LEU cc_start: 0.9622 (tp) cc_final: 0.9389 (tp) REVERT: B 615 TRP cc_start: 0.5167 (t-100) cc_final: 0.4141 (t-100) REVERT: B 619 ASN cc_start: 0.4450 (m-40) cc_final: 0.3136 (t0) outliers start: 15 outliers final: 13 residues processed: 101 average time/residue: 0.6216 time to fit residues: 88.6295 Evaluate side-chains 97 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.980 ------------------------------------------------------------------------------- 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 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 118 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.074552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.056352 restraints weight = 161865.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.058982 restraints weight = 73496.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.060440 restraints weight = 45522.770| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3572 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= 0.115 Angle : 0.487 8.701 16845 Z= 0.240 Chirality : 0.038 0.151 1921 Planarity : 0.004 0.073 2122 Dihedral : 4.386 58.613 1637 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.11 % Allowed : 12.00 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1475 helix: 2.20 (0.19), residues: 696 sheet: -1.50 (0.32), residues: 231 loop : -0.59 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 293 HIS 0.004 0.000 HIS A 693 PHE 0.015 0.001 PHE A1084 TYR 0.011 0.001 TYR A1050 ARG 0.013 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 620) hydrogen bonds : angle 4.25667 ( 1776) covalent geometry : bond 0.00249 (12428) covalent geometry : angle 0.48731 (16845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7677.32 seconds wall clock time: 136 minutes 18.54 seconds (8178.54 seconds total)