Starting phenix.real_space_refine on Thu Sep 26 02:57:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xfb_38300/09_2024/8xfb_38300.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xfb_38300/09_2024/8xfb_38300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xfb_38300/09_2024/8xfb_38300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xfb_38300/09_2024/8xfb_38300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xfb_38300/09_2024/8xfb_38300.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xfb_38300/09_2024/8xfb_38300.cif" } resolution = 3.4 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= 0.001 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7555 2.51 5 N 2043 2.21 5 O 2176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11837 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1147 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain: "A" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2485 Classifications: {'peptide': 314} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 297} Chain breaks: 7 Chain: "B" Number of atoms: 8205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8205 Classifications: {'peptide': 1038} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 996} Chain breaks: 8 Time building chain proxies: 7.79, per 1000 atoms: 0.66 Number of scatterers: 11837 At special positions: 0 Unit cell: (102.85, 113.9, 173.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2176 8.00 N 2043 7.00 C 7555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D1029 " - pdb=" SG CYS B1029 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.7 seconds 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2834 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 19 sheets defined 37.0% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'D' and resid 973 through 990 removed outlier: 3.513A pdb=" N LYS D 990 " --> pdb=" O LEU D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1007 removed outlier: 4.404A pdb=" N LYS D 999 " --> pdb=" O ASP D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1018 removed outlier: 3.723A pdb=" N LEU D1016 " --> pdb=" O ARG D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1026 through 1040 Processing helix chain 'D' and resid 1048 through 1061 removed outlier: 3.633A pdb=" N GLY D1061 " --> pdb=" O MET D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1062 through 1074 removed outlier: 3.716A pdb=" N GLY D1066 " --> pdb=" O LYS D1062 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP D1074 " --> pdb=" O LEU D1070 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1087 Processing helix chain 'D' and resid 1088 through 1099 Processing helix chain 'D' and resid 1101 through 1116 removed outlier: 3.703A pdb=" N ALA D1106 " --> pdb=" O PRO D1102 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASP D1107 " --> pdb=" O GLU D1103 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D1108 " --> pdb=" O GLU D1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.052A pdb=" N THR A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 409 removed outlier: 4.253A pdb=" N THR A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 removed outlier: 4.290A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 450 removed outlier: 3.642A pdb=" N LEU A 445 " --> pdb=" O HIS A 441 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 448 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 543 removed outlier: 3.813A pdb=" N LYS A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.541A pdb=" N ASP A 593 " --> pdb=" O THR A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 645 removed outlier: 3.710A pdb=" N ASN A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 720 removed outlier: 3.757A pdb=" N TRP A 720 " --> pdb=" O GLU A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 748 removed outlier: 3.550A pdb=" N HIS A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 776 removed outlier: 4.496A pdb=" N ASN A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 764 " --> pdb=" O HIS A 760 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 766 " --> pdb=" O SER A 762 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 24 removed outlier: 3.802A pdb=" N LYS B 24 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 430 removed outlier: 4.140A pdb=" N SER B 426 " --> pdb=" O PRO B 423 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU B 427 " --> pdb=" O ASP B 424 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ASP B 428 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 484 removed outlier: 3.703A pdb=" N TYR B 484 " --> pdb=" O ILE B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 848 through 861 removed outlier: 3.805A pdb=" N LEU B 853 " --> pdb=" O PRO B 849 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 854 " --> pdb=" O ARG B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 875 removed outlier: 3.755A pdb=" N HIS B 874 " --> pdb=" O ASP B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 893 Processing helix chain 'B' and resid 895 through 903 Processing helix chain 'B' and resid 908 through 921 Processing helix chain 'B' and resid 923 through 941 Processing helix chain 'B' and resid 972 through 990 removed outlier: 3.652A pdb=" N PHE B 979 " --> pdb=" O TYR B 975 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 987 " --> pdb=" O ARG B 983 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 990 " --> pdb=" O LEU B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1008 Processing helix chain 'B' and resid 1009 through 1018 removed outlier: 4.590A pdb=" N GLN B1015 " --> pdb=" O ASP B1011 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU B1016 " --> pdb=" O ARG B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1040 removed outlier: 3.698A pdb=" N THR B1038 " --> pdb=" O ALA B1034 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR B1039 " --> pdb=" O CYS B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1046 No H-bonds generated for 'chain 'B' and resid 1044 through 1046' Processing helix chain 'B' and resid 1047 through 1060 Processing helix chain 'B' and resid 1063 through 1074 removed outlier: 3.948A pdb=" N LEU B1069 " --> pdb=" O GLU B1065 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP B1074 " --> pdb=" O LEU B1070 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1086 Processing helix chain 'B' and resid 1088 through 1099 Processing helix chain 'B' and resid 1104 through 1117 removed outlier: 3.655A pdb=" N VAL B1108 " --> pdb=" O GLU B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1135 removed outlier: 3.512A pdb=" N LEU B1129 " --> pdb=" O SER B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1136 through 1147 Processing helix chain 'B' and resid 1149 through 1164 removed outlier: 3.783A pdb=" N LEU B1155 " --> pdb=" O ASP B1151 " (cutoff:3.500A) Processing helix chain 'B' and resid 1172 through 1191 Processing helix chain 'B' and resid 1192 through 1204 removed outlier: 3.623A pdb=" N ALA B1196 " --> pdb=" O PHE B1192 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B1204 " --> pdb=" O ALA B1200 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1215 Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 380 removed outlier: 6.749A pdb=" N LEU A 501 " --> pdb=" O ILE A 522 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 412 Processing sheet with id=AA3, first strand: chain 'A' and resid 504 through 505 Processing sheet with id=AA4, first strand: chain 'A' and resid 580 through 583 removed outlier: 6.781A pdb=" N ARG A 569 " --> pdb=" O HIS A 605 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 600 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 612 through 618 removed outlier: 3.502A pdb=" N VAL A 614 " --> pdb=" O MET A 658 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 618 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 654 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR A 655 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU A 725 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR A 657 " --> pdb=" O LEU A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 15 removed outlier: 3.862A pdb=" N ASP B 800 " --> pdb=" O ALA B 812 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 29 removed outlier: 6.428A pdb=" N VAL B 43 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 56 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 45 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 69 removed outlier: 3.628A pdb=" N LYS B 66 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE B 95 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU B 108 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL B 97 " --> pdb=" O GLN B 106 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 104 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 119 through 121 removed outlier: 4.212A pdb=" N TRP B 153 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 166 removed outlier: 6.985A pdb=" N LEU B 177 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE B 164 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR B 175 " --> pdb=" O PHE B 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 249 through 252 removed outlier: 4.221A pdb=" N GLN B 249 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 251 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET B 260 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY B 280 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP B 272 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR B 278 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 291 through 296 removed outlier: 7.026A pdb=" N ILE B 312 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLN B 346 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU B 314 " --> pdb=" O ARG B 344 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 358 through 363 removed outlier: 3.982A pdb=" N SER B 360 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 380 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU B 459 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE B 382 " --> pdb=" O THR B 457 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 470 through 472 removed outlier: 6.604A pdb=" N VAL B 497 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU B 510 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 499 " --> pdb=" O HIS B 508 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 518 through 523 removed outlier: 7.012A pdb=" N VAL B 518 " --> pdb=" O THR B 534 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THR B 534 " --> pdb=" O VAL B 518 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY B 520 " --> pdb=" O PHE B 532 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 571 through 576 removed outlier: 4.937A pdb=" N MET B 573 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 586 " --> pdb=" O MET B 573 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU B 594 " --> pdb=" O LEU B 603 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 615 through 618 removed outlier: 3.599A pdb=" N ALA B 615 " --> pdb=" O THR B 682 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 717 through 719 removed outlier: 3.712A pdb=" N LEU B 732 " --> pdb=" O ILE B 745 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE B 745 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG B 743 " --> pdb=" O PHE B 734 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 754 through 757 removed outlier: 3.819A pdb=" N LYS B 754 " --> pdb=" O MET B 769 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY B 773 " --> pdb=" O TYR B 770 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA B 774 " --> pdb=" O SER B 787 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N SER B 787 " --> pdb=" O ALA B 774 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL B 776 " --> pdb=" O VAL B 785 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1380 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: 4.65 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2387 1.33 - 1.45: 2920 1.45 - 1.58: 6688 1.58 - 1.71: 0 1.71 - 1.83: 86 Bond restraints: 12081 Sorted by residual: bond pdb=" N ASP B 589 " pdb=" CA ASP B 589 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.24e+00 bond pdb=" N LEU B 592 " pdb=" CA LEU B 592 " ideal model delta sigma weight residual 1.455 1.488 -0.034 1.27e-02 6.20e+03 7.04e+00 bond pdb=" C PRO B 591 " pdb=" O PRO B 591 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.30e-02 5.92e+03 5.97e+00 bond pdb=" N LEU B 594 " pdb=" CA LEU B 594 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.29e-02 6.01e+03 4.59e+00 bond pdb=" N GLU B 593 " pdb=" CA GLU B 593 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.19e-02 7.06e+03 4.43e+00 ... (remaining 12076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 16002 1.44 - 2.89: 314 2.89 - 4.33: 52 4.33 - 5.78: 14 5.78 - 7.22: 5 Bond angle restraints: 16387 Sorted by residual: angle pdb=" N VAL B 275 " pdb=" CA VAL B 275 " pdb=" C VAL B 275 " ideal model delta sigma weight residual 112.96 109.13 3.83 1.00e+00 1.00e+00 1.47e+01 angle pdb=" C GLU B 593 " pdb=" CA GLU B 593 " pdb=" CB GLU B 593 " ideal model delta sigma weight residual 110.14 104.88 5.26 1.60e+00 3.91e-01 1.08e+01 angle pdb=" CA LEU B 592 " pdb=" C LEU B 592 " pdb=" O LEU B 592 " ideal model delta sigma weight residual 121.56 118.01 3.55 1.09e+00 8.42e-01 1.06e+01 angle pdb=" N PRO B 591 " pdb=" CA PRO B 591 " pdb=" C PRO B 591 " ideal model delta sigma weight residual 112.47 118.58 -6.11 2.06e+00 2.36e-01 8.79e+00 angle pdb=" CA LEU B 594 " pdb=" C LEU B 594 " pdb=" O LEU B 594 " ideal model delta sigma weight residual 120.54 117.22 3.32 1.13e+00 7.83e-01 8.63e+00 ... (remaining 16382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 6489 17.44 - 34.87: 615 34.87 - 52.31: 102 52.31 - 69.75: 18 69.75 - 87.18: 16 Dihedral angle restraints: 7240 sinusoidal: 2885 harmonic: 4355 Sorted by residual: dihedral pdb=" CA ASP B1074 " pdb=" C ASP B1074 " pdb=" N LYS B1075 " pdb=" CA LYS B1075 " ideal model delta harmonic sigma weight residual -180.00 -157.43 -22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CB CYS D1029 " pdb=" SG CYS D1029 " pdb=" SG CYS B1029 " pdb=" CB CYS B1029 " ideal model delta sinusoidal sigma weight residual -86.00 -119.97 33.97 1 1.00e+01 1.00e-02 1.64e+01 dihedral pdb=" CA CYS D1029 " pdb=" CB CYS D1029 " pdb=" SG CYS D1029 " pdb=" SG CYS B1029 " ideal model delta sinusoidal sigma weight residual 79.00 7.72 71.28 1 2.00e+01 2.50e-03 1.63e+01 ... (remaining 7237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1705 0.062 - 0.125: 180 0.125 - 0.187: 2 0.187 - 0.250: 0 0.250 - 0.312: 2 Chirality restraints: 1889 Sorted by residual: chirality pdb=" CA GLU B 593 " pdb=" N GLU B 593 " pdb=" C GLU B 593 " pdb=" CB GLU B 593 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB ILE B1073 " pdb=" CA ILE B1073 " pdb=" CG1 ILE B1073 " pdb=" CG2 ILE B1073 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ILE A 729 " pdb=" N ILE A 729 " pdb=" C ILE A 729 " pdb=" CB ILE A 729 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1886 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 877 " -0.069 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO B 878 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO B 878 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 878 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 582 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO A 583 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 465 " -0.058 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO B 466 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 466 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 466 " -0.048 5.00e-02 4.00e+02 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 172 2.69 - 3.24: 10664 3.24 - 3.79: 16798 3.79 - 4.35: 22700 4.35 - 4.90: 37983 Nonbonded interactions: 88317 Sorted by model distance: nonbonded pdb=" OG SER B 426 " pdb=" OD1 ASP B 428 " model vdw 2.134 3.040 nonbonded pdb=" NH1 ARG B 604 " pdb=" O GLU B 605 " model vdw 2.210 3.120 nonbonded pdb=" ND2 ASN B 23 " pdb=" O VAL B 64 " model vdw 2.291 3.120 nonbonded pdb=" O LEU D 981 " pdb=" ND2 ASN D 985 " model vdw 2.321 3.120 nonbonded pdb=" OG SER B 786 " pdb=" O MET B 823 " model vdw 2.341 3.040 ... (remaining 88312 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 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: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.340 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 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 : 0.002 0.057 12081 Z= 0.140 Angle : 0.515 7.221 16387 Z= 0.284 Chirality : 0.039 0.312 1889 Planarity : 0.005 0.106 2070 Dihedral : 14.022 87.185 4403 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.23 % Allowed : 0.61 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1460 helix: 0.90 (0.23), residues: 479 sheet: 1.16 (0.30), residues: 307 loop : -0.86 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D1112 HIS 0.002 0.000 HIS B1115 PHE 0.019 0.001 PHE B 298 TYR 0.018 0.001 TYR D 975 ARG 0.006 0.000 ARG D1081 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 312 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 TYR cc_start: 0.8055 (m-10) cc_final: 0.7815 (m-10) REVERT: A 568 ASP cc_start: 0.6863 (m-30) cc_final: 0.6640 (m-30) REVERT: A 593 ASP cc_start: 0.6773 (t0) cc_final: 0.6447 (t0) REVERT: A 658 MET cc_start: 0.7475 (mmm) cc_final: 0.6620 (mmm) REVERT: A 738 ARG cc_start: 0.7057 (ttp-110) cc_final: 0.6809 (ttp-110) REVERT: A 810 LYS cc_start: 0.7576 (ptmt) cc_final: 0.7257 (pttt) REVERT: B 312 ILE cc_start: 0.8341 (mt) cc_final: 0.8106 (mt) REVERT: B 348 ASP cc_start: 0.7344 (m-30) cc_final: 0.7077 (m-30) REVERT: B 404 LEU cc_start: 0.7897 (mt) cc_final: 0.7609 (mt) REVERT: B 428 ASP cc_start: 0.7370 (p0) cc_final: 0.6931 (p0) REVERT: B 528 SER cc_start: 0.8676 (t) cc_final: 0.8429 (t) REVERT: B 618 TRP cc_start: 0.7982 (m100) cc_final: 0.7488 (m100) REVERT: B 765 LYS cc_start: 0.7217 (ptpp) cc_final: 0.7000 (mtmm) REVERT: B 1032 LEU cc_start: 0.8107 (mt) cc_final: 0.7907 (mt) REVERT: B 1111 ARG cc_start: 0.7225 (ttm170) cc_final: 0.7012 (mtm-85) REVERT: B 1193 LYS cc_start: 0.7749 (ttmt) cc_final: 0.7396 (ttmm) outliers start: 3 outliers final: 0 residues processed: 314 average time/residue: 0.2690 time to fit residues: 117.2639 Evaluate side-chains 272 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 HIS B 112 HIS B 125 GLN B 258 ASN B 299 GLN B 501 HIS B 514 HIS B 763 ASN B 835 GLN B1060 ASN B1068 GLN B1090 ASN ** B1120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 ASN ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12081 Z= 0.351 Angle : 0.648 8.766 16387 Z= 0.340 Chirality : 0.044 0.148 1889 Planarity : 0.006 0.088 2070 Dihedral : 4.078 21.072 1595 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.75 % Allowed : 10.36 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.00 (0.22), residues: 1460 helix: 0.80 (0.23), residues: 501 sheet: 0.74 (0.28), residues: 334 loop : -1.06 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 383 HIS 0.007 0.001 HIS B 690 PHE 0.032 0.002 PHE A 618 TYR 0.021 0.002 TYR B1028 ARG 0.004 0.001 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 276 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 979 PHE cc_start: 0.7753 (m-10) cc_final: 0.7502 (m-10) REVERT: A 503 SER cc_start: 0.7771 (t) cc_final: 0.7446 (m) REVERT: A 593 ASP cc_start: 0.6918 (t0) cc_final: 0.6573 (t0) REVERT: A 598 SER cc_start: 0.8279 (p) cc_final: 0.7890 (m) REVERT: A 602 ILE cc_start: 0.8183 (mm) cc_final: 0.7911 (mt) REVERT: A 658 MET cc_start: 0.7535 (mmm) cc_final: 0.6908 (mmm) REVERT: A 738 ARG cc_start: 0.7431 (ttp-110) cc_final: 0.7094 (ttp-110) REVERT: A 810 LYS cc_start: 0.7840 (ptmt) cc_final: 0.7501 (pttt) REVERT: B 348 ASP cc_start: 0.7552 (m-30) cc_final: 0.7247 (m-30) REVERT: B 428 ASP cc_start: 0.7762 (p0) cc_final: 0.7525 (p0) REVERT: B 510 GLU cc_start: 0.6950 (tp30) cc_final: 0.6605 (tp30) REVERT: B 582 TYR cc_start: 0.7927 (m-80) cc_final: 0.7557 (m-80) REVERT: B 604 ARG cc_start: 0.7535 (tmt-80) cc_final: 0.7305 (tmt-80) REVERT: B 618 TRP cc_start: 0.7979 (m100) cc_final: 0.7729 (m100) REVERT: B 805 THR cc_start: 0.8768 (t) cc_final: 0.8314 (p) REVERT: B 810 ILE cc_start: 0.8441 (mt) cc_final: 0.8157 (tt) REVERT: B 813 SER cc_start: 0.8145 (m) cc_final: 0.7756 (p) REVERT: B 823 MET cc_start: 0.8002 (mmm) cc_final: 0.7547 (mpp) REVERT: B 1193 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7476 (ttmm) outliers start: 23 outliers final: 14 residues processed: 289 average time/residue: 0.2631 time to fit residues: 105.7789 Evaluate side-chains 269 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 255 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain A residue 605 HIS Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1121 VAL Chi-restraints excluded: chain B residue 1171 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 145 optimal weight: 0.2980 chunk 119 optimal weight: 0.0040 chunk 133 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN A 615 HIS B 125 GLN B 258 ASN B 299 GLN B 514 HIS ** B 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1060 ASN B1120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12081 Z= 0.197 Angle : 0.523 8.875 16387 Z= 0.274 Chirality : 0.041 0.143 1889 Planarity : 0.004 0.074 2070 Dihedral : 3.830 22.073 1595 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.52 % Allowed : 12.80 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.20 (0.22), residues: 1460 helix: 1.11 (0.23), residues: 502 sheet: 0.85 (0.29), residues: 333 loop : -1.08 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1094 HIS 0.004 0.001 HIS B 690 PHE 0.031 0.001 PHE A 618 TYR 0.011 0.001 TYR B1028 ARG 0.004 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 262 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1002 ASP cc_start: 0.7333 (m-30) cc_final: 0.7113 (m-30) REVERT: A 406 MET cc_start: 0.6524 (mmm) cc_final: 0.5970 (mmt) REVERT: A 503 SER cc_start: 0.7859 (t) cc_final: 0.7501 (m) REVERT: A 593 ASP cc_start: 0.6922 (t0) cc_final: 0.6593 (t0) REVERT: A 658 MET cc_start: 0.7437 (mmm) cc_final: 0.6955 (mmm) REVERT: A 738 ARG cc_start: 0.7349 (ttp-110) cc_final: 0.7010 (ttp-110) REVERT: A 810 LYS cc_start: 0.7802 (ptmt) cc_final: 0.7466 (pttt) REVERT: B 348 ASP cc_start: 0.7475 (m-30) cc_final: 0.7168 (m-30) REVERT: B 356 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8496 (t) REVERT: B 428 ASP cc_start: 0.7732 (p0) cc_final: 0.7376 (p0) REVERT: B 510 GLU cc_start: 0.6980 (tp30) cc_final: 0.6632 (tp30) REVERT: B 573 MET cc_start: 0.7953 (ptt) cc_final: 0.7675 (ptm) REVERT: B 604 ARG cc_start: 0.7459 (tmt-80) cc_final: 0.7148 (tmt170) REVERT: B 618 TRP cc_start: 0.7934 (m100) cc_final: 0.7683 (m100) REVERT: B 754 LYS cc_start: 0.7614 (ptmt) cc_final: 0.7342 (ptmt) REVERT: B 805 THR cc_start: 0.8796 (t) cc_final: 0.8332 (p) REVERT: B 810 ILE cc_start: 0.8349 (mt) cc_final: 0.8105 (tt) REVERT: B 813 SER cc_start: 0.8083 (m) cc_final: 0.7703 (p) REVERT: B 1177 THR cc_start: 0.8256 (m) cc_final: 0.6985 (t) REVERT: B 1193 LYS cc_start: 0.7749 (ttmt) cc_final: 0.7418 (ttmm) outliers start: 20 outliers final: 11 residues processed: 271 average time/residue: 0.2573 time to fit residues: 97.3929 Evaluate side-chains 263 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 251 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 605 HIS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1171 ASP Chi-restraints excluded: chain B residue 1201 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.0670 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 14 optimal weight: 7.9990 chunk 64 optimal weight: 0.0060 chunk 90 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN B 258 ASN B 514 HIS B 545 ASN ** B 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12081 Z= 0.165 Angle : 0.505 11.339 16387 Z= 0.262 Chirality : 0.040 0.141 1889 Planarity : 0.004 0.074 2070 Dihedral : 3.731 22.023 1595 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.90 % Allowed : 14.39 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.27 (0.22), residues: 1460 helix: 1.22 (0.23), residues: 504 sheet: 0.89 (0.30), residues: 328 loop : -1.08 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1094 HIS 0.003 0.001 HIS B 578 PHE 0.031 0.001 PHE A 618 TYR 0.015 0.001 TYR D 975 ARG 0.003 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 271 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1002 ASP cc_start: 0.7342 (m-30) cc_final: 0.7066 (m-30) REVERT: A 503 SER cc_start: 0.7899 (t) cc_final: 0.7537 (m) REVERT: A 528 GLU cc_start: 0.7241 (mp0) cc_final: 0.6976 (mp0) REVERT: A 593 ASP cc_start: 0.6993 (t0) cc_final: 0.6639 (t0) REVERT: A 658 MET cc_start: 0.7402 (mmm) cc_final: 0.7047 (mmm) REVERT: A 738 ARG cc_start: 0.7379 (ttp-110) cc_final: 0.7028 (ttp-110) REVERT: A 810 LYS cc_start: 0.7784 (ptmt) cc_final: 0.7456 (pttt) REVERT: B 348 ASP cc_start: 0.7455 (m-30) cc_final: 0.7166 (m-30) REVERT: B 356 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8550 (t) REVERT: B 428 ASP cc_start: 0.7733 (p0) cc_final: 0.7404 (p0) REVERT: B 510 GLU cc_start: 0.6954 (tp30) cc_final: 0.6673 (tp30) REVERT: B 573 MET cc_start: 0.7989 (ptt) cc_final: 0.7704 (ptm) REVERT: B 604 ARG cc_start: 0.7457 (tmt-80) cc_final: 0.7109 (tmt170) REVERT: B 618 TRP cc_start: 0.7923 (m100) cc_final: 0.7676 (m100) REVERT: B 754 LYS cc_start: 0.7576 (ptmt) cc_final: 0.7267 (ptmt) REVERT: B 805 THR cc_start: 0.8792 (t) cc_final: 0.8298 (p) REVERT: B 813 SER cc_start: 0.8068 (m) cc_final: 0.7726 (p) REVERT: B 823 MET cc_start: 0.7646 (mmm) cc_final: 0.7384 (mmm) REVERT: B 1177 THR cc_start: 0.8228 (m) cc_final: 0.6958 (t) REVERT: B 1193 LYS cc_start: 0.7703 (ttmt) cc_final: 0.7410 (ttmm) outliers start: 25 outliers final: 20 residues processed: 285 average time/residue: 0.2539 time to fit residues: 101.6247 Evaluate side-chains 279 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 258 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 605 HIS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1104 GLU Chi-restraints excluded: chain B residue 1142 GLU Chi-restraints excluded: chain B residue 1171 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.2980 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 98 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 0.0570 chunk 128 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN B 429 ASN B 514 HIS B 888 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12081 Z= 0.168 Angle : 0.510 13.694 16387 Z= 0.264 Chirality : 0.040 0.142 1889 Planarity : 0.004 0.071 2070 Dihedral : 3.698 22.368 1595 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.98 % Allowed : 15.84 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.30 (0.22), residues: 1460 helix: 1.31 (0.24), residues: 505 sheet: 0.86 (0.30), residues: 329 loop : -1.10 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 153 HIS 0.003 0.001 HIS B 690 PHE 0.033 0.001 PHE A 618 TYR 0.012 0.001 TYR B1028 ARG 0.003 0.000 ARG B 831 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 269 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1002 ASP cc_start: 0.7352 (m-30) cc_final: 0.7076 (m-30) REVERT: A 503 SER cc_start: 0.7926 (t) cc_final: 0.7548 (m) REVERT: A 528 GLU cc_start: 0.7268 (mp0) cc_final: 0.6995 (mp0) REVERT: A 593 ASP cc_start: 0.7008 (t0) cc_final: 0.6652 (t0) REVERT: A 658 MET cc_start: 0.7402 (mmm) cc_final: 0.7060 (mmm) REVERT: A 738 ARG cc_start: 0.7365 (ttp-110) cc_final: 0.7014 (ttp-110) REVERT: B 348 ASP cc_start: 0.7455 (m-30) cc_final: 0.7166 (m-30) REVERT: B 428 ASP cc_start: 0.7732 (p0) cc_final: 0.7412 (p0) REVERT: B 510 GLU cc_start: 0.6993 (tp30) cc_final: 0.6669 (tp30) REVERT: B 573 MET cc_start: 0.7976 (ptt) cc_final: 0.7710 (ptm) REVERT: B 604 ARG cc_start: 0.7451 (tmt-80) cc_final: 0.7083 (tmt170) REVERT: B 618 TRP cc_start: 0.7988 (m100) cc_final: 0.7760 (m100) REVERT: B 754 LYS cc_start: 0.7568 (ptmt) cc_final: 0.7254 (ptmt) REVERT: B 813 SER cc_start: 0.8056 (m) cc_final: 0.7719 (p) REVERT: B 823 MET cc_start: 0.7626 (mmm) cc_final: 0.7327 (mmm) REVERT: B 1177 THR cc_start: 0.8231 (m) cc_final: 0.7824 (p) REVERT: B 1193 LYS cc_start: 0.7702 (ttmt) cc_final: 0.7394 (ttmm) outliers start: 26 outliers final: 20 residues processed: 281 average time/residue: 0.2640 time to fit residues: 103.6769 Evaluate side-chains 284 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 264 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 605 HIS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1104 GLU Chi-restraints excluded: chain B residue 1142 GLU Chi-restraints excluded: chain B residue 1171 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 28 optimal weight: 0.0470 chunk 83 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN B 501 HIS B 514 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12081 Z= 0.229 Angle : 0.540 11.674 16387 Z= 0.282 Chirality : 0.041 0.144 1889 Planarity : 0.004 0.071 2070 Dihedral : 3.846 22.042 1595 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.21 % Allowed : 16.37 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.26 (0.22), residues: 1460 helix: 1.29 (0.23), residues: 505 sheet: 0.83 (0.30), residues: 329 loop : -1.14 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1094 HIS 0.005 0.001 HIS A 521 PHE 0.033 0.002 PHE A 618 TYR 0.012 0.001 TYR B1028 ARG 0.004 0.000 ARG B 831 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 271 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1002 ASP cc_start: 0.7388 (m-30) cc_final: 0.7090 (m-30) REVERT: A 503 SER cc_start: 0.8025 (t) cc_final: 0.7647 (m) REVERT: A 528 GLU cc_start: 0.7257 (mp0) cc_final: 0.6940 (mp0) REVERT: A 593 ASP cc_start: 0.6974 (t0) cc_final: 0.6623 (t0) REVERT: A 658 MET cc_start: 0.7431 (mmm) cc_final: 0.6879 (mmm) REVERT: A 738 ARG cc_start: 0.7392 (ttp-110) cc_final: 0.7088 (ttp-110) REVERT: B 348 ASP cc_start: 0.7476 (m-30) cc_final: 0.7188 (m-30) REVERT: B 428 ASP cc_start: 0.7748 (p0) cc_final: 0.7433 (p0) REVERT: B 510 GLU cc_start: 0.7014 (tp30) cc_final: 0.6790 (tp30) REVERT: B 573 MET cc_start: 0.7986 (ptt) cc_final: 0.7725 (ptm) REVERT: B 617 GLU cc_start: 0.7149 (tp30) cc_final: 0.6831 (tp30) REVERT: B 754 LYS cc_start: 0.7546 (ptmt) cc_final: 0.7236 (ptmt) REVERT: B 823 MET cc_start: 0.7626 (mmm) cc_final: 0.7373 (mmm) REVERT: B 1193 LYS cc_start: 0.7791 (ttmt) cc_final: 0.7432 (ttmm) outliers start: 29 outliers final: 23 residues processed: 285 average time/residue: 0.2670 time to fit residues: 105.3826 Evaluate side-chains 288 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 265 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 605 HIS Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1104 GLU Chi-restraints excluded: chain B residue 1142 GLU Chi-restraints excluded: chain B residue 1147 MET Chi-restraints excluded: chain B residue 1201 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 0.0670 chunk 104 optimal weight: 0.0970 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN B 501 HIS B 514 HIS B1047 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12081 Z= 0.177 Angle : 0.520 14.097 16387 Z= 0.270 Chirality : 0.041 0.143 1889 Planarity : 0.004 0.068 2070 Dihedral : 3.763 21.902 1595 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.06 % Allowed : 17.29 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.30 (0.22), residues: 1460 helix: 1.36 (0.23), residues: 505 sheet: 0.84 (0.30), residues: 323 loop : -1.13 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 153 HIS 0.003 0.001 HIS B 578 PHE 0.034 0.001 PHE A 618 TYR 0.014 0.001 TYR D 975 ARG 0.004 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 266 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1002 ASP cc_start: 0.7342 (m-30) cc_final: 0.7052 (m-30) REVERT: A 503 SER cc_start: 0.8034 (t) cc_final: 0.7644 (m) REVERT: A 528 GLU cc_start: 0.7249 (mp0) cc_final: 0.6975 (mp0) REVERT: A 559 LYS cc_start: 0.7652 (mtpp) cc_final: 0.7264 (mtpp) REVERT: A 593 ASP cc_start: 0.6999 (t0) cc_final: 0.6651 (t0) REVERT: A 658 MET cc_start: 0.7417 (mmm) cc_final: 0.6946 (mmm) REVERT: A 738 ARG cc_start: 0.7402 (ttp-110) cc_final: 0.7088 (ttp-110) REVERT: B 348 ASP cc_start: 0.7450 (m-30) cc_final: 0.7183 (m-30) REVERT: B 510 GLU cc_start: 0.6984 (tp30) cc_final: 0.6770 (tp30) REVERT: B 573 MET cc_start: 0.7956 (ptt) cc_final: 0.7704 (ptm) REVERT: B 617 GLU cc_start: 0.7153 (tp30) cc_final: 0.6816 (tp30) REVERT: B 754 LYS cc_start: 0.7537 (ptmt) cc_final: 0.7242 (ptmt) REVERT: B 823 MET cc_start: 0.7676 (mmm) cc_final: 0.7372 (mmm) REVERT: B 1177 THR cc_start: 0.8194 (m) cc_final: 0.6944 (t) REVERT: B 1193 LYS cc_start: 0.7687 (ttmt) cc_final: 0.7414 (ttmm) outliers start: 27 outliers final: 24 residues processed: 280 average time/residue: 0.2692 time to fit residues: 105.0082 Evaluate side-chains 285 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 261 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 605 HIS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1104 GLU Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1142 GLU Chi-restraints excluded: chain B residue 1147 MET Chi-restraints excluded: chain B residue 1201 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 112 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN B 501 HIS B 514 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12081 Z= 0.259 Angle : 0.558 13.279 16387 Z= 0.290 Chirality : 0.042 0.144 1889 Planarity : 0.004 0.070 2070 Dihedral : 3.939 22.686 1595 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.13 % Allowed : 17.59 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1460 helix: 1.30 (0.23), residues: 508 sheet: 0.68 (0.30), residues: 332 loop : -1.11 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1094 HIS 0.004 0.001 HIS A 521 PHE 0.031 0.002 PHE A 618 TYR 0.015 0.001 TYR B1028 ARG 0.003 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 273 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1002 ASP cc_start: 0.7399 (m-30) cc_final: 0.7098 (m-30) REVERT: A 503 SER cc_start: 0.8082 (t) cc_final: 0.7686 (m) REVERT: A 528 GLU cc_start: 0.7285 (mp0) cc_final: 0.6938 (mp0) REVERT: A 593 ASP cc_start: 0.6982 (t0) cc_final: 0.6633 (t0) REVERT: A 658 MET cc_start: 0.7469 (mmm) cc_final: 0.6921 (mmm) REVERT: A 738 ARG cc_start: 0.7430 (ttp-110) cc_final: 0.7129 (ttp-110) REVERT: B 348 ASP cc_start: 0.7465 (m-30) cc_final: 0.7200 (m-30) REVERT: B 510 GLU cc_start: 0.6986 (tp30) cc_final: 0.6780 (tp30) REVERT: B 573 MET cc_start: 0.7963 (ptt) cc_final: 0.7713 (ptm) REVERT: B 617 GLU cc_start: 0.7154 (tp30) cc_final: 0.6806 (tp30) REVERT: B 754 LYS cc_start: 0.7565 (ptmt) cc_final: 0.7235 (ptmt) REVERT: B 831 ARG cc_start: 0.7590 (mtp-110) cc_final: 0.7323 (mtm110) REVERT: B 1051 LYS cc_start: 0.8079 (ttmt) cc_final: 0.7869 (ttmm) REVERT: B 1193 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7477 (ttmm) outliers start: 28 outliers final: 27 residues processed: 288 average time/residue: 0.2777 time to fit residues: 108.5682 Evaluate side-chains 292 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 265 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 605 HIS Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1104 GLU Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1142 GLU Chi-restraints excluded: chain B residue 1147 MET Chi-restraints excluded: chain B residue 1171 ASP Chi-restraints excluded: chain B residue 1201 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1068 GLN A 565 GLN ** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 173 HIS B 514 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12081 Z= 0.288 Angle : 0.583 13.201 16387 Z= 0.301 Chirality : 0.043 0.148 1889 Planarity : 0.004 0.069 2070 Dihedral : 4.102 22.404 1595 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.28 % Allowed : 18.51 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.16 (0.22), residues: 1460 helix: 1.23 (0.23), residues: 506 sheet: 0.70 (0.30), residues: 329 loop : -1.16 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1094 HIS 0.004 0.001 HIS A 521 PHE 0.031 0.002 PHE A 618 TYR 0.015 0.001 TYR B1028 ARG 0.009 0.000 ARG A 558 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 272 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1002 ASP cc_start: 0.7420 (m-30) cc_final: 0.7096 (m-30) REVERT: A 406 MET cc_start: 0.5912 (mmm) cc_final: 0.5211 (mmt) REVERT: A 503 SER cc_start: 0.8125 (t) cc_final: 0.7711 (m) REVERT: A 528 GLU cc_start: 0.7263 (mp0) cc_final: 0.7002 (mp0) REVERT: A 559 LYS cc_start: 0.7679 (mtpp) cc_final: 0.7376 (mtpp) REVERT: A 593 ASP cc_start: 0.6995 (t0) cc_final: 0.6643 (t0) REVERT: A 658 MET cc_start: 0.7502 (mmm) cc_final: 0.6899 (mmm) REVERT: A 738 ARG cc_start: 0.7428 (ttp-110) cc_final: 0.7092 (ttp-110) REVERT: B 348 ASP cc_start: 0.7485 (m-30) cc_final: 0.7212 (m-30) REVERT: B 510 GLU cc_start: 0.6968 (tp30) cc_final: 0.6763 (tp30) REVERT: B 573 MET cc_start: 0.7919 (ptt) cc_final: 0.7673 (ptm) REVERT: B 617 GLU cc_start: 0.7153 (tp30) cc_final: 0.6794 (tp30) REVERT: B 618 TRP cc_start: 0.8090 (m100) cc_final: 0.7318 (m100) REVERT: B 754 LYS cc_start: 0.7537 (ptmt) cc_final: 0.7216 (ptmt) REVERT: B 1177 THR cc_start: 0.8209 (m) cc_final: 0.6973 (t) REVERT: B 1193 LYS cc_start: 0.7808 (ttmt) cc_final: 0.7510 (ttmm) outliers start: 30 outliers final: 25 residues processed: 289 average time/residue: 0.2820 time to fit residues: 111.6620 Evaluate side-chains 289 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 264 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 605 HIS Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1104 GLU Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1142 GLU Chi-restraints excluded: chain B residue 1171 ASP Chi-restraints excluded: chain B residue 1201 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 985 ASN ** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 HIS B 865 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12081 Z= 0.279 Angle : 0.587 12.567 16387 Z= 0.303 Chirality : 0.043 0.150 1889 Planarity : 0.004 0.070 2070 Dihedral : 4.126 22.618 1595 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.90 % Allowed : 19.04 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.12 (0.22), residues: 1460 helix: 1.25 (0.23), residues: 506 sheet: 0.67 (0.30), residues: 324 loop : -1.22 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1094 HIS 0.004 0.001 HIS A 521 PHE 0.031 0.002 PHE A 618 TYR 0.015 0.001 TYR B1028 ARG 0.006 0.000 ARG A 558 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 270 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1002 ASP cc_start: 0.7392 (m-30) cc_final: 0.7094 (m-30) REVERT: A 406 MET cc_start: 0.5894 (mmm) cc_final: 0.5201 (mmt) REVERT: A 503 SER cc_start: 0.8139 (t) cc_final: 0.7721 (m) REVERT: A 528 GLU cc_start: 0.7285 (mp0) cc_final: 0.6929 (mp0) REVERT: A 559 LYS cc_start: 0.7679 (mtpp) cc_final: 0.7394 (mtpp) REVERT: A 593 ASP cc_start: 0.6994 (t0) cc_final: 0.6647 (t0) REVERT: A 634 MET cc_start: 0.8422 (mtm) cc_final: 0.8221 (mtp) REVERT: A 658 MET cc_start: 0.7503 (mmm) cc_final: 0.6839 (mmm) REVERT: A 738 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.7105 (ttp-110) REVERT: B 180 GLU cc_start: 0.6860 (mp0) cc_final: 0.6556 (mp0) REVERT: B 348 ASP cc_start: 0.7503 (m-30) cc_final: 0.7222 (m-30) REVERT: B 573 MET cc_start: 0.7915 (ptt) cc_final: 0.7666 (ptm) REVERT: B 617 GLU cc_start: 0.7146 (tp30) cc_final: 0.6787 (tp30) REVERT: B 618 TRP cc_start: 0.8096 (m100) cc_final: 0.7359 (m100) REVERT: B 754 LYS cc_start: 0.7532 (ptmt) cc_final: 0.7250 (ptmt) REVERT: B 831 ARG cc_start: 0.7556 (mtp-110) cc_final: 0.7327 (mtm110) REVERT: B 1177 THR cc_start: 0.8198 (m) cc_final: 0.6963 (t) REVERT: B 1193 LYS cc_start: 0.7822 (ttmt) cc_final: 0.7476 (ttmm) outliers start: 25 outliers final: 25 residues processed: 285 average time/residue: 0.2659 time to fit residues: 103.7455 Evaluate side-chains 287 residues out of total 1313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 262 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 605 HIS Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1104 GLU Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1142 GLU Chi-restraints excluded: chain B residue 1171 ASP Chi-restraints excluded: chain B residue 1201 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.9980 chunk 108 optimal weight: 0.3980 chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 120 optimal weight: 0.0070 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN B 514 HIS B1068 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.134767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108150 restraints weight = 18625.873| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.48 r_work: 0.3222 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12081 Z= 0.223 Angle : 0.565 12.535 16387 Z= 0.291 Chirality : 0.042 0.142 1889 Planarity : 0.004 0.068 2070 Dihedral : 4.026 22.298 1595 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.98 % Allowed : 19.04 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.18 (0.22), residues: 1460 helix: 1.34 (0.23), residues: 504 sheet: 0.71 (0.30), residues: 326 loop : -1.23 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1094 HIS 0.008 0.001 HIS B 501 PHE 0.032 0.001 PHE A 618 TYR 0.014 0.001 TYR B1028 ARG 0.004 0.000 ARG B 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3193.92 seconds wall clock time: 58 minutes 52.87 seconds (3532.87 seconds total)