Starting phenix.real_space_refine on Wed Sep 17 22:40:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xfb_38300/09_2025/8xfb_38300.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xfb_38300/09_2025/8xfb_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/cci-nas-00/data/ceres_data/8xfb_38300/09_2025/8xfb_38300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xfb_38300/09_2025/8xfb_38300.map" model { file = "/net/cci-nas-00/data/ceres_data/8xfb_38300/09_2025/8xfb_38300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xfb_38300/09_2025/8xfb_38300.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.00, per 1000 atoms: 0.25 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: 0.91 Conformation dependent library (CDL) restraints added in 634.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.38 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: 2.04 Time building geometry restraints manager: 1.28 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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.250 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.350 ------------------------------------------------------------------------------- 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 12082 Z= 0.116 Angle : 0.515 7.221 16389 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.22), 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 ARG 0.006 0.000 ARG D1081 TYR 0.018 0.001 TYR D 975 PHE 0.019 0.001 PHE B 298 TRP 0.006 0.001 TRP D1112 HIS 0.002 0.000 HIS B1115 Details of bonding type rmsd covalent geometry : bond 0.00216 (12081) covalent geometry : angle 0.51457 (16387) SS BOND : bond 0.00780 ( 1) SS BOND : angle 2.81024 ( 2) hydrogen bonds : bond 0.26223 ( 490) hydrogen bonds : angle 7.08813 ( 1380) *********************** 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 to be fit. rotamer outliers: 3 poor density : 312 time to evaluate : 0.504 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: 0.1251 time to fit residues: 54.7266 Evaluate side-chains 272 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0070 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 835 GLN B1060 ASN B1068 GLN B1090 ASN ** B1120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113613 restraints weight = 18930.632| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.41 r_work: 0.3303 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12082 Z= 0.153 Angle : 0.570 6.954 16389 Z= 0.300 Chirality : 0.042 0.150 1889 Planarity : 0.005 0.079 2070 Dihedral : 3.608 20.650 1595 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.22 % Allowed : 9.82 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.22), residues: 1460 helix: 1.05 (0.24), residues: 502 sheet: 0.95 (0.29), residues: 334 loop : -0.91 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 912 TYR 0.016 0.001 TYR B1028 PHE 0.028 0.002 PHE A 618 TRP 0.013 0.001 TRP B 523 HIS 0.005 0.001 HIS B 690 Details of bonding type rmsd covalent geometry : bond 0.00355 (12081) covalent geometry : angle 0.56921 (16387) SS BOND : bond 0.00070 ( 1) SS BOND : angle 3.21158 ( 2) hydrogen bonds : bond 0.05096 ( 490) hydrogen bonds : angle 4.89920 ( 1380) *********************** 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 294 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 278 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 SER cc_start: 0.7610 (t) cc_final: 0.7281 (m) REVERT: A 568 ASP cc_start: 0.8004 (m-30) cc_final: 0.7605 (m-30) REVERT: A 593 ASP cc_start: 0.7769 (t0) cc_final: 0.7417 (t0) REVERT: A 598 SER cc_start: 0.8434 (p) cc_final: 0.8107 (m) REVERT: A 602 ILE cc_start: 0.8330 (mm) cc_final: 0.8085 (mm) REVERT: A 658 MET cc_start: 0.8137 (mmm) cc_final: 0.7584 (mmm) REVERT: A 738 ARG cc_start: 0.7765 (ttp-110) cc_final: 0.7518 (ttp-110) REVERT: A 810 LYS cc_start: 0.8036 (ptmt) cc_final: 0.7647 (pttt) REVERT: B 338 GLU cc_start: 0.7254 (mp0) cc_final: 0.7028 (mp0) REVERT: B 348 ASP cc_start: 0.7941 (m-30) cc_final: 0.7595 (m-30) REVERT: B 428 ASP cc_start: 0.8242 (p0) cc_final: 0.7902 (p0) REVERT: B 510 GLU cc_start: 0.7714 (tp30) cc_final: 0.7134 (tp30) REVERT: B 522 GLU cc_start: 0.7642 (mp0) cc_final: 0.7397 (mm-30) REVERT: B 604 ARG cc_start: 0.7908 (tmt-80) cc_final: 0.7546 (tmt-80) REVERT: B 618 TRP cc_start: 0.8012 (m100) cc_final: 0.7756 (m100) REVERT: B 805 THR cc_start: 0.8809 (t) cc_final: 0.8274 (p) REVERT: B 810 ILE cc_start: 0.8627 (mt) cc_final: 0.8336 (tt) REVERT: B 823 MET cc_start: 0.8357 (mmm) cc_final: 0.8029 (mpp) REVERT: B 1173 GLU cc_start: 0.7356 (pt0) cc_final: 0.6827 (pt0) outliers start: 16 outliers final: 11 residues processed: 288 average time/residue: 0.1189 time to fit residues: 48.4718 Evaluate side-chains 276 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 265 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 592 LEU 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 1171 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 58 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 18 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 125 GLN B 258 ASN B 299 GLN B 514 HIS ** B 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.138704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111558 restraints weight = 19100.369| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.51 r_work: 0.3264 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12082 Z= 0.142 Angle : 0.537 8.699 16389 Z= 0.280 Chirality : 0.041 0.141 1889 Planarity : 0.004 0.073 2070 Dihedral : 3.723 21.301 1595 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.83 % Allowed : 11.81 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.22), residues: 1460 helix: 1.26 (0.24), residues: 502 sheet: 0.86 (0.29), residues: 333 loop : -0.99 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 448 TYR 0.015 0.001 TYR B1028 PHE 0.028 0.002 PHE A 618 TRP 0.011 0.001 TRP B1094 HIS 0.004 0.001 HIS B 690 Details of bonding type rmsd covalent geometry : bond 0.00336 (12081) covalent geometry : angle 0.53693 (16387) SS BOND : bond 0.00165 ( 1) SS BOND : angle 2.14718 ( 2) hydrogen bonds : bond 0.04619 ( 490) hydrogen bonds : angle 4.49536 ( 1380) *********************** 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 278 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 979 PHE cc_start: 0.8284 (m-10) cc_final: 0.8023 (m-10) REVERT: A 503 SER cc_start: 0.7865 (t) cc_final: 0.7505 (m) REVERT: A 593 ASP cc_start: 0.7892 (t0) cc_final: 0.7542 (t0) REVERT: A 658 MET cc_start: 0.8103 (mmm) cc_final: 0.7624 (mmm) REVERT: A 738 ARG cc_start: 0.7745 (ttp-110) cc_final: 0.7389 (ttp-110) REVERT: A 810 LYS cc_start: 0.8126 (ptmt) cc_final: 0.7724 (pttt) REVERT: B 111 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6943 (tm-30) REVERT: B 338 GLU cc_start: 0.7334 (mp0) cc_final: 0.7060 (mp0) REVERT: B 348 ASP cc_start: 0.8007 (m-30) cc_final: 0.7657 (m-30) REVERT: B 356 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8181 (t) REVERT: B 428 ASP cc_start: 0.8325 (p0) cc_final: 0.7988 (p0) REVERT: B 510 GLU cc_start: 0.7789 (tp30) cc_final: 0.7403 (tp30) REVERT: B 522 GLU cc_start: 0.7673 (mp0) cc_final: 0.7466 (mm-30) REVERT: B 573 MET cc_start: 0.8403 (ptm) cc_final: 0.8124 (ptm) REVERT: B 604 ARG cc_start: 0.7955 (tmt-80) cc_final: 0.7591 (tmt170) REVERT: B 618 TRP cc_start: 0.8088 (m100) cc_final: 0.7857 (m100) REVERT: B 805 THR cc_start: 0.8834 (t) cc_final: 0.8328 (p) REVERT: B 810 ILE cc_start: 0.8618 (mt) cc_final: 0.8316 (tt) REVERT: B 813 SER cc_start: 0.8357 (m) cc_final: 0.7977 (p) REVERT: B 823 MET cc_start: 0.8377 (mmm) cc_final: 0.8044 (mmm) outliers start: 24 outliers final: 16 residues processed: 264 average time/residue: 0.1225 time to fit residues: 45.4103 Evaluate side-chains 264 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 247 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 605 HIS Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1171 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 3 optimal weight: 0.0770 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 chunk 89 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN A 660 ASN B 258 ASN B 299 GLN B 514 HIS B 763 ASN ** B 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111490 restraints weight = 18881.813| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.44 r_work: 0.3266 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12082 Z= 0.125 Angle : 0.513 9.756 16389 Z= 0.266 Chirality : 0.041 0.143 1889 Planarity : 0.004 0.073 2070 Dihedral : 3.705 21.133 1595 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.75 % Allowed : 13.25 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.22), residues: 1460 helix: 1.30 (0.24), residues: 502 sheet: 0.93 (0.30), residues: 328 loop : -1.05 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 912 TYR 0.012 0.001 TYR B1028 PHE 0.029 0.001 PHE A 618 TRP 0.010 0.001 TRP B1094 HIS 0.004 0.001 HIS B 578 Details of bonding type rmsd covalent geometry : bond 0.00296 (12081) covalent geometry : angle 0.51260 (16387) SS BOND : bond 0.00420 ( 1) SS BOND : angle 1.80179 ( 2) hydrogen bonds : bond 0.03978 ( 490) hydrogen bonds : angle 4.30023 ( 1380) *********************** 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 287 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 264 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 979 PHE cc_start: 0.8224 (m-10) cc_final: 0.7965 (m-10) REVERT: A 406 MET cc_start: 0.6517 (mmm) cc_final: 0.5908 (mmt) REVERT: A 503 SER cc_start: 0.7942 (t) cc_final: 0.7588 (m) REVERT: A 593 ASP cc_start: 0.7953 (t0) cc_final: 0.7593 (t0) REVERT: A 658 MET cc_start: 0.8049 (mmm) cc_final: 0.7663 (mmm) REVERT: A 738 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.7319 (ttp-110) REVERT: A 810 LYS cc_start: 0.8113 (ptmt) cc_final: 0.7728 (pttt) REVERT: B 111 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6876 (tm-30) REVERT: B 338 GLU cc_start: 0.7335 (mp0) cc_final: 0.7070 (mp0) REVERT: B 348 ASP cc_start: 0.8024 (m-30) cc_final: 0.7689 (m-30) REVERT: B 351 ARG cc_start: 0.7977 (mtt90) cc_final: 0.7735 (mmt90) REVERT: B 356 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8365 (t) REVERT: B 385 LEU cc_start: 0.8836 (tp) cc_final: 0.8586 (mp) REVERT: B 428 ASP cc_start: 0.8368 (p0) cc_final: 0.8034 (p0) REVERT: B 510 GLU cc_start: 0.7759 (tp30) cc_final: 0.7382 (tp30) REVERT: B 604 ARG cc_start: 0.7949 (tmt-80) cc_final: 0.7563 (tmt170) REVERT: B 618 TRP cc_start: 0.8107 (m100) cc_final: 0.7886 (m100) REVERT: B 754 LYS cc_start: 0.7956 (ptmt) cc_final: 0.7673 (ptmt) REVERT: B 805 THR cc_start: 0.8842 (t) cc_final: 0.8343 (p) REVERT: B 810 ILE cc_start: 0.8622 (mt) cc_final: 0.8342 (tt) REVERT: B 813 SER cc_start: 0.8354 (m) cc_final: 0.7990 (p) REVERT: B 1193 LYS cc_start: 0.8069 (ttmt) cc_final: 0.7785 (ttmm) outliers start: 23 outliers final: 18 residues processed: 274 average time/residue: 0.1187 time to fit residues: 45.5807 Evaluate side-chains 271 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 252 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 605 HIS Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 356 VAL 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 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 1007 LEU Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1073 ILE 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 53 optimal weight: 0.9980 chunk 46 optimal weight: 0.0020 chunk 137 optimal weight: 0.0470 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 overall best weight: 0.4486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN B 514 HIS ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 888 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111389 restraints weight = 18978.363| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.48 r_work: 0.3261 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12082 Z= 0.121 Angle : 0.512 12.540 16389 Z= 0.265 Chirality : 0.040 0.141 1889 Planarity : 0.004 0.071 2070 Dihedral : 3.697 21.850 1595 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.36 % Allowed : 14.39 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.22), residues: 1460 helix: 1.36 (0.24), residues: 503 sheet: 0.90 (0.29), residues: 335 loop : -1.08 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 831 TYR 0.012 0.001 TYR B1028 PHE 0.030 0.001 PHE A 618 TRP 0.009 0.001 TRP B1094 HIS 0.003 0.001 HIS B 578 Details of bonding type rmsd covalent geometry : bond 0.00284 (12081) covalent geometry : angle 0.51122 (16387) SS BOND : bond 0.00275 ( 1) SS BOND : angle 2.24728 ( 2) hydrogen bonds : bond 0.03811 ( 490) hydrogen bonds : angle 4.20094 ( 1380) *********************** 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 305 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 274 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 979 PHE cc_start: 0.8220 (m-10) cc_final: 0.7941 (m-10) REVERT: A 503 SER cc_start: 0.8003 (t) cc_final: 0.7632 (m) REVERT: A 528 GLU cc_start: 0.7787 (mp0) cc_final: 0.7441 (mp0) REVERT: A 593 ASP cc_start: 0.7987 (t0) cc_final: 0.7619 (t0) REVERT: A 658 MET cc_start: 0.8060 (mmm) cc_final: 0.7660 (mmm) REVERT: A 738 ARG cc_start: 0.7658 (ttp-110) cc_final: 0.7289 (ttp-110) REVERT: B 111 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6796 (tm-30) REVERT: B 180 GLU cc_start: 0.7437 (mp0) cc_final: 0.7021 (mp0) REVERT: B 338 GLU cc_start: 0.7342 (mp0) cc_final: 0.7066 (mp0) REVERT: B 348 ASP cc_start: 0.8001 (m-30) cc_final: 0.7641 (m-30) REVERT: B 351 ARG cc_start: 0.7992 (mtt90) cc_final: 0.7763 (mmt90) REVERT: B 356 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8373 (t) REVERT: B 428 ASP cc_start: 0.8373 (p0) cc_final: 0.8064 (p0) REVERT: B 510 GLU cc_start: 0.7817 (tp30) cc_final: 0.7415 (tp30) REVERT: B 604 ARG cc_start: 0.7936 (tmt-80) cc_final: 0.7496 (tmt170) REVERT: B 618 TRP cc_start: 0.8073 (m100) cc_final: 0.7818 (m100) REVERT: B 754 LYS cc_start: 0.7940 (ptmt) cc_final: 0.7676 (ptmt) REVERT: B 810 ILE cc_start: 0.8588 (mt) cc_final: 0.8324 (tt) REVERT: B 813 SER cc_start: 0.8354 (m) cc_final: 0.8003 (p) REVERT: B 823 MET cc_start: 0.8245 (mmm) cc_final: 0.8026 (mmm) REVERT: B 1193 LYS cc_start: 0.8064 (ttmt) cc_final: 0.7764 (ttmm) outliers start: 31 outliers final: 20 residues processed: 292 average time/residue: 0.1187 time to fit residues: 48.2482 Evaluate side-chains 286 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 265 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 605 HIS 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 356 VAL Chi-restraints excluded: chain B residue 516 CYS 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 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 986 LEU Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1104 GLU Chi-restraints excluded: chain B residue 1201 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 0.3980 chunk 65 optimal weight: 0.0870 chunk 16 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 501 HIS B 514 HIS B 545 ASN B1068 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.137655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110644 restraints weight = 19017.895| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.49 r_work: 0.3254 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12082 Z= 0.117 Angle : 0.511 13.783 16389 Z= 0.263 Chirality : 0.040 0.143 1889 Planarity : 0.004 0.069 2070 Dihedral : 3.677 21.461 1595 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.21 % Allowed : 15.16 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.23), residues: 1460 helix: 1.41 (0.24), residues: 504 sheet: 0.90 (0.30), residues: 330 loop : -1.03 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 831 TYR 0.010 0.001 TYR B1028 PHE 0.033 0.001 PHE A 618 TRP 0.010 0.001 TRP B 153 HIS 0.004 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00275 (12081) covalent geometry : angle 0.51035 (16387) SS BOND : bond 0.00264 ( 1) SS BOND : angle 1.82821 ( 2) hydrogen bonds : bond 0.03669 ( 490) hydrogen bonds : angle 4.12014 ( 1380) *********************** 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 297 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 979 PHE cc_start: 0.8222 (m-10) cc_final: 0.7948 (m-10) REVERT: A 503 SER cc_start: 0.8024 (t) cc_final: 0.7644 (m) REVERT: A 528 GLU cc_start: 0.7795 (mp0) cc_final: 0.7452 (mp0) REVERT: A 559 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7776 (mtpp) REVERT: A 593 ASP cc_start: 0.8020 (t0) cc_final: 0.7664 (t0) REVERT: A 658 MET cc_start: 0.8081 (mmm) cc_final: 0.7632 (mmm) REVERT: A 738 ARG cc_start: 0.7689 (ttp-110) cc_final: 0.7316 (ttp-110) REVERT: B 338 GLU cc_start: 0.7363 (mp0) cc_final: 0.7084 (mp0) REVERT: B 348 ASP cc_start: 0.7982 (m-30) cc_final: 0.7648 (m-30) REVERT: B 351 ARG cc_start: 0.8083 (mtt90) cc_final: 0.7816 (mmt90) REVERT: B 356 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8398 (t) REVERT: B 428 ASP cc_start: 0.8334 (p0) cc_final: 0.8037 (p0) REVERT: B 510 GLU cc_start: 0.7794 (tp30) cc_final: 0.7412 (tp30) REVERT: B 604 ARG cc_start: 0.7935 (tmt-80) cc_final: 0.7478 (tmt170) REVERT: B 617 GLU cc_start: 0.7795 (tp30) cc_final: 0.7499 (tp30) REVERT: B 618 TRP cc_start: 0.8120 (m100) cc_final: 0.7541 (m100) REVERT: B 754 LYS cc_start: 0.7949 (ptmt) cc_final: 0.7685 (ptmt) REVERT: B 810 ILE cc_start: 0.8598 (mt) cc_final: 0.8310 (tt) REVERT: B 823 MET cc_start: 0.8205 (mmm) cc_final: 0.7932 (mmm) REVERT: B 1193 LYS cc_start: 0.8039 (ttmt) cc_final: 0.7722 (ttmm) outliers start: 29 outliers final: 22 residues processed: 282 average time/residue: 0.1231 time to fit residues: 48.0268 Evaluate side-chains 288 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 265 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 516 CYS 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 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 986 LEU Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1016 LEU 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 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 31 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN B 501 HIS B 514 HIS B 545 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109235 restraints weight = 18701.554| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.46 r_work: 0.3232 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12082 Z= 0.164 Angle : 0.551 13.143 16389 Z= 0.286 Chirality : 0.042 0.141 1889 Planarity : 0.004 0.070 2070 Dihedral : 3.895 21.972 1595 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.13 % Allowed : 16.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.22), residues: 1460 helix: 1.37 (0.24), residues: 504 sheet: 0.80 (0.30), residues: 330 loop : -1.09 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 831 TYR 0.012 0.001 TYR B 935 PHE 0.030 0.002 PHE A 618 TRP 0.012 0.002 TRP B1094 HIS 0.004 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00390 (12081) covalent geometry : angle 0.55051 (16387) SS BOND : bond 0.00472 ( 1) SS BOND : angle 2.19047 ( 2) hydrogen bonds : bond 0.04471 ( 490) hydrogen bonds : angle 4.26160 ( 1380) *********************** 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 303 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 275 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 979 PHE cc_start: 0.8258 (m-10) cc_final: 0.7995 (m-10) REVERT: A 503 SER cc_start: 0.8119 (t) cc_final: 0.7750 (m) REVERT: A 528 GLU cc_start: 0.7805 (mp0) cc_final: 0.7431 (mp0) REVERT: A 593 ASP cc_start: 0.7929 (t0) cc_final: 0.7572 (t0) REVERT: A 658 MET cc_start: 0.8126 (mmm) cc_final: 0.7586 (mmm) REVERT: A 738 ARG cc_start: 0.7693 (ttp-110) cc_final: 0.7315 (ttp-110) REVERT: B 338 GLU cc_start: 0.7375 (mp0) cc_final: 0.7065 (mp0) REVERT: B 348 ASP cc_start: 0.7985 (m-30) cc_final: 0.7649 (m-30) REVERT: B 356 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8473 (t) REVERT: B 428 ASP cc_start: 0.8280 (p0) cc_final: 0.7923 (p0) REVERT: B 510 GLU cc_start: 0.7779 (tp30) cc_final: 0.7484 (tp30) REVERT: B 617 GLU cc_start: 0.7778 (tp30) cc_final: 0.7441 (tp30) REVERT: B 754 LYS cc_start: 0.7970 (ptmt) cc_final: 0.7714 (ptmt) REVERT: B 810 ILE cc_start: 0.8644 (mt) cc_final: 0.8312 (tt) REVERT: B 823 MET cc_start: 0.8233 (mmm) cc_final: 0.8011 (mmm) REVERT: B 972 GLU cc_start: 0.7444 (mp0) cc_final: 0.7239 (mt-10) REVERT: B 1151 ASP cc_start: 0.8104 (t0) cc_final: 0.7823 (p0) REVERT: B 1177 THR cc_start: 0.8472 (m) cc_final: 0.7270 (t) REVERT: B 1193 LYS cc_start: 0.8136 (ttmt) cc_final: 0.7856 (ttmm) outliers start: 28 outliers final: 23 residues processed: 291 average time/residue: 0.1258 time to fit residues: 50.8093 Evaluate side-chains 285 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 516 CYS 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 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 986 LEU Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1016 LEU 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 1147 MET Chi-restraints excluded: chain B residue 1171 ASP 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 31 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 61 optimal weight: 0.4980 chunk 134 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN B 258 ASN B 501 HIS B 514 HIS ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.136506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.109896 restraints weight = 18781.056| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.41 r_work: 0.3250 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12082 Z= 0.132 Angle : 0.534 12.442 16389 Z= 0.276 Chirality : 0.041 0.144 1889 Planarity : 0.004 0.068 2070 Dihedral : 3.854 22.463 1595 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.83 % Allowed : 17.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.23), residues: 1460 helix: 1.42 (0.24), residues: 505 sheet: 0.81 (0.30), residues: 331 loop : -1.11 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 831 TYR 0.010 0.001 TYR B1028 PHE 0.029 0.001 PHE A 618 TRP 0.011 0.001 TRP B 153 HIS 0.003 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00315 (12081) covalent geometry : angle 0.53409 (16387) SS BOND : bond 0.00312 ( 1) SS BOND : angle 1.94088 ( 2) hydrogen bonds : bond 0.03903 ( 490) hydrogen bonds : angle 4.14019 ( 1380) *********************** 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 288 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 979 PHE cc_start: 0.8259 (m-10) cc_final: 0.7982 (m-10) REVERT: A 503 SER cc_start: 0.8123 (t) cc_final: 0.7766 (m) REVERT: A 528 GLU cc_start: 0.7812 (mp0) cc_final: 0.7430 (mp0) REVERT: A 559 LYS cc_start: 0.8147 (mtpp) cc_final: 0.7766 (mtpp) REVERT: A 593 ASP cc_start: 0.7922 (t0) cc_final: 0.7569 (t0) REVERT: A 658 MET cc_start: 0.8098 (mmm) cc_final: 0.7576 (mmm) REVERT: A 738 ARG cc_start: 0.7709 (ttp-110) cc_final: 0.7323 (ttp-110) REVERT: B 338 GLU cc_start: 0.7379 (mp0) cc_final: 0.7088 (mp0) REVERT: B 348 ASP cc_start: 0.7958 (m-30) cc_final: 0.7620 (m-30) REVERT: B 356 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8492 (t) REVERT: B 428 ASP cc_start: 0.8290 (p0) cc_final: 0.7947 (p0) REVERT: B 510 GLU cc_start: 0.7747 (tp30) cc_final: 0.7447 (tp30) REVERT: B 617 GLU cc_start: 0.7773 (tp30) cc_final: 0.7404 (tp30) REVERT: B 754 LYS cc_start: 0.7999 (ptmt) cc_final: 0.7745 (ptmt) REVERT: B 810 ILE cc_start: 0.8618 (mt) cc_final: 0.8310 (tt) REVERT: B 823 MET cc_start: 0.8234 (mmm) cc_final: 0.7979 (mmm) REVERT: B 1151 ASP cc_start: 0.8073 (t0) cc_final: 0.7801 (p0) REVERT: B 1177 THR cc_start: 0.8403 (m) cc_final: 0.7198 (t) REVERT: B 1193 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7781 (ttmm) outliers start: 24 outliers final: 20 residues processed: 276 average time/residue: 0.1295 time to fit residues: 49.4683 Evaluate side-chains 280 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 259 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 165 SER Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 516 CYS 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 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 986 LEU Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1104 GLU 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 103 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 120 optimal weight: 0.0870 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 985 ASN A 565 GLN B 125 GLN B 258 ASN B 514 HIS B 545 ASN B1060 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.135418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108850 restraints weight = 18602.032| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.40 r_work: 0.3223 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12082 Z= 0.170 Angle : 0.573 11.803 16389 Z= 0.298 Chirality : 0.042 0.146 1889 Planarity : 0.004 0.070 2070 Dihedral : 4.043 22.614 1595 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.13 % Allowed : 17.52 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.22), residues: 1460 helix: 1.29 (0.23), residues: 505 sheet: 0.73 (0.30), residues: 325 loop : -1.18 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 831 TYR 0.012 0.001 TYR B 935 PHE 0.028 0.002 PHE A 618 TRP 0.011 0.002 TRP B1094 HIS 0.004 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00409 (12081) covalent geometry : angle 0.57238 (16387) SS BOND : bond 0.00517 ( 1) SS BOND : angle 2.27691 ( 2) hydrogen bonds : bond 0.04630 ( 490) hydrogen bonds : angle 4.28511 ( 1380) *********************** 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 305 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 979 PHE cc_start: 0.8230 (m-10) cc_final: 0.7988 (m-10) REVERT: A 406 MET cc_start: 0.6182 (mmm) cc_final: 0.5539 (mmt) REVERT: A 503 SER cc_start: 0.8203 (t) cc_final: 0.7828 (m) REVERT: A 528 GLU cc_start: 0.7834 (mp0) cc_final: 0.7426 (mp0) REVERT: A 593 ASP cc_start: 0.7935 (t0) cc_final: 0.7576 (t0) REVERT: A 658 MET cc_start: 0.8147 (mmm) cc_final: 0.7562 (mmm) REVERT: A 738 ARG cc_start: 0.7766 (ttp-110) cc_final: 0.7374 (ttp-110) REVERT: B 338 GLU cc_start: 0.7431 (mp0) cc_final: 0.7141 (mp0) REVERT: B 348 ASP cc_start: 0.7991 (m-30) cc_final: 0.7647 (m-30) REVERT: B 356 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8523 (t) REVERT: B 428 ASP cc_start: 0.8309 (p0) cc_final: 0.7966 (p0) REVERT: B 510 GLU cc_start: 0.7729 (tp30) cc_final: 0.7452 (tp30) REVERT: B 617 GLU cc_start: 0.7747 (tp30) cc_final: 0.7373 (tp30) REVERT: B 618 TRP cc_start: 0.8194 (m100) cc_final: 0.7478 (m100) REVERT: B 754 LYS cc_start: 0.7991 (ptmt) cc_final: 0.7768 (ptmt) REVERT: B 810 ILE cc_start: 0.8660 (mt) cc_final: 0.8445 (tt) REVERT: B 1151 ASP cc_start: 0.8075 (t0) cc_final: 0.7853 (p0) REVERT: B 1177 THR cc_start: 0.8403 (m) cc_final: 0.7210 (t) REVERT: B 1193 LYS cc_start: 0.8158 (ttmt) cc_final: 0.7834 (ttmm) outliers start: 28 outliers final: 23 residues processed: 292 average time/residue: 0.1364 time to fit residues: 54.3624 Evaluate side-chains 291 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 267 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 A residue 610 ILE 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 356 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 545 ASN 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 986 LEU Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1073 ILE 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 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 141 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 0.0370 chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 0.0370 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN B 258 ASN ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 HIS B 545 ASN B1047 GLN B1060 ASN B1068 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.136252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109847 restraints weight = 18938.602| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.43 r_work: 0.3246 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12082 Z= 0.115 Angle : 0.566 17.135 16389 Z= 0.288 Chirality : 0.041 0.149 1889 Planarity : 0.004 0.067 2070 Dihedral : 3.905 22.703 1595 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.98 % Allowed : 18.28 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.22), residues: 1460 helix: 1.43 (0.24), residues: 499 sheet: 0.73 (0.30), residues: 328 loop : -1.15 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 558 TYR 0.009 0.001 TYR B1028 PHE 0.032 0.001 PHE A 618 TRP 0.011 0.001 TRP B 153 HIS 0.004 0.001 HIS B 501 Details of bonding type rmsd covalent geometry : bond 0.00270 (12081) covalent geometry : angle 0.56589 (16387) SS BOND : bond 0.00238 ( 1) SS BOND : angle 1.72988 ( 2) hydrogen bonds : bond 0.03665 ( 490) hydrogen bonds : angle 4.12718 ( 1380) ********************** 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 294 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 268 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 979 PHE cc_start: 0.8261 (m-10) cc_final: 0.7990 (m-10) REVERT: A 503 SER cc_start: 0.8200 (t) cc_final: 0.7824 (m) REVERT: A 528 GLU cc_start: 0.7815 (mp0) cc_final: 0.7475 (mp0) REVERT: A 559 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7724 (mtpp) REVERT: A 593 ASP cc_start: 0.7945 (t0) cc_final: 0.7579 (t0) REVERT: A 658 MET cc_start: 0.8133 (mmm) cc_final: 0.7646 (mmm) REVERT: A 738 ARG cc_start: 0.7730 (ttp-110) cc_final: 0.7335 (ttp-110) REVERT: B 338 GLU cc_start: 0.7460 (mp0) cc_final: 0.7187 (mp0) REVERT: B 348 ASP cc_start: 0.7962 (m-30) cc_final: 0.7622 (m-30) REVERT: B 356 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8522 (t) REVERT: B 428 ASP cc_start: 0.8318 (p0) cc_final: 0.7957 (p0) REVERT: B 510 GLU cc_start: 0.7756 (tp30) cc_final: 0.7451 (tp30) REVERT: B 617 GLU cc_start: 0.7804 (tp30) cc_final: 0.7429 (tp30) REVERT: B 618 TRP cc_start: 0.8186 (m100) cc_final: 0.7465 (m100) REVERT: B 754 LYS cc_start: 0.7979 (ptmt) cc_final: 0.7768 (ptmt) REVERT: B 810 ILE cc_start: 0.8620 (mt) cc_final: 0.8296 (tt) REVERT: B 1177 THR cc_start: 0.8369 (m) cc_final: 0.7101 (t) REVERT: B 1193 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7817 (ttmm) outliers start: 26 outliers final: 20 residues processed: 282 average time/residue: 0.1277 time to fit residues: 49.7457 Evaluate side-chains 285 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 264 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 526 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 986 LEU Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1060 ASN Chi-restraints excluded: chain B residue 1073 ILE 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 100 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 37 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN A 768 GLN B 125 GLN ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 HIS ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1060 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108730 restraints weight = 18762.881| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.41 r_work: 0.3229 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12082 Z= 0.154 Angle : 0.580 16.209 16389 Z= 0.296 Chirality : 0.042 0.148 1889 Planarity : 0.004 0.070 2070 Dihedral : 3.978 22.497 1595 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.90 % Allowed : 18.35 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.22), residues: 1460 helix: 1.39 (0.24), residues: 501 sheet: 0.76 (0.30), residues: 325 loop : -1.20 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 558 TYR 0.011 0.001 TYR B1028 PHE 0.030 0.002 PHE A 618 TRP 0.011 0.001 TRP B1094 HIS 0.004 0.001 HIS B 578 Details of bonding type rmsd covalent geometry : bond 0.00372 (12081) covalent geometry : angle 0.57950 (16387) SS BOND : bond 0.00485 ( 1) SS BOND : angle 2.13384 ( 2) hydrogen bonds : bond 0.04176 ( 490) hydrogen bonds : angle 4.20059 ( 1380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3266.59 seconds wall clock time: 56 minutes 34.02 seconds (3394.02 seconds total)