Starting phenix.real_space_refine on Wed Apr 30 19:35:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqr_37752/04_2025/8wqr_37752.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqr_37752/04_2025/8wqr_37752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wqr_37752/04_2025/8wqr_37752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqr_37752/04_2025/8wqr_37752.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqr_37752/04_2025/8wqr_37752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqr_37752/04_2025/8wqr_37752.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.036 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 43 5.16 5 C 6136 2.51 5 N 1720 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9681 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2763 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 18, 'TRANS': 337} Chain breaks: 5 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 6918 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 416} Link IDs: {'PTRANS': 38, 'TRANS': 1020} Chain breaks: 14 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1448 Unresolved non-hydrogen angles: 1837 Unresolved non-hydrogen dihedrals: 1170 Unresolved non-hydrogen chiralities: 126 Planarities with less than four sites: {'GLN:plan1': 24, 'HIS:plan': 9, 'TYR:plan': 10, 'ASN:plan1': 25, 'TRP:plan': 3, 'ASP:plan': 32, 'PHE:plan': 14, 'GLU:plan': 52, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 826 Time building chain proxies: 6.30, per 1000 atoms: 0.65 Number of scatterers: 9681 At special positions: 0 Unit cell: (94.35, 87.55, 147.9, 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 43 16.00 O 1782 8.00 N 1720 7.00 C 6136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.3 seconds 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 31 sheets defined 6.1% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'B' and resid 8 through 18 removed outlier: 4.046A pdb=" N ILE B 12 " --> pdb=" O ASN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 38 Processing helix chain 'B' and resid 927 through 931 removed outlier: 3.731A pdb=" N LEU B 931 " --> pdb=" O PRO B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 989 No H-bonds generated for 'chain 'B' and resid 987 through 989' Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 1044 through 1054 removed outlier: 3.504A pdb=" N TYR A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N MET A1054 " --> pdb=" O LEU A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1060 removed outlier: 4.287A pdb=" N LEU A1058 " --> pdb=" O GLN A1055 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A1060 " --> pdb=" O ARG A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1075 Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1101 through 1108 removed outlier: 4.237A pdb=" N GLU A1107 " --> pdb=" O PRO A1103 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A1108 " --> pdb=" O LYS A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1135 removed outlier: 3.753A pdb=" N LYS A1131 " --> pdb=" O ASP A1127 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A1132 " --> pdb=" O ASP A1128 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A1135 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 44 through 45 removed outlier: 3.541A pdb=" N VAL B1034 " --> pdb=" O TYR B1026 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B1025 " --> pdb=" O ARG B1015 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER B1013 " --> pdb=" O GLY B1027 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 61 removed outlier: 5.242A pdb=" N LEU B 59 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ALA B 69 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN B 76 " --> pdb=" O HIS B 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 102 removed outlier: 6.581A pdb=" N GLY B 114 " --> pdb=" O TRP B 99 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL B 101 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA B 112 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B 119 " --> pdb=" O CYS B 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 146 removed outlier: 3.568A pdb=" N ALA B 144 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 152 " --> pdb=" O TRP B 163 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TRP B 163 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 174 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 183 through 188 removed outlier: 7.239A pdb=" N VAL B 183 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL B 200 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 185 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU B 862 " --> pdb=" O GLN B 885 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLN B 885 " --> pdb=" O LEU B 862 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TRP B 864 " --> pdb=" O LEU B 883 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU B 883 " --> pdb=" O TRP B 864 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 896 through 897 removed outlier: 3.873A pdb=" N ASP B 896 " --> pdb=" O ALA B 905 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 905 " --> pdb=" O ASP B 896 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 944 through 949 removed outlier: 4.191A pdb=" N SER B 946 " --> pdb=" O GLY B 959 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 956 " --> pdb=" O PHE B 979 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 979 " --> pdb=" O VAL B 956 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA B 976 " --> pdb=" O ASN B 996 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASN B 996 " --> pdb=" O ALA B 976 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL B 978 " --> pdb=" O VAL B 994 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 980 " --> pdb=" O ARG B 992 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1004 through 1008 removed outlier: 6.538A pdb=" N GLY A1031 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE A1007 " --> pdb=" O LEU A1029 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A1029 " --> pdb=" O PHE A1007 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A1030 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A1038 " --> pdb=" O PHE A1030 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 5 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A1089 " --> pdb=" O ASN A 4 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.584A pdb=" N GLY A 17 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU A 39 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLU A 54 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE A 41 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 21 through 25 removed outlier: 3.826A pdb=" N GLY A 21 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE A 23 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ASP A 28 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 61 through 67 removed outlier: 3.772A pdb=" N GLU A 65 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 104 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU A 90 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N THR A 102 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS A 92 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE A 100 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.687A pdb=" N ILE A 121 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 135 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.762A pdb=" N ASP A 166 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 180 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 190 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 210 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 218 through 221 Processing sheet with id=AB6, first strand: chain 'A' and resid 237 through 241 removed outlier: 3.529A pdb=" N LEU A 246 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 241 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 258 through 263 removed outlier: 6.158A pdb=" N GLY A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N HIS A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG A 263 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ARG A 270 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 273 " --> pdb=" O PHE A 281 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 313 through 318 removed outlier: 5.519A pdb=" N LEU A 314 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY A 325 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N TYR A 316 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE A 323 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 318 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 362 through 365 removed outlier: 3.646A pdb=" N CYS A 363 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 713 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.646A pdb=" N GLY A 409 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 428 " --> pdb=" O GLY A 409 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP A 411 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 426 " --> pdb=" O TRP A 411 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 457 through 459 removed outlier: 6.446A pdb=" N VAL A 476 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU A 489 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU A 478 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 485 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 507 through 512 removed outlier: 6.716A pdb=" N LEU A 516 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N HIS A 531 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR A 518 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 527 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 525 " --> pdb=" O HIS A 522 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 538 through 542 removed outlier: 4.945A pdb=" N CYS A 540 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 559 " --> pdb=" O CYS A 540 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 542 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 565 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA A 566 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS A 579 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A 568 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 575 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 588 through 594 Processing sheet with id=AC6, first strand: chain 'A' and resid 637 through 641 removed outlier: 3.513A pdb=" N VAL A 637 " --> pdb=" O CYS A 652 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS A 652 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 678 through 681 removed outlier: 3.711A pdb=" N TYR A 678 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 700 " --> pdb=" O LEU A 693 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 724 through 725 removed outlier: 3.751A pdb=" N CYS A 725 " --> pdb=" O GLY A 734 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 764 through 765 removed outlier: 6.201A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 812 through 817 removed outlier: 4.142A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 815 " --> pdb=" O GLY A 832 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 883 through 884 removed outlier: 3.504A pdb=" N ILE A 884 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 915 through 916 removed outlier: 7.123A pdb=" N VAL A 930 " --> pdb=" O ARG A 947 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG A 947 " --> pdb=" O VAL A 930 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU A 932 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 941 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 954 through 957 removed outlier: 7.162A pdb=" N ALA A 968 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 976 " --> pdb=" O GLY A 996 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 996 " --> pdb=" O VAL A 976 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3280 1.34 - 1.46: 2210 1.46 - 1.58: 4281 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 9837 Sorted by residual: bond pdb=" N ASN B 137 " pdb=" CA ASN B 137 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.52e+00 bond pdb=" CB LYS B 86 " pdb=" CG LYS B 86 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" N PRO A 250 " pdb=" CA PRO A 250 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.31e-02 5.83e+03 6.81e-01 bond pdb=" CB ARG A1074 " pdb=" CG ARG A1074 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.21e-01 bond pdb=" CB TRP A1073 " pdb=" CG TRP A1073 " ideal model delta sigma weight residual 1.498 1.474 0.024 3.10e-02 1.04e+03 5.93e-01 ... (remaining 9832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 13166 1.72 - 3.44: 221 3.44 - 5.16: 36 5.16 - 6.88: 3 6.88 - 8.60: 2 Bond angle restraints: 13428 Sorted by residual: angle pdb=" CB LYS B 86 " pdb=" CG LYS B 86 " pdb=" CD LYS B 86 " ideal model delta sigma weight residual 111.30 119.17 -7.87 2.30e+00 1.89e-01 1.17e+01 angle pdb=" N VAL B 975 " pdb=" CA VAL B 975 " pdb=" C VAL B 975 " ideal model delta sigma weight residual 113.42 109.73 3.69 1.17e+00 7.31e-01 9.96e+00 angle pdb=" N VAL A1033 " pdb=" CA VAL A1033 " pdb=" C VAL A1033 " ideal model delta sigma weight residual 113.16 108.77 4.39 1.49e+00 4.50e-01 8.66e+00 angle pdb=" CA LEU A 881 " pdb=" CB LEU A 881 " pdb=" CG LEU A 881 " ideal model delta sigma weight residual 116.30 124.90 -8.60 3.50e+00 8.16e-02 6.03e+00 angle pdb=" CG MET A 927 " pdb=" SD MET A 927 " pdb=" CE MET A 927 " ideal model delta sigma weight residual 100.90 106.08 -5.18 2.20e+00 2.07e-01 5.55e+00 ... (remaining 13423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 5358 17.17 - 34.34: 349 34.34 - 51.51: 60 51.51 - 68.69: 4 68.69 - 85.86: 7 Dihedral angle restraints: 5778 sinusoidal: 1716 harmonic: 4062 Sorted by residual: dihedral pdb=" CA PHE B 57 " pdb=" C PHE B 57 " pdb=" N LEU B 58 " pdb=" CA LEU B 58 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA THR B 937 " pdb=" C THR B 937 " pdb=" N LYS B 938 " pdb=" CA LYS B 938 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PHE A1076 " pdb=" C PHE A1076 " pdb=" N HIS A1077 " pdb=" CA HIS A1077 " ideal model delta harmonic sigma weight residual 180.00 -163.86 -16.14 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 5775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 931 0.028 - 0.057: 421 0.057 - 0.085: 120 0.085 - 0.113: 125 0.113 - 0.141: 37 Chirality restraints: 1634 Sorted by residual: chirality pdb=" CA ASN B 137 " pdb=" N ASN B 137 " pdb=" C ASN B 137 " pdb=" CB ASN B 137 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CG LEU A 89 " pdb=" CB LEU A 89 " pdb=" CD1 LEU A 89 " pdb=" CD2 LEU A 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE A 959 " pdb=" N ILE A 959 " pdb=" C ILE A 959 " pdb=" CB ILE A 959 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 1631 not shown) Planarity restraints: 1739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 146 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO B 147 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 147 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 147 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 189 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO B 190 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 190 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 190 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 125 " -0.026 5.00e-02 4.00e+02 4.04e-02 2.62e+00 pdb=" N PRO A 126 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.023 5.00e-02 4.00e+02 ... (remaining 1736 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 372 2.71 - 3.26: 9380 3.26 - 3.81: 14974 3.81 - 4.35: 17457 4.35 - 4.90: 29919 Nonbonded interactions: 72102 Sorted by model distance: nonbonded pdb=" OG SER B 136 " pdb=" OD1 ASN B 138 " model vdw 2.166 3.040 nonbonded pdb=" O LEU A1093 " pdb=" OG SER A1096 " model vdw 2.194 3.040 nonbonded pdb=" NH1 ARG B 980 " pdb=" O LEU B 981 " model vdw 2.227 3.120 nonbonded pdb=" NH2 ARG B 18 " pdb=" OG SER A 720 " model vdw 2.228 3.120 nonbonded pdb=" OG SER A 196 " pdb=" OE1 GLU A 199 " model vdw 2.233 3.040 ... (remaining 72097 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.650 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 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 : 0.003 0.034 9837 Z= 0.124 Angle : 0.577 8.596 13428 Z= 0.312 Chirality : 0.045 0.141 1634 Planarity : 0.004 0.047 1739 Dihedral : 12.193 85.857 3142 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.77 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.22), residues: 1373 helix: -0.60 (0.69), residues: 60 sheet: -1.40 (0.23), residues: 514 loop : -1.90 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1073 HIS 0.004 0.001 HIS A1070 PHE 0.011 0.001 PHE A 829 TYR 0.015 0.001 TYR A 3 ARG 0.008 0.000 ARG B1015 Details of bonding type rmsd hydrogen bonds : bond 0.31437 ( 269) hydrogen bonds : angle 11.31558 ( 702) covalent geometry : bond 0.00252 ( 9837) covalent geometry : angle 0.57683 (13428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: B 896 ASP cc_start: 0.8282 (t70) cc_final: 0.8059 (t0) REVERT: A 326 SER cc_start: 0.8200 (t) cc_final: 0.7584 (p) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1923 time to fit residues: 30.2144 Evaluate side-chains 80 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS A 4 ASN A 36 ASN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 HIS A1034 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.120000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.099430 restraints weight = 39275.169| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 5.03 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9837 Z= 0.191 Angle : 0.620 7.062 13428 Z= 0.326 Chirality : 0.047 0.147 1634 Planarity : 0.005 0.052 1739 Dihedral : 4.377 19.247 1469 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.65 % Favored : 92.21 % Rotamer: Outliers : 1.11 % Allowed : 9.65 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.22), residues: 1373 helix: -0.37 (0.70), residues: 62 sheet: -1.44 (0.22), residues: 544 loop : -2.01 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 865 HIS 0.005 0.001 HIS A 711 PHE 0.015 0.002 PHE B 907 TYR 0.020 0.002 TYR A 3 ARG 0.009 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.05090 ( 269) hydrogen bonds : angle 7.84983 ( 702) covalent geometry : bond 0.00421 ( 9837) covalent geometry : angle 0.62010 (13428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 1.199 Fit side-chains REVERT: B 16 ARG cc_start: 0.8042 (mmp-170) cc_final: 0.7761 (mmp-170) REVERT: B 896 ASP cc_start: 0.8326 (t70) cc_final: 0.8113 (t70) outliers start: 9 outliers final: 6 residues processed: 92 average time/residue: 0.2424 time to fit residues: 33.2582 Evaluate side-chains 85 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 872 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 60 optimal weight: 5.9990 chunk 83 optimal weight: 40.0000 chunk 8 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 0.0670 chunk 95 optimal weight: 1.9990 chunk 88 optimal weight: 40.0000 chunk 130 optimal weight: 8.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS B 150 GLN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.118013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.097246 restraints weight = 39068.216| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 4.95 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9837 Z= 0.232 Angle : 0.663 8.037 13428 Z= 0.345 Chirality : 0.048 0.166 1634 Planarity : 0.005 0.053 1739 Dihedral : 4.700 21.369 1469 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.23 % Favored : 91.62 % Rotamer: Outliers : 1.49 % Allowed : 13.99 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.21), residues: 1373 helix: -1.08 (0.60), residues: 79 sheet: -1.66 (0.22), residues: 538 loop : -2.24 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1047 HIS 0.006 0.001 HIS A 711 PHE 0.023 0.002 PHE A 155 TYR 0.022 0.002 TYR A 3 ARG 0.003 0.001 ARG A 847 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 269) hydrogen bonds : angle 7.28135 ( 702) covalent geometry : bond 0.00515 ( 9837) covalent geometry : angle 0.66301 (13428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: B 16 ARG cc_start: 0.8007 (mmp-170) cc_final: 0.7694 (mmp-170) REVERT: B 896 ASP cc_start: 0.8383 (t70) cc_final: 0.8154 (t70) REVERT: B 938 LYS cc_start: 0.7755 (mttt) cc_final: 0.7331 (mttt) REVERT: A 914 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7510 (mp) outliers start: 12 outliers final: 9 residues processed: 89 average time/residue: 0.2445 time to fit residues: 32.0908 Evaluate side-chains 85 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 885 GLN Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 914 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 108 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 40.0000 chunk 127 optimal weight: 20.0000 chunk 49 optimal weight: 0.0050 chunk 70 optimal weight: 0.0040 chunk 98 optimal weight: 50.0000 chunk 31 optimal weight: 0.9990 overall best weight: 0.7610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 HIS B 150 GLN A 4 ASN ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 ASN A1070 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.120583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.100479 restraints weight = 38962.154| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 5.05 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9837 Z= 0.104 Angle : 0.554 9.448 13428 Z= 0.285 Chirality : 0.046 0.145 1634 Planarity : 0.004 0.050 1739 Dihedral : 4.152 18.400 1469 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.48 % Favored : 93.37 % Rotamer: Outliers : 1.61 % Allowed : 15.59 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.22), residues: 1373 helix: -0.53 (0.64), residues: 75 sheet: -1.40 (0.22), residues: 564 loop : -2.21 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 865 HIS 0.004 0.001 HIS B 985 PHE 0.013 0.001 PHE A 155 TYR 0.013 0.001 TYR A 3 ARG 0.004 0.000 ARG B1015 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 269) hydrogen bonds : angle 6.46399 ( 702) covalent geometry : bond 0.00230 ( 9837) covalent geometry : angle 0.55382 (13428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 896 ASP cc_start: 0.8446 (t70) cc_final: 0.8152 (t70) REVERT: B 938 LYS cc_start: 0.7636 (mttt) cc_final: 0.7102 (mttt) outliers start: 13 outliers final: 8 residues processed: 103 average time/residue: 0.2076 time to fit residues: 31.6436 Evaluate side-chains 92 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1073 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 40.0000 chunk 29 optimal weight: 10.0000 chunk 103 optimal weight: 40.0000 chunk 82 optimal weight: 0.0050 chunk 138 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 50.0000 chunk 44 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.115885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.095107 restraints weight = 39296.593| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 4.88 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 9837 Z= 0.283 Angle : 0.713 12.254 13428 Z= 0.370 Chirality : 0.049 0.159 1634 Planarity : 0.005 0.058 1739 Dihedral : 4.906 23.791 1469 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.91 % Favored : 89.95 % Rotamer: Outliers : 4.46 % Allowed : 15.72 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.21), residues: 1373 helix: -1.30 (0.59), residues: 79 sheet: -1.68 (0.22), residues: 532 loop : -2.35 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1047 HIS 0.006 0.001 HIS A 711 PHE 0.025 0.002 PHE A 829 TYR 0.021 0.002 TYR A 3 ARG 0.005 0.001 ARG A 847 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 269) hydrogen bonds : angle 6.99301 ( 702) covalent geometry : bond 0.00630 ( 9837) covalent geometry : angle 0.71294 (13428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: B 896 ASP cc_start: 0.8425 (t70) cc_final: 0.8202 (t0) REVERT: B 938 LYS cc_start: 0.7818 (mttt) cc_final: 0.7507 (mttt) REVERT: A 914 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7658 (mp) REVERT: A 1070 HIS cc_start: 0.7781 (OUTLIER) cc_final: 0.7542 (t-170) outliers start: 36 outliers final: 17 residues processed: 108 average time/residue: 0.2207 time to fit residues: 34.6100 Evaluate side-chains 96 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1070 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 105 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 62 optimal weight: 0.0060 chunk 50 optimal weight: 3.9990 chunk 127 optimal weight: 0.0170 chunk 23 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 92 optimal weight: 20.0000 overall best weight: 0.5234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 GLN ** A1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.119450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.099014 restraints weight = 38797.813| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 5.01 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9837 Z= 0.107 Angle : 0.604 13.922 13428 Z= 0.302 Chirality : 0.046 0.149 1634 Planarity : 0.004 0.052 1739 Dihedral : 4.321 19.820 1469 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.41 % Favored : 93.45 % Rotamer: Outliers : 2.10 % Allowed : 18.19 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.21), residues: 1373 helix: -0.90 (0.61), residues: 75 sheet: -1.47 (0.22), residues: 532 loop : -2.15 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 865 HIS 0.003 0.001 HIS B 72 PHE 0.015 0.002 PHE B 162 TYR 0.011 0.001 TYR A1048 ARG 0.007 0.000 ARG B1015 Details of bonding type rmsd hydrogen bonds : bond 0.02958 ( 269) hydrogen bonds : angle 6.30369 ( 702) covalent geometry : bond 0.00245 ( 9837) covalent geometry : angle 0.60412 (13428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: B 896 ASP cc_start: 0.8432 (t70) cc_final: 0.8056 (t70) REVERT: B 938 LYS cc_start: 0.7675 (mttt) cc_final: 0.7296 (mttt) REVERT: A 166 ASP cc_start: 0.8154 (t70) cc_final: 0.7942 (t70) outliers start: 17 outliers final: 13 residues processed: 101 average time/residue: 0.2275 time to fit residues: 34.3948 Evaluate side-chains 93 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 1073 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 17 optimal weight: 9.9990 chunk 87 optimal weight: 50.0000 chunk 40 optimal weight: 0.0000 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.119654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.099312 restraints weight = 39016.863| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 5.06 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9837 Z= 0.104 Angle : 0.578 14.025 13428 Z= 0.288 Chirality : 0.045 0.168 1634 Planarity : 0.004 0.051 1739 Dihedral : 4.101 18.463 1469 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.70 % Favored : 93.15 % Rotamer: Outliers : 2.35 % Allowed : 18.69 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.22), residues: 1373 helix: -0.82 (0.62), residues: 75 sheet: -1.39 (0.22), residues: 537 loop : -2.11 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 865 HIS 0.003 0.001 HIS B 72 PHE 0.014 0.001 PHE B 162 TYR 0.012 0.001 TYR A 3 ARG 0.004 0.000 ARG B1015 Details of bonding type rmsd hydrogen bonds : bond 0.02846 ( 269) hydrogen bonds : angle 5.97038 ( 702) covalent geometry : bond 0.00234 ( 9837) covalent geometry : angle 0.57832 (13428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: B 896 ASP cc_start: 0.8403 (t70) cc_final: 0.8049 (t0) REVERT: B 938 LYS cc_start: 0.7725 (mttt) cc_final: 0.7298 (mttt) REVERT: A 166 ASP cc_start: 0.8136 (t70) cc_final: 0.7931 (t70) outliers start: 19 outliers final: 15 residues processed: 102 average time/residue: 0.1956 time to fit residues: 29.6347 Evaluate side-chains 96 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 885 GLN Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 1073 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 139 optimal weight: 4.9990 chunk 96 optimal weight: 30.0000 chunk 118 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 41 optimal weight: 1.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.116911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.096312 restraints weight = 39362.730| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 4.98 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9837 Z= 0.199 Angle : 0.649 12.830 13428 Z= 0.329 Chirality : 0.047 0.173 1634 Planarity : 0.005 0.054 1739 Dihedral : 4.482 22.271 1469 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.59 % Favored : 91.33 % Rotamer: Outliers : 2.97 % Allowed : 18.07 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.21), residues: 1373 helix: -1.18 (0.61), residues: 77 sheet: -1.44 (0.22), residues: 526 loop : -2.24 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1047 HIS 0.005 0.001 HIS A 711 PHE 0.020 0.002 PHE A 829 TYR 0.015 0.002 TYR A 3 ARG 0.006 0.001 ARG B1015 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 269) hydrogen bonds : angle 6.37350 ( 702) covalent geometry : bond 0.00444 ( 9837) covalent geometry : angle 0.64861 (13428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 896 ASP cc_start: 0.8437 (t70) cc_final: 0.8152 (t0) REVERT: B 938 LYS cc_start: 0.7727 (mttt) cc_final: 0.7270 (mttt) REVERT: A 166 ASP cc_start: 0.8412 (t70) cc_final: 0.8158 (t70) outliers start: 24 outliers final: 18 residues processed: 95 average time/residue: 0.2218 time to fit residues: 30.6579 Evaluate side-chains 96 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 885 GLN Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1073 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 4 optimal weight: 20.0000 chunk 125 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 GLN ** A1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.118170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.097749 restraints weight = 38784.657| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 4.97 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9837 Z= 0.130 Angle : 0.607 12.463 13428 Z= 0.303 Chirality : 0.046 0.164 1634 Planarity : 0.004 0.050 1739 Dihedral : 4.322 20.083 1469 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.14 % Favored : 92.79 % Rotamer: Outliers : 2.48 % Allowed : 18.69 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.22), residues: 1373 helix: -0.84 (0.63), residues: 74 sheet: -1.42 (0.22), residues: 533 loop : -2.17 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1047 HIS 0.015 0.001 HIS A1070 PHE 0.025 0.001 PHE B 162 TYR 0.011 0.001 TYR A1048 ARG 0.006 0.000 ARG B1015 Details of bonding type rmsd hydrogen bonds : bond 0.02972 ( 269) hydrogen bonds : angle 6.13643 ( 702) covalent geometry : bond 0.00296 ( 9837) covalent geometry : angle 0.60705 (13428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 MET cc_start: 0.4737 (mmt) cc_final: 0.4228 (mmt) REVERT: B 896 ASP cc_start: 0.8399 (t70) cc_final: 0.8029 (t0) REVERT: B 938 LYS cc_start: 0.7704 (mttt) cc_final: 0.7241 (mttt) outliers start: 20 outliers final: 17 residues processed: 93 average time/residue: 0.2116 time to fit residues: 28.6841 Evaluate side-chains 95 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 885 GLN Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 1073 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 71 optimal weight: 0.8980 chunk 82 optimal weight: 40.0000 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.0670 chunk 52 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 125 optimal weight: 0.4980 chunk 3 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.118938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.098661 restraints weight = 39236.818| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 5.04 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9837 Z= 0.112 Angle : 0.590 11.809 13428 Z= 0.293 Chirality : 0.046 0.156 1634 Planarity : 0.004 0.051 1739 Dihedral : 4.136 18.901 1469 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.21 % Favored : 92.72 % Rotamer: Outliers : 2.10 % Allowed : 18.81 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.22), residues: 1373 helix: -0.73 (0.63), residues: 74 sheet: -1.35 (0.22), residues: 535 loop : -2.06 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1016 HIS 0.014 0.001 HIS A1070 PHE 0.016 0.001 PHE B 162 TYR 0.010 0.001 TYR A1048 ARG 0.006 0.000 ARG B1015 Details of bonding type rmsd hydrogen bonds : bond 0.02843 ( 269) hydrogen bonds : angle 5.92044 ( 702) covalent geometry : bond 0.00257 ( 9837) covalent geometry : angle 0.58972 (13428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: B 16 ARG cc_start: 0.7875 (mmp-170) cc_final: 0.7622 (mmp-170) REVERT: B 23 MET cc_start: 0.4439 (mmt) cc_final: 0.3911 (mmt) REVERT: B 896 ASP cc_start: 0.8369 (t70) cc_final: 0.8006 (t0) REVERT: B 938 LYS cc_start: 0.7649 (mttt) cc_final: 0.7215 (mttt) REVERT: B 1016 TRP cc_start: 0.7807 (m100) cc_final: 0.7598 (m100) outliers start: 17 outliers final: 16 residues processed: 93 average time/residue: 0.2054 time to fit residues: 28.4480 Evaluate side-chains 95 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 1073 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 96 optimal weight: 50.0000 chunk 110 optimal weight: 8.9990 chunk 80 optimal weight: 40.0000 chunk 90 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 98 optimal weight: 50.0000 chunk 111 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 HIS ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN A1009 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.115925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.095373 restraints weight = 39712.177| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 4.95 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9837 Z= 0.251 Angle : 0.707 10.113 13428 Z= 0.360 Chirality : 0.048 0.188 1634 Planarity : 0.005 0.057 1739 Dihedral : 4.811 25.032 1469 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.83 % Favored : 90.09 % Rotamer: Outliers : 2.72 % Allowed : 18.56 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.21), residues: 1373 helix: -1.44 (0.59), residues: 78 sheet: -1.50 (0.22), residues: 527 loop : -2.29 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1047 HIS 0.010 0.001 HIS A1070 PHE 0.026 0.002 PHE A 829 TYR 0.019 0.002 TYR B 936 ARG 0.005 0.001 ARG B 16 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 269) hydrogen bonds : angle 6.56548 ( 702) covalent geometry : bond 0.00563 ( 9837) covalent geometry : angle 0.70669 (13428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4353.63 seconds wall clock time: 77 minutes 8.47 seconds (4628.47 seconds total)