Starting phenix.real_space_refine on Mon Dec 30 23:00:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s9w_24939/12_2024/7s9w_24939.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s9w_24939/12_2024/7s9w_24939.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/7s9w_24939/12_2024/7s9w_24939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s9w_24939/12_2024/7s9w_24939.map" model { file = "/net/cci-nas-00/data/ceres_data/7s9w_24939/12_2024/7s9w_24939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s9w_24939/12_2024/7s9w_24939.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 73 5.16 5 C 8825 2.51 5 N 2508 2.21 5 O 2637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14052 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1238, 9746 Classifications: {'peptide': 1238} Link IDs: {'PCIS': 2, 'PTRANS': 63, 'TRANS': 1172} Chain breaks: 2 Chain: "B" Number of atoms: 4139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4139 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 491} Chain breaks: 3 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.64, per 1000 atoms: 0.61 Number of scatterers: 14052 At special positions: 0 Unit cell: (97.9, 123.2, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 P 9 15.00 O 2637 8.00 N 2508 7.00 C 8825 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: 3.37 Conformation dependent library (CDL) restraints added in 1.9 seconds 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3284 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 18 sheets defined 36.8% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.791A pdb=" N TYR A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.987A pdb=" N GLN A 42 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.721A pdb=" N ILE A 93 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.870A pdb=" N ASP A 102 " --> pdb=" O PRO A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 119 Proline residue: A 117 - end of helix Processing helix chain 'A' and resid 132 through 149 removed outlier: 4.034A pdb=" N ILE A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.628A pdb=" N GLU A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 removed outlier: 3.627A pdb=" N TRP A 347 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.584A pdb=" N ALA A 458 " --> pdb=" O GLN A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 484 removed outlier: 3.991A pdb=" N VAL A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 491 removed outlier: 3.565A pdb=" N ALA A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 522 removed outlier: 4.066A pdb=" N ARG A 504 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N CYS A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 506 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 551 removed outlier: 4.284A pdb=" N LEU A 544 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 4.345A pdb=" N SER A 567 " --> pdb=" O LYS A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 Proline residue: A 581 - end of helix removed outlier: 3.928A pdb=" N ASP A 585 " --> pdb=" O PRO A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 626 removed outlier: 3.578A pdb=" N GLY A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 617 " --> pdb=" O ALA A 613 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG A 626 " --> pdb=" O MET A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 677 removed outlier: 3.731A pdb=" N GLN A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 658 " --> pdb=" O GLN A 654 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 662 " --> pdb=" O ARG A 658 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 712 removed outlier: 3.618A pdb=" N ILE A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 775 removed outlier: 4.198A pdb=" N THR A 774 " --> pdb=" O LYS A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 792 Processing helix chain 'A' and resid 802 through 809 removed outlier: 3.521A pdb=" N ALA A 805 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET A 807 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA A 808 " --> pdb=" O ALA A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 816 removed outlier: 3.626A pdb=" N ARG A 814 " --> pdb=" O GLY A 811 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A 815 " --> pdb=" O GLN A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 871 Processing helix chain 'A' and resid 872 through 890 removed outlier: 3.665A pdb=" N MET A 878 " --> pdb=" O PRO A 874 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 886 " --> pdb=" O TYR A 882 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS A 890 " --> pdb=" O VAL A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 removed outlier: 3.579A pdb=" N GLN A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 987 removed outlier: 3.643A pdb=" N ARG A 970 " --> pdb=" O ALA A 966 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 980 " --> pdb=" O LEU A 976 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS A 985 " --> pdb=" O GLU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 994 Proline residue: A 992 - end of helix Processing helix chain 'A' and resid 1002 through 1023 removed outlier: 3.778A pdb=" N ARG A1011 " --> pdb=" O GLY A1007 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A1012 " --> pdb=" O GLY A1008 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL A1017 " --> pdb=" O ALA A1013 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN A1018 " --> pdb=" O GLU A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1061 Processing helix chain 'A' and resid 1117 through 1125 Processing helix chain 'A' and resid 1144 through 1153 removed outlier: 3.530A pdb=" N THR A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1158 Processing helix chain 'A' and resid 1161 through 1165 removed outlier: 3.956A pdb=" N VAL A1165 " --> pdb=" O TYR A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1194 removed outlier: 4.022A pdb=" N ARG A1180 " --> pdb=" O ARG A1176 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A1182 " --> pdb=" O MET A1178 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR A1183 " --> pdb=" O ASP A1179 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLY A1184 " --> pdb=" O ARG A1180 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A1192 " --> pdb=" O SER A1188 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A1194 " --> pdb=" O MET A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1203 removed outlier: 4.127A pdb=" N ALA A1203 " --> pdb=" O ASN A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1212 No H-bonds generated for 'chain 'A' and resid 1210 through 1212' Processing helix chain 'A' and resid 1213 through 1230 removed outlier: 4.113A pdb=" N ALA A1217 " --> pdb=" O GLU A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1254 removed outlier: 3.622A pdb=" N LYS A1235 " --> pdb=" O ASP A1231 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A1237 " --> pdb=" O ALA A1233 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A1252 " --> pdb=" O GLU A1248 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A1254 " --> pdb=" O ALA A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1270 removed outlier: 4.309A pdb=" N ASP A1270 " --> pdb=" O PRO A1267 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 19 removed outlier: 4.092A pdb=" N LEU B 18 " --> pdb=" O SER B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 42 Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.631A pdb=" N ARG B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS B 47 " --> pdb=" O ARG B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 47' Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.748A pdb=" N ALA B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.650A pdb=" N THR B 129 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 removed outlier: 3.772A pdb=" N HIS B 174 " --> pdb=" O HIS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.529A pdb=" N PHE B 215 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLY B 216 " --> pdb=" O HIS B 213 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS B 217 " --> pdb=" O ALA B 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 212 through 217' Processing helix chain 'B' and resid 218 through 223 removed outlier: 3.576A pdb=" N ASN B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 346 removed outlier: 4.318A pdb=" N GLU B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 removed outlier: 4.058A pdb=" N ILE B 369 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 442 removed outlier: 3.648A pdb=" N LEU B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 464 removed outlier: 3.688A pdb=" N SER B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 497 removed outlier: 3.699A pdb=" N ALA B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 501 No H-bonds generated for 'chain 'B' and resid 499 through 501' Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 541 through 556 removed outlier: 3.985A pdb=" N GLY B 546 " --> pdb=" O PRO B 542 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 555 " --> pdb=" O GLN B 551 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.633A pdb=" N LEU B 603 " --> pdb=" O ASP B 600 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 6.973A pdb=" N ILE A 50 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL A 62 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 52 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG A 61 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN A 84 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY A 63 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET A 82 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ILE A 65 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP A 80 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 67 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 160 removed outlier: 4.525A pdb=" N GLY A 258 " --> pdb=" O GLN A 350 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN A 350 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N TYR A 260 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N VAL A 348 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 173 removed outlier: 8.651A pdb=" N VAL A 348 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N TYR A 260 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN A 350 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY A 258 " --> pdb=" O GLN A 350 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 250 through 262 current: chain 'A' and resid 402 through 407 Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 298 removed outlier: 3.526A pdb=" N GLY A 239 " --> pdb=" O HIS A 399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 424 through 427 removed outlier: 3.500A pdb=" N ARG A 952 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A 953 " --> pdb=" O VAL A1136 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR A1138 " --> pdb=" O ARG A 953 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 955 " --> pdb=" O THR A1138 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET A 996 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ALA A1093 " --> pdb=" O MET A 996 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY A 998 " --> pdb=" O ALA A1093 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 431 Processing sheet with id=AA7, first strand: chain 'A' and resid 782 through 783 removed outlier: 6.636A pdb=" N ILE A 688 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 800 " --> pdb=" O TRP A 691 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 643 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ASP A 866 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG A 645 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N TYR A 598 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ALA A 905 " --> pdb=" O TYR A 598 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASP A 600 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR A 907 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU A 602 " --> pdb=" O THR A 907 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 743 through 745 Processing sheet with id=AA9, first strand: chain 'A' and resid 828 through 829 removed outlier: 3.559A pdb=" N LYS A 852 " --> pdb=" O GLU A 823 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 894 removed outlier: 3.524A pdb=" N TRP A 892 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1068 through 1070 Processing sheet with id=AB3, first strand: chain 'A' and resid 1259 through 1261 Processing sheet with id=AB4, first strand: chain 'B' and resid 6 through 12 removed outlier: 6.883A pdb=" N LEU A1302 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU B 11 " --> pdb=" O VAL A1300 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A1300 " --> pdb=" O GLU B 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 49 through 50 removed outlier: 4.611A pdb=" N LEU B 70 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 419 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 10.476A pdb=" N TRP B 418 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N LEU B 388 " --> pdb=" O TRP B 418 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALA B 386 " --> pdb=" O PRO B 420 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN B 422 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 384 " --> pdb=" O ASN B 422 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL B 424 " --> pdb=" O ARG B 382 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG B 382 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY B 426 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG B 380 " --> pdb=" O GLY B 426 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 374 " --> pdb=" O GLN B 432 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N MET B 358 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 256 through 263 removed outlier: 3.960A pdb=" N GLY B 389 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B 260 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU B 387 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA B 262 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASN B 385 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 374 " --> pdb=" O GLN B 432 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG B 380 " --> pdb=" O GLY B 426 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY B 426 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG B 382 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL B 424 " --> pdb=" O ARG B 382 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 384 " --> pdb=" O ASN B 422 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN B 422 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALA B 386 " --> pdb=" O PRO B 420 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N LEU B 388 " --> pdb=" O TRP B 418 " (cutoff:3.500A) removed outlier: 10.476A pdb=" N TRP B 418 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLU B 427 " --> pdb=" O THR B 524 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 524 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 117 through 120 removed outlier: 5.712A pdb=" N PHE B 131 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 150 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 135 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS B 146 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 108 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU B 184 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP B 199 " --> pdb=" O PHE B 187 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AB9, first strand: chain 'B' and resid 229 through 230 494 hydrogen bonds defined for protein. 1356 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: 6.20 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.31: 2357 1.31 - 1.61: 11891 1.61 - 1.91: 119 1.91 - 2.21: 0 2.21 - 2.51: 1 Bond restraints: 14368 Sorted by residual: bond pdb=" CB PRO A 960 " pdb=" CG PRO A 960 " ideal model delta sigma weight residual 1.492 2.510 -1.018 5.00e-02 4.00e+02 4.15e+02 bond pdb=" CG PRO A 960 " pdb=" CD PRO A 960 " ideal model delta sigma weight residual 1.503 1.013 0.490 3.40e-02 8.65e+02 2.08e+02 bond pdb=" N PRO A 960 " pdb=" CD PRO A 960 " ideal model delta sigma weight residual 1.473 1.597 -0.124 1.40e-02 5.10e+03 7.89e+01 bond pdb=" CG PRO B 74 " pdb=" CD PRO B 74 " ideal model delta sigma weight residual 1.503 1.268 0.235 3.40e-02 8.65e+02 4.78e+01 bond pdb=" N PRO A 960 " pdb=" CA PRO A 960 " ideal model delta sigma weight residual 1.467 1.401 0.066 1.21e-02 6.83e+03 2.95e+01 ... (remaining 14363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 19502 21.21 - 42.41: 2 42.41 - 63.62: 0 63.62 - 84.83: 0 84.83 - 106.03: 1 Bond angle restraints: 19505 Sorted by residual: angle pdb=" CB PRO A 960 " pdb=" CG PRO A 960 " pdb=" CD PRO A 960 " ideal model delta sigma weight residual 106.10 0.07 106.03 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO A 960 " pdb=" N PRO A 960 " pdb=" CD PRO A 960 " ideal model delta sigma weight residual 112.00 87.66 24.34 1.40e+00 5.10e-01 3.02e+02 angle pdb=" N PRO A 960 " pdb=" CA PRO A 960 " pdb=" CB PRO A 960 " ideal model delta sigma weight residual 103.31 91.44 11.87 8.90e-01 1.26e+00 1.78e+02 angle pdb=" CA PRO B 74 " pdb=" N PRO B 74 " pdb=" CD PRO B 74 " ideal model delta sigma weight residual 112.00 96.69 15.31 1.40e+00 5.10e-01 1.20e+02 angle pdb=" CA PRO A 960 " pdb=" CB PRO A 960 " pdb=" CG PRO A 960 " ideal model delta sigma weight residual 104.50 88.84 15.66 1.90e+00 2.77e-01 6.79e+01 ... (remaining 19500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.32: 8406 34.32 - 68.64: 258 68.64 - 102.96: 20 102.96 - 137.28: 0 137.28 - 171.60: 1 Dihedral angle restraints: 8685 sinusoidal: 3603 harmonic: 5082 Sorted by residual: dihedral pdb=" CA ASP A 937 " pdb=" C ASP A 937 " pdb=" N ASN A 938 " pdb=" CA ASN A 938 " ideal model delta harmonic sigma weight residual 180.00 152.27 27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" N PRO A 960 " pdb=" CG PRO A 960 " pdb=" CD PRO A 960 " pdb=" CB PRO A 960 " ideal model delta sinusoidal sigma weight residual -30.00 -95.63 65.63 1 1.50e+01 4.44e-03 2.51e+01 dihedral pdb=" N PRO A 960 " pdb=" C PRO A 960 " pdb=" CA PRO A 960 " pdb=" CB PRO A 960 " ideal model delta harmonic sigma weight residual 115.10 103.01 12.09 0 2.50e+00 1.60e-01 2.34e+01 ... (remaining 8682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1854 0.069 - 0.139: 278 0.139 - 0.208: 18 0.208 - 0.277: 0 0.277 - 0.347: 2 Chirality restraints: 2152 Sorted by residual: chirality pdb=" CA PRO B 74 " pdb=" N PRO B 74 " pdb=" C PRO B 74 " pdb=" CB PRO B 74 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CG LEU A 650 " pdb=" CB LEU A 650 " pdb=" CD1 LEU A 650 " pdb=" CD2 LEU A 650 " both_signs ideal model delta sigma weight residual False -2.59 -2.89 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" P DT C 5 " pdb=" OP1 DT C 5 " pdb=" OP2 DT C 5 " pdb=" O5' DT C 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 2149 not shown) Planarity restraints: 2529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 73 " -0.107 5.00e-02 4.00e+02 1.47e-01 3.48e+01 pdb=" N PRO B 74 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO B 74 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 74 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 547 " 0.352 9.50e-02 1.11e+02 1.58e-01 1.53e+01 pdb=" NE ARG B 547 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 547 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 547 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 547 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 959 " -0.066 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO A 960 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 960 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 960 " -0.048 5.00e-02 4.00e+02 ... (remaining 2526 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4130 2.83 - 3.34: 11386 3.34 - 3.86: 20644 3.86 - 4.38: 23071 4.38 - 4.90: 41825 Nonbonded interactions: 101056 Sorted by model distance: nonbonded pdb=" O ILE A 969 " pdb=" OG1 THR A 973 " model vdw 2.308 3.040 nonbonded pdb=" O ASP A1015 " pdb=" OG1 THR A1019 " model vdw 2.311 3.040 nonbonded pdb=" O ASP A 111 " pdb=" OG1 THR A 115 " model vdw 2.324 3.040 nonbonded pdb=" O ASP A1268 " pdb=" OG1 THR A1272 " model vdw 2.325 3.040 nonbonded pdb=" OE1 GLN B 235 " pdb=" NH2 ARG B 413 " model vdw 2.330 3.120 ... (remaining 101051 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: 1.730 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: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.520 Find NCS groups from input model: 0.110 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.011 1.018 14368 Z= 0.946 Angle : 1.155 106.034 19505 Z= 0.545 Chirality : 0.049 0.347 2152 Planarity : 0.008 0.158 2529 Dihedral : 15.908 171.599 5401 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.28 % Favored : 97.66 % Rotamer: Outliers : 0.47 % Allowed : 14.86 % Favored : 84.67 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.18), residues: 1753 helix: -0.44 (0.22), residues: 497 sheet: 0.17 (0.31), residues: 288 loop : -0.94 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 568 HIS 0.021 0.001 HIS B 170 PHE 0.051 0.002 PHE A 620 TYR 0.055 0.002 TYR A 614 ARG 0.008 0.000 ARG A1301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 230 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 232 average time/residue: 0.3007 time to fit residues: 99.2559 Evaluate side-chains 231 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 226 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1057 TYR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 528 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 2.9990 chunk 132 optimal weight: 0.0870 chunk 73 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 0.0370 chunk 137 optimal weight: 6.9990 chunk 53 optimal weight: 0.2980 chunk 83 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 158 optimal weight: 0.1980 overall best weight: 0.1836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN B 170 HIS ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.102 14368 Z= 0.168 Angle : 0.561 10.366 19505 Z= 0.288 Chirality : 0.042 0.156 2152 Planarity : 0.005 0.081 2529 Dihedral : 8.463 168.340 2017 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.67 % Allowed : 13.19 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 1753 helix: 0.58 (0.23), residues: 522 sheet: 0.50 (0.31), residues: 290 loop : -0.78 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 691 HIS 0.007 0.001 HIS B 170 PHE 0.010 0.001 PHE A 331 TYR 0.008 0.001 TYR A 614 ARG 0.003 0.000 ARG A1037 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 1.599 Fit side-chains revert: symmetry clash REVERT: A 391 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7480 (t0) REVERT: A 563 LEU cc_start: 0.8604 (tt) cc_final: 0.8375 (tt) REVERT: A 644 MET cc_start: 0.7701 (ttp) cc_final: 0.7467 (mtp) REVERT: B 471 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6925 (mt-10) outliers start: 25 outliers final: 13 residues processed: 265 average time/residue: 0.2800 time to fit residues: 107.8464 Evaluate side-chains 240 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 575 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.4980 chunk 49 optimal weight: 0.0000 chunk 132 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 157 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN B 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14368 Z= 0.164 Angle : 0.537 8.315 19505 Z= 0.274 Chirality : 0.043 0.145 2152 Planarity : 0.004 0.044 2529 Dihedral : 8.249 170.389 2008 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.48 % Allowed : 13.19 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1753 helix: 0.99 (0.24), residues: 508 sheet: 0.60 (0.31), residues: 293 loop : -0.72 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 281 HIS 0.004 0.001 HIS B 170 PHE 0.013 0.001 PHE A1154 TYR 0.012 0.001 TYR A 614 ARG 0.002 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 1.527 Fit side-chains REVERT: A 65 ILE cc_start: 0.8688 (mt) cc_final: 0.8429 (mm) REVERT: A 391 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7628 (t0) REVERT: A 563 LEU cc_start: 0.8654 (tt) cc_final: 0.8395 (tt) REVERT: A 644 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7626 (mtp) REVERT: A 656 PHE cc_start: 0.7759 (t80) cc_final: 0.7508 (t80) REVERT: A 980 GLN cc_start: 0.8155 (tp40) cc_final: 0.7856 (tp-100) REVERT: A 1211 GLN cc_start: 0.8061 (mt0) cc_final: 0.7717 (mt0) REVERT: B 547 ARG cc_start: 0.6936 (tpp-160) cc_final: 0.6600 (tpp-160) outliers start: 37 outliers final: 25 residues processed: 251 average time/residue: 0.2774 time to fit residues: 102.1295 Evaluate side-chains 252 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1292 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 575 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 0.0030 chunk 106 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 169 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14368 Z= 0.198 Angle : 0.549 9.161 19505 Z= 0.279 Chirality : 0.043 0.143 2152 Planarity : 0.004 0.045 2529 Dihedral : 8.233 169.925 2008 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.74 % Allowed : 13.86 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1753 helix: 1.05 (0.24), residues: 520 sheet: 0.56 (0.31), residues: 293 loop : -0.71 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 281 HIS 0.004 0.001 HIS A 41 PHE 0.015 0.001 PHE A1154 TYR 0.015 0.001 TYR A 614 ARG 0.006 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 243 time to evaluate : 1.652 Fit side-chains REVERT: A 65 ILE cc_start: 0.8748 (mt) cc_final: 0.8524 (mm) REVERT: A 391 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7634 (t0) REVERT: A 563 LEU cc_start: 0.8664 (tt) cc_final: 0.8392 (tt) REVERT: A 644 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7674 (mtp) REVERT: A 980 GLN cc_start: 0.8208 (tp40) cc_final: 0.7887 (tp-100) REVERT: A 1211 GLN cc_start: 0.8113 (mt0) cc_final: 0.7798 (mt0) REVERT: B 26 LEU cc_start: 0.9035 (tp) cc_final: 0.8618 (tp) REVERT: B 547 ARG cc_start: 0.6998 (tpp-160) cc_final: 0.6570 (tpp-160) REVERT: B 561 SER cc_start: 0.7513 (p) cc_final: 0.7102 (p) outliers start: 41 outliers final: 30 residues processed: 263 average time/residue: 0.2738 time to fit residues: 104.8777 Evaluate side-chains 266 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 575 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 7.9990 chunk 96 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 0.0670 chunk 69 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.0050 chunk 151 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 overall best weight: 0.3332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14368 Z= 0.136 Angle : 0.513 6.546 19505 Z= 0.260 Chirality : 0.042 0.138 2152 Planarity : 0.004 0.043 2529 Dihedral : 8.133 171.899 2008 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.21 % Allowed : 15.06 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1753 helix: 1.29 (0.24), residues: 519 sheet: 0.70 (0.31), residues: 287 loop : -0.66 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 603 HIS 0.002 0.001 HIS B 232 PHE 0.009 0.001 PHE A 571 TYR 0.010 0.001 TYR A 614 ARG 0.006 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 1.533 Fit side-chains REVERT: A 42 GLN cc_start: 0.7585 (tp-100) cc_final: 0.7354 (mm-40) REVERT: A 65 ILE cc_start: 0.8702 (mt) cc_final: 0.8499 (mm) REVERT: A 391 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7619 (t0) REVERT: A 563 LEU cc_start: 0.8667 (tt) cc_final: 0.8353 (tt) REVERT: A 644 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7609 (mtt) REVERT: A 1211 GLN cc_start: 0.8143 (mt0) cc_final: 0.7868 (mt0) REVERT: B 26 LEU cc_start: 0.9053 (tp) cc_final: 0.8789 (tp) REVERT: B 547 ARG cc_start: 0.7004 (tpp-160) cc_final: 0.6514 (tpp-160) outliers start: 33 outliers final: 26 residues processed: 257 average time/residue: 0.2696 time to fit residues: 100.9772 Evaluate side-chains 255 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 572 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14368 Z= 0.223 Angle : 0.549 7.675 19505 Z= 0.281 Chirality : 0.043 0.141 2152 Planarity : 0.004 0.045 2529 Dihedral : 8.189 170.678 2008 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.15 % Allowed : 14.73 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1753 helix: 1.25 (0.24), residues: 520 sheet: 0.57 (0.31), residues: 295 loop : -0.68 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 281 HIS 0.004 0.001 HIS B 232 PHE 0.015 0.001 PHE A 529 TYR 0.036 0.001 TYR A 614 ARG 0.006 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 1.641 Fit side-chains revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8798 (mt) cc_final: 0.8546 (mm) REVERT: A 391 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7632 (t0) REVERT: A 446 MET cc_start: 0.8608 (ttm) cc_final: 0.8155 (ttp) REVERT: A 563 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8428 (tt) REVERT: A 644 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7621 (mtp) REVERT: A 826 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7754 (ttm-80) REVERT: A 1211 GLN cc_start: 0.8084 (mt0) cc_final: 0.7827 (mt0) REVERT: A 1244 GLU cc_start: 0.8718 (tp30) cc_final: 0.8508 (tp30) REVERT: B 547 ARG cc_start: 0.7063 (tpp-160) cc_final: 0.6830 (tpp-160) REVERT: B 561 SER cc_start: 0.7470 (p) cc_final: 0.7057 (p) outliers start: 47 outliers final: 33 residues processed: 264 average time/residue: 0.2822 time to fit residues: 108.3295 Evaluate side-chains 265 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1161 PHE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 572 LYS Chi-restraints excluded: chain B residue 575 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.0470 chunk 96 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 142 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 168 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14368 Z= 0.171 Angle : 0.538 8.918 19505 Z= 0.272 Chirality : 0.043 0.159 2152 Planarity : 0.004 0.045 2529 Dihedral : 8.145 171.326 2008 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.54 % Allowed : 15.53 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1753 helix: 1.34 (0.24), residues: 518 sheet: 0.60 (0.32), residues: 276 loop : -0.62 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 603 HIS 0.005 0.001 HIS B 133 PHE 0.012 0.001 PHE A 529 TYR 0.030 0.001 TYR A 614 ARG 0.006 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8790 (mt) cc_final: 0.8556 (mm) REVERT: A 391 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7671 (t0) REVERT: A 446 MET cc_start: 0.8575 (ttm) cc_final: 0.8167 (ttp) REVERT: A 563 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8392 (tt) REVERT: A 564 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8627 (ptpt) REVERT: A 826 ARG cc_start: 0.8049 (ttm170) cc_final: 0.7694 (ttm-80) REVERT: A 1001 ASN cc_start: 0.8201 (t0) cc_final: 0.7723 (t0) REVERT: B 547 ARG cc_start: 0.7047 (tpp-160) cc_final: 0.6792 (tpp-160) REVERT: B 561 SER cc_start: 0.7419 (p) cc_final: 0.6989 (p) outliers start: 38 outliers final: 30 residues processed: 252 average time/residue: 0.3095 time to fit residues: 112.7654 Evaluate side-chains 260 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1161 PHE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 572 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN A1211 GLN B 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14368 Z= 0.203 Angle : 0.550 8.143 19505 Z= 0.280 Chirality : 0.043 0.147 2152 Planarity : 0.004 0.046 2529 Dihedral : 8.171 170.750 2008 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.61 % Allowed : 15.33 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1753 helix: 1.32 (0.24), residues: 517 sheet: 0.47 (0.32), residues: 285 loop : -0.61 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 603 HIS 0.006 0.001 HIS B 232 PHE 0.014 0.001 PHE A 529 TYR 0.028 0.001 TYR A 614 ARG 0.007 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 1.637 Fit side-chains revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8848 (mt) cc_final: 0.8627 (mm) REVERT: A 391 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7623 (t0) REVERT: A 446 MET cc_start: 0.8575 (ttm) cc_final: 0.8200 (ttp) REVERT: A 563 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8453 (tt) REVERT: A 564 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8638 (ptpt) REVERT: A 654 GLN cc_start: 0.7818 (mp10) cc_final: 0.7598 (mp10) REVERT: A 826 ARG cc_start: 0.8072 (ttm170) cc_final: 0.7729 (ttm-80) REVERT: A 1001 ASN cc_start: 0.8207 (t0) cc_final: 0.7762 (t0) REVERT: B 547 ARG cc_start: 0.6997 (tpp-160) cc_final: 0.6721 (tpp-160) REVERT: B 561 SER cc_start: 0.7433 (p) cc_final: 0.7020 (p) outliers start: 39 outliers final: 33 residues processed: 257 average time/residue: 0.2959 time to fit residues: 110.2321 Evaluate side-chains 269 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1161 PHE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 572 LYS Chi-restraints excluded: chain B residue 575 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.8980 chunk 147 optimal weight: 0.0040 chunk 157 optimal weight: 0.0030 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 142 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14368 Z= 0.147 Angle : 0.528 9.981 19505 Z= 0.267 Chirality : 0.042 0.139 2152 Planarity : 0.004 0.043 2529 Dihedral : 8.065 173.197 2008 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.14 % Allowed : 16.00 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1753 helix: 1.44 (0.24), residues: 517 sheet: 0.60 (0.31), residues: 298 loop : -0.61 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 603 HIS 0.006 0.001 HIS B 232 PHE 0.010 0.001 PHE A 571 TYR 0.028 0.001 TYR A 614 ARG 0.007 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8778 (mt) cc_final: 0.8560 (mm) REVERT: A 176 ARG cc_start: 0.7172 (mtp-110) cc_final: 0.6871 (mpp80) REVERT: A 446 MET cc_start: 0.8557 (ttm) cc_final: 0.8212 (ttp) REVERT: A 563 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8372 (tt) REVERT: A 564 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8631 (ptpt) REVERT: A 593 LYS cc_start: 0.7661 (pttt) cc_final: 0.7405 (pttp) REVERT: A 826 ARG cc_start: 0.8052 (ttm170) cc_final: 0.7726 (ttm-80) REVERT: A 1001 ASN cc_start: 0.8194 (t0) cc_final: 0.7762 (t0) REVERT: B 18 LEU cc_start: 0.8736 (mt) cc_final: 0.8410 (mt) REVERT: B 561 SER cc_start: 0.7335 (p) cc_final: 0.6917 (p) outliers start: 32 outliers final: 25 residues processed: 255 average time/residue: 0.2885 time to fit residues: 106.3233 Evaluate side-chains 261 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 575 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 174 optimal weight: 0.0270 chunk 160 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14368 Z= 0.184 Angle : 0.547 9.615 19505 Z= 0.277 Chirality : 0.043 0.164 2152 Planarity : 0.004 0.044 2529 Dihedral : 8.088 171.945 2008 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.07 % Allowed : 16.06 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1753 helix: 1.41 (0.24), residues: 517 sheet: 0.48 (0.31), residues: 303 loop : -0.58 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 603 HIS 0.006 0.001 HIS B 232 PHE 0.016 0.001 PHE A 620 TYR 0.023 0.001 TYR A 614 ARG 0.007 0.000 ARG A1144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 1.734 Fit side-chains revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8830 (mt) cc_final: 0.8579 (mm) REVERT: A 176 ARG cc_start: 0.7174 (mtp-110) cc_final: 0.6899 (mpp80) REVERT: A 446 MET cc_start: 0.8564 (ttm) cc_final: 0.8251 (ttp) REVERT: A 563 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8399 (tt) REVERT: A 564 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8639 (ptpt) REVERT: A 826 ARG cc_start: 0.8046 (ttm170) cc_final: 0.7716 (ttm-80) REVERT: A 1001 ASN cc_start: 0.8241 (t0) cc_final: 0.7785 (t0) REVERT: B 547 ARG cc_start: 0.6842 (tpp-160) cc_final: 0.6549 (tpp-160) REVERT: B 561 SER cc_start: 0.7768 (p) cc_final: 0.7340 (p) outliers start: 31 outliers final: 26 residues processed: 255 average time/residue: 0.3000 time to fit residues: 110.3799 Evaluate side-chains 258 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 575 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 139 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 17 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN B 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.177981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.141480 restraints weight = 15605.692| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.39 r_work: 0.3352 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14368 Z= 0.141 Angle : 0.532 9.161 19505 Z= 0.267 Chirality : 0.042 0.192 2152 Planarity : 0.004 0.044 2529 Dihedral : 8.001 173.268 2008 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.94 % Allowed : 16.00 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1753 helix: 1.50 (0.24), residues: 517 sheet: 0.59 (0.30), residues: 315 loop : -0.55 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 603 HIS 0.007 0.001 HIS B 232 PHE 0.015 0.001 PHE A 620 TYR 0.021 0.001 TYR A 614 ARG 0.009 0.000 ARG A 810 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3108.99 seconds wall clock time: 57 minutes 59.02 seconds (3479.02 seconds total)