Starting phenix.real_space_refine on Sat Sep 12 06:18:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s9w_24939/09_2026/7s9w_24939.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s9w_24939/09_2026/7s9w_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 { model { file = "/net/cci-nas-00/data/ceres_data/7s9w_24939/09_2026/7s9w_24939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s9w_24939/09_2026/7s9w_24939.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7s9w_24939/09_2026/7s9w_24939.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s9w_24939/09_2026/7s9w_24939.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s9w_24939/09_2026/7s9w_24939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s9w_24939/09_2026/7s9w_24939.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 3.09, per 1000 atoms: 0.22 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: 0.88 Conformation dependent library (CDL) restraints added in 627.3 milliseconds 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: 0.51 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: 2.62 Time building geometry restraints manager: 1.31 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 2.34 -2.54 -0.20 2.00e-01 2.50e+01 9.99e-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: 3.660 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.480 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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= 0.326 Angle : 1.160 106.034 19505 Z= 0.565 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 : 2.82 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.000 ARG A1301 TYR 0.055 0.002 TYR A 614 PHE 0.051 0.002 PHE A 620 TRP 0.016 0.002 TRP A 568 HIS 0.021 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.01076 / 0.33 (14368) covalent geometry : angle 1.15993 / 0.56 (19505) hydrogen bonds : bond 0.23382 / 15.49 ( 483) hydrogen bonds : angle 7.20632 / 5.17 ( 1356) *********************** 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 : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1031 ARG cc_start: 0.7975 (mmm-85) cc_final: 0.7674 (mmm-85) outliers start: 7 outliers final: 5 residues processed: 232 average time/residue: 0.1308 time to fit residues: 43.5458 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 : 0.522 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0060 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 ASN B 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.175760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139711 restraints weight = 15791.706| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.42 r_work: 0.3317 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 14368 Z= 0.130 Angle : 0.586 10.378 19505 Z= 0.303 Chirality : 0.044 0.273 2152 Planarity : 0.005 0.081 2529 Dihedral : 8.578 165.680 2017 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.81 % Allowed : 13.52 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.19), residues: 1753 helix: 0.59 (0.24), residues: 514 sheet: 0.36 (0.31), residues: 296 loop : -0.81 (0.18), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1037 TYR 0.010 0.001 TYR B 171 PHE 0.013 0.001 PHE A1154 TRP 0.012 0.001 TRP A 281 HIS 0.006 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (14368) covalent geometry : angle 0.58603 / 0.30 (19505) hydrogen bonds : bond 0.05611 / 3.66 ( 483) hydrogen bonds : angle 5.07105 / 3.66 ( 1356) *********************** 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 276 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 391 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7738 (t0) REVERT: A 563 LEU cc_start: 0.8659 (tt) cc_final: 0.8436 (tt) REVERT: A 644 MET cc_start: 0.7346 (ttp) cc_final: 0.7135 (mtp) REVERT: A 888 GLU cc_start: 0.7752 (tp30) cc_final: 0.7518 (tp30) REVERT: B 471 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6791 (mt-10) outliers start: 27 outliers final: 19 residues processed: 261 average time/residue: 0.1236 time to fit residues: 47.0796 Evaluate side-chains 246 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 802 ASP 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 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 119 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 0.0010 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 ASN B 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.174626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138605 restraints weight = 15904.517| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.40 r_work: 0.3299 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14368 Z= 0.137 Angle : 0.566 8.401 19505 Z= 0.292 Chirality : 0.044 0.243 2152 Planarity : 0.004 0.048 2529 Dihedral : 8.395 170.323 2010 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.74 % Allowed : 13.99 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.19), residues: 1753 helix: 0.90 (0.24), residues: 509 sheet: 0.47 (0.31), residues: 293 loop : -0.82 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1031 TYR 0.013 0.001 TYR A 614 PHE 0.016 0.001 PHE A1154 TRP 0.014 0.001 TRP A 281 HIS 0.004 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (14368) covalent geometry : angle 0.56599 / 0.29 (19505) hydrogen bonds : bond 0.05331 / 3.47 ( 483) hydrogen bonds : angle 4.80010 / 3.47 ( 1356) *********************** 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 277 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 0.542 Fit side-chains REVERT: A 391 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7818 (t0) REVERT: A 563 LEU cc_start: 0.8701 (tt) cc_final: 0.8450 (tt) REVERT: A 1211 GLN cc_start: 0.8211 (mt0) cc_final: 0.7894 (mt0) REVERT: B 471 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7076 (mt-10) REVERT: B 547 ARG cc_start: 0.7304 (tpp-160) cc_final: 0.6975 (tpp-160) REVERT: B 561 SER cc_start: 0.7705 (p) cc_final: 0.7316 (p) outliers start: 41 outliers final: 27 residues processed: 259 average time/residue: 0.1214 time to fit residues: 46.4294 Evaluate side-chains 260 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 430 THR 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 774 THR Chi-restraints excluded: chain A residue 857 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 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 64 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 98 optimal weight: 0.0070 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 69 ASN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.174554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139310 restraints weight = 15803.004| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.39 r_work: 0.3317 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14368 Z= 0.130 Angle : 0.551 7.427 19505 Z= 0.282 Chirality : 0.043 0.234 2152 Planarity : 0.004 0.043 2529 Dihedral : 8.339 171.202 2010 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.88 % Allowed : 15.13 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1753 helix: 1.04 (0.24), residues: 518 sheet: 0.49 (0.31), residues: 293 loop : -0.79 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1144 TYR 0.011 0.001 TYR A 614 PHE 0.014 0.001 PHE A1154 TRP 0.011 0.001 TRP A 281 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (14368) covalent geometry : angle 0.55144 / 0.28 (19505) hydrogen bonds : bond 0.04880 / 3.18 ( 483) hydrogen bonds : angle 4.65754 / 3.36 ( 1356) *********************** 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 289 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 246 time to evaluate : 0.500 Fit side-chains REVERT: A 391 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7857 (t0) REVERT: A 563 LEU cc_start: 0.8677 (tt) cc_final: 0.8406 (tt) REVERT: A 1211 GLN cc_start: 0.8227 (mt0) cc_final: 0.7934 (mt0) REVERT: B 26 LEU cc_start: 0.9129 (tp) cc_final: 0.8750 (tp) REVERT: B 547 ARG cc_start: 0.7299 (tpp-160) cc_final: 0.6867 (tpp-160) REVERT: B 561 SER cc_start: 0.7622 (p) cc_final: 0.7215 (p) outliers start: 43 outliers final: 31 residues processed: 271 average time/residue: 0.1268 time to fit residues: 50.7186 Evaluate side-chains 264 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU 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 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 774 THR Chi-restraints excluded: chain A residue 857 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 1161 PHE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain B residue 7 THR 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 119 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 15 optimal weight: 0.0270 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 483 GLN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.174687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139586 restraints weight = 15845.445| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.41 r_work: 0.3312 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14368 Z= 0.123 Angle : 0.541 7.664 19505 Z= 0.277 Chirality : 0.043 0.229 2152 Planarity : 0.004 0.044 2529 Dihedral : 8.273 173.079 2008 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.08 % Allowed : 14.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.20), residues: 1753 helix: 1.10 (0.24), residues: 517 sheet: 0.57 (0.31), residues: 290 loop : -0.78 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1144 TYR 0.009 0.001 TYR B 171 PHE 0.013 0.001 PHE A 529 TRP 0.012 0.001 TRP A 603 HIS 0.002 0.001 HIS B 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (14368) covalent geometry : angle 0.54070 / 0.28 (19505) hydrogen bonds : bond 0.04657 / 3.03 ( 483) hydrogen bonds : angle 4.56444 / 3.30 ( 1356) *********************** 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 288 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 0.551 Fit side-chains REVERT: A 391 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7849 (t0) REVERT: A 563 LEU cc_start: 0.8669 (tt) cc_final: 0.8374 (tt) REVERT: A 593 LYS cc_start: 0.7751 (pttt) cc_final: 0.7524 (pttp) REVERT: A 996 MET cc_start: 0.8486 (ttt) cc_final: 0.8185 (tmm) REVERT: A 1211 GLN cc_start: 0.8187 (mt0) cc_final: 0.7928 (mt0) REVERT: A 1244 GLU cc_start: 0.8801 (tp30) cc_final: 0.8518 (tp30) REVERT: B 547 ARG cc_start: 0.7388 (tpp-160) cc_final: 0.6950 (tpp-160) REVERT: B 561 SER cc_start: 0.7579 (p) cc_final: 0.7170 (p) outliers start: 46 outliers final: 33 residues processed: 269 average time/residue: 0.1151 time to fit residues: 45.8532 Evaluate side-chains 265 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 397 VAL 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 603 TRP Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 857 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 1091 VAL Chi-restraints excluded: chain A residue 1094 THR 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 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 575 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 110 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 0.0370 chunk 62 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 483 GLN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.173816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.138498 restraints weight = 15841.538| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.40 r_work: 0.3300 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14368 Z= 0.138 Angle : 0.561 9.847 19505 Z= 0.285 Chirality : 0.043 0.220 2152 Planarity : 0.004 0.045 2529 Dihedral : 8.283 173.529 2008 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.35 % Allowed : 15.39 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.20), residues: 1753 helix: 1.10 (0.24), residues: 517 sheet: 0.45 (0.31), residues: 286 loop : -0.76 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1144 TYR 0.010 0.001 TYR B 171 PHE 0.014 0.001 PHE A 529 TRP 0.012 0.001 TRP A 603 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (14368) covalent geometry : angle 0.56125 / 0.29 (19505) hydrogen bonds : bond 0.04892 / 3.18 ( 483) hydrogen bonds : angle 4.56780 / 3.30 ( 1356) *********************** 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 290 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 0.523 Fit side-chains REVERT: A 391 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7872 (t0) REVERT: A 563 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8419 (tt) REVERT: A 996 MET cc_start: 0.8511 (ttt) cc_final: 0.8247 (tmm) REVERT: B 547 ARG cc_start: 0.7404 (tpp-160) cc_final: 0.7176 (tpp-160) REVERT: B 561 SER cc_start: 0.7587 (p) cc_final: 0.7177 (p) outliers start: 50 outliers final: 36 residues processed: 270 average time/residue: 0.1222 time to fit residues: 48.3104 Evaluate side-chains 273 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 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 774 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 857 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 1015 ASP 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 575 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 483 GLN B 69 ASN B 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.171004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.136447 restraints weight = 15930.938| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.51 r_work: 0.3272 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14368 Z= 0.184 Angle : 0.599 8.284 19505 Z= 0.309 Chirality : 0.045 0.227 2152 Planarity : 0.004 0.046 2529 Dihedral : 8.400 171.489 2008 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.41 % Allowed : 16.20 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.20), residues: 1753 helix: 0.89 (0.23), residues: 517 sheet: 0.43 (0.32), residues: 289 loop : -0.88 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1144 TYR 0.015 0.001 TYR A 614 PHE 0.015 0.002 PHE A 529 TRP 0.015 0.002 TRP A 603 HIS 0.008 0.001 HIS B 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (14368) covalent geometry : angle 0.59935 / 0.31 (19505) hydrogen bonds : bond 0.05725 / 3.73 ( 483) hydrogen bonds : angle 4.69775 / 3.39 ( 1356) *********************** 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 286 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 0.521 Fit side-chains REVERT: A 1244 GLU cc_start: 0.8869 (tp30) cc_final: 0.8632 (tp30) REVERT: B 166 ASP cc_start: 0.8424 (m-30) cc_final: 0.7744 (m-30) REVERT: B 547 ARG cc_start: 0.7442 (tpp-160) cc_final: 0.7184 (tpp-160) REVERT: B 561 SER cc_start: 0.7725 (p) cc_final: 0.7322 (p) outliers start: 51 outliers final: 37 residues processed: 268 average time/residue: 0.1198 time to fit residues: 46.7352 Evaluate side-chains 268 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 412 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 538 THR 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 774 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 857 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 1015 ASP 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 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 505 GLU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 575 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 3 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 483 GLN A 980 GLN B 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.172240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.137155 restraints weight = 15865.371| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.43 r_work: 0.3278 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14368 Z= 0.153 Angle : 0.579 8.102 19505 Z= 0.296 Chirality : 0.044 0.226 2152 Planarity : 0.004 0.047 2529 Dihedral : 8.346 171.782 2008 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.95 % Allowed : 16.87 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 1753 helix: 0.99 (0.24), residues: 515 sheet: 0.41 (0.33), residues: 269 loop : -0.87 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1144 TYR 0.011 0.001 TYR A 614 PHE 0.015 0.001 PHE A 529 TRP 0.014 0.001 TRP A 603 HIS 0.007 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (14368) covalent geometry : angle 0.57931 / 0.30 (19505) hydrogen bonds : bond 0.05175 / 3.36 ( 483) hydrogen bonds : angle 4.62765 / 3.34 ( 1356) *********************** 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 288 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 446 MET cc_start: 0.8611 (ttm) cc_final: 0.8297 (ttp) REVERT: A 563 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8401 (tt) REVERT: A 564 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8578 (ptpt) REVERT: B 166 ASP cc_start: 0.8369 (m-30) cc_final: 0.7660 (m-30) REVERT: B 547 ARG cc_start: 0.7415 (tpp-160) cc_final: 0.7147 (tpp-160) REVERT: B 561 SER cc_start: 0.7591 (p) cc_final: 0.7195 (p) outliers start: 44 outliers final: 37 residues processed: 272 average time/residue: 0.1261 time to fit residues: 49.9482 Evaluate side-chains 275 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 412 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 538 THR 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 681 LEU 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 857 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 1015 ASP 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 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 491 GLU Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 520 ILE 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 93 optimal weight: 0.2980 chunk 89 optimal weight: 0.4980 chunk 142 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 136 optimal weight: 0.4980 chunk 150 optimal weight: 0.0670 chunk 56 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 483 GLN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.174272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139313 restraints weight = 15975.910| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.45 r_work: 0.3307 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14368 Z= 0.107 Angle : 0.544 7.021 19505 Z= 0.278 Chirality : 0.043 0.224 2152 Planarity : 0.004 0.044 2529 Dihedral : 8.234 174.982 2008 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.48 % Allowed : 17.60 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.20), residues: 1753 helix: 1.25 (0.24), residues: 515 sheet: 0.47 (0.32), residues: 274 loop : -0.80 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1144 TYR 0.007 0.001 TYR A 614 PHE 0.016 0.001 PHE A 620 TRP 0.012 0.001 TRP A 603 HIS 0.008 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (14368) covalent geometry : angle 0.54411 / 0.28 (19505) hydrogen bonds : bond 0.04258 / 2.76 ( 483) hydrogen bonds : angle 4.47175 / 3.25 ( 1356) *********************** 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 281 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8818 (mt) cc_final: 0.8564 (mm) REVERT: A 446 MET cc_start: 0.8555 (ttm) cc_final: 0.8262 (ttp) REVERT: A 563 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8369 (tt) REVERT: A 564 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8556 (ptpt) REVERT: A 802 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7405 (m-30) REVERT: A 1292 SER cc_start: 0.8472 (p) cc_final: 0.8254 (t) REVERT: B 547 ARG cc_start: 0.7447 (tpp-160) cc_final: 0.7157 (tpp-160) REVERT: B 561 SER cc_start: 0.7540 (p) cc_final: 0.7142 (p) outliers start: 37 outliers final: 29 residues processed: 267 average time/residue: 0.1261 time to fit residues: 48.9522 Evaluate side-chains 270 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 412 THR Chi-restraints excluded: chain A residue 466 VAL 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 774 THR Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 857 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 7 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 149 optimal weight: 0.0570 chunk 119 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 483 GLN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.174189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139248 restraints weight = 15905.492| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.44 r_work: 0.3305 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14368 Z= 0.116 Angle : 0.560 9.945 19505 Z= 0.283 Chirality : 0.043 0.219 2152 Planarity : 0.004 0.044 2529 Dihedral : 8.207 175.993 2008 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.21 % Allowed : 17.87 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.20), residues: 1753 helix: 1.32 (0.24), residues: 515 sheet: 0.47 (0.32), residues: 279 loop : -0.74 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1144 TYR 0.031 0.001 TYR A 614 PHE 0.025 0.001 PHE A 620 TRP 0.012 0.001 TRP A 603 HIS 0.007 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (14368) covalent geometry : angle 0.55959 / 0.28 (19505) hydrogen bonds : bond 0.04345 / 2.82 ( 483) hydrogen bonds : angle 4.46426 / 3.26 ( 1356) ********************** 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 273 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7251 (mtp-110) cc_final: 0.6942 (mtp-110) REVERT: A 446 MET cc_start: 0.8588 (ttm) cc_final: 0.8336 (ttp) REVERT: A 563 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8352 (tt) REVERT: A 564 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8557 (ptpt) REVERT: A 1001 ASN cc_start: 0.8273 (t0) cc_final: 0.7831 (t0) REVERT: A 1292 SER cc_start: 0.8488 (p) cc_final: 0.8257 (t) REVERT: B 547 ARG cc_start: 0.7482 (tpp-160) cc_final: 0.7192 (tpp-160) REVERT: B 561 SER cc_start: 0.7513 (p) cc_final: 0.7100 (p) outliers start: 33 outliers final: 29 residues processed: 260 average time/residue: 0.1277 time to fit residues: 47.9289 Evaluate side-chains 268 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 412 THR Chi-restraints excluded: chain A residue 466 VAL 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 774 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 857 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 146 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 483 GLN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.170283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135818 restraints weight = 15933.550| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.47 r_work: 0.3270 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14368 Z= 0.204 Angle : 0.633 8.997 19505 Z= 0.325 Chirality : 0.046 0.224 2152 Planarity : 0.005 0.048 2529 Dihedral : 8.386 171.845 2008 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.41 % Allowed : 17.67 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.20), residues: 1753 helix: 0.85 (0.23), residues: 522 sheet: 0.29 (0.32), residues: 292 loop : -0.89 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1144 TYR 0.030 0.002 TYR A 614 PHE 0.027 0.002 PHE A 620 TRP 0.016 0.002 TRP A 603 HIS 0.007 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (14368) covalent geometry : angle 0.63308 / 0.33 (19505) hydrogen bonds : bond 0.05916 / 3.85 ( 483) hydrogen bonds : angle 4.75179 / 3.46 ( 1356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3167.98 seconds wall clock time: 55 minutes 7.01 seconds (3307.01 seconds total)