Starting phenix.real_space_refine on Sat May 17 11:15:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ezy_50091/05_2025/9ezy_50091.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ezy_50091/05_2025/9ezy_50091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ezy_50091/05_2025/9ezy_50091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ezy_50091/05_2025/9ezy_50091.map" model { file = "/net/cci-nas-00/data/ceres_data/9ezy_50091/05_2025/9ezy_50091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ezy_50091/05_2025/9ezy_50091.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 52 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 9750 2.51 5 N 2662 2.21 5 O 3046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15547 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9130 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 34, 'TRANS': 1094} Chain breaks: 7 Chain: "B" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5356 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 33, 'TRANS': 623} Chain breaks: 2 Chain: "C" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 286 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "E" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 382 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.74, per 1000 atoms: 0.76 Number of scatterers: 15547 At special positions: 0 Unit cell: (132.6, 153.4, 117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 52 15.00 Mg 1 11.99 O 3046 8.00 N 2662 7.00 C 9750 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: 4.54 Conformation dependent library (CDL) restraints added in 1.9 seconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 19 sheets defined 52.9% alpha, 15.8% beta 18 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 5.66 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 20 through 38 Proline residue: A 29 - end of helix Processing helix chain 'A' and resid 54 through 77 Processing helix chain 'A' and resid 94 through 112 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.629A pdb=" N CYS A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 158 through 161 removed outlier: 3.829A pdb=" N ALA A 161 " --> pdb=" O ASN A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 158 through 161' Processing helix chain 'A' and resid 162 through 177 removed outlier: 3.583A pdb=" N ARG A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 209 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.661A pdb=" N LYS A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 259 through 264 removed outlier: 3.935A pdb=" N LEU A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.621A pdb=" N VAL A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 307 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.560A pdb=" N PHE A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 402 through 432 Processing helix chain 'A' and resid 445 through 460 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 475 removed outlier: 4.060A pdb=" N THR A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.644A pdb=" N HIS A 496 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 604 through 615 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 636 through 657 Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 694 removed outlier: 3.520A pdb=" N PHE A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.646A pdb=" N SER A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 removed outlier: 3.782A pdb=" N GLY A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 807 Processing helix chain 'A' and resid 811 through 824 Processing helix chain 'A' and resid 827 through 837 removed outlier: 3.707A pdb=" N GLN A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 856 removed outlier: 4.047A pdb=" N GLN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 880 removed outlier: 4.463A pdb=" N GLU A 876 " --> pdb=" O SER A 872 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 877 " --> pdb=" O GLY A 873 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 removed outlier: 4.355A pdb=" N LEU A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 900 Processing helix chain 'A' and resid 910 through 938 Processing helix chain 'A' and resid 942 through 960 removed outlier: 4.001A pdb=" N GLN A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 992 through 996 removed outlier: 3.668A pdb=" N PHE A 996 " --> pdb=" O PRO A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1002 No H-bonds generated for 'chain 'A' and resid 1000 through 1002' Processing helix chain 'A' and resid 1014 through 1019 Processing helix chain 'A' and resid 1023 through 1032 removed outlier: 3.539A pdb=" N TRP A1027 " --> pdb=" O TYR A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1052 Processing helix chain 'A' and resid 1052 through 1068 Processing helix chain 'A' and resid 1077 through 1081 Processing helix chain 'A' and resid 1102 through 1106 removed outlier: 4.395A pdb=" N LYS A1105 " --> pdb=" O LYS A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1127 removed outlier: 3.747A pdb=" N GLU A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1190 removed outlier: 3.815A pdb=" N SER A1190 " --> pdb=" O TRP A1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 31 Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.769A pdb=" N VAL B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N THR B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER B 56 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY B 62 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 105 through 121 Proline residue: B 118 - end of helix Processing helix chain 'B' and resid 165 through 168 removed outlier: 3.997A pdb=" N GLY B 168 " --> pdb=" O ALA B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 249 through 266 removed outlier: 3.543A pdb=" N LYS B 262 " --> pdb=" O MET B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 301 Processing helix chain 'B' and resid 315 through 329 removed outlier: 4.155A pdb=" N ALA B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 357 through 360 Processing helix chain 'B' and resid 361 through 370 Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 391 through 411 removed outlier: 3.905A pdb=" N VAL B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 462 through 474 removed outlier: 3.642A pdb=" N GLY B 474 " --> pdb=" O GLU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 511 through 527 Processing helix chain 'B' and resid 531 through 542 removed outlier: 3.740A pdb=" N LEU B 535 " --> pdb=" O PRO B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 557 removed outlier: 3.868A pdb=" N ALA B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 removed outlier: 4.352A pdb=" N THR B 571 " --> pdb=" O GLU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 589 Processing helix chain 'B' and resid 605 through 609 Processing helix chain 'B' and resid 650 through 655 removed outlier: 4.078A pdb=" N ASN B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 650 through 655' Processing helix chain 'B' and resid 670 through 683 Processing helix chain 'B' and resid 684 through 687 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 47 removed outlier: 6.226A pdb=" N TYR A 89 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP A 272 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 91 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 88 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU A 242 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR A 90 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 133 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N THR A 243 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 removed outlier: 3.533A pdb=" N GLU A 117 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 343 removed outlier: 6.173A pdb=" N ALA A 341 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE A 385 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A 343 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N SER A 387 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 595 through 601 removed outlier: 6.461A pdb=" N VAL A 595 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU A 868 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR A 597 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL A 870 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS A 599 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE A 774 " --> pdb=" O PHE A 869 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASP A 871 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU A 776 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS A 698 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE A 730 " --> pdb=" O LYS A 698 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE A 700 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N THR A 732 " --> pdb=" O PHE A 700 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 744 through 745 Processing sheet with id=AA8, first strand: chain 'A' and resid 755 through 757 Processing sheet with id=AA9, first strand: chain 'A' and resid 962 through 963 removed outlier: 3.506A pdb=" N ASN A1042 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 997 through 998 Processing sheet with id=AB2, first strand: chain 'A' and resid 1072 through 1074 removed outlier: 3.778A pdb=" N ASN A1086 " --> pdb=" O LEU A1099 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE A1097 " --> pdb=" O VAL A1088 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE A1131 " --> pdb=" O ILE A1162 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE A1164 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR A1133 " --> pdb=" O ILE A1164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1137 through 1138 Processing sheet with id=AB4, first strand: chain 'B' and resid 269 through 275 removed outlier: 6.692A pdb=" N SER B 270 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE B 21 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS B 272 " --> pdb=" O GLU B 19 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU B 17 " --> pdb=" O GLN B 274 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 14 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN B 507 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 10.106A pdb=" N ILE B 18 " --> pdb=" O GLY B 505 " (cutoff:3.500A) removed outlier: 13.675A pdb=" N GLY B 505 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 19.772A pdb=" N GLN B 20 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 23.155A pdb=" N ASP B 503 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 30.471A pdb=" N SER B 22 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 33.943A pdb=" N PHE B 501 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU B 638 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N HIS B 637 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA B 622 " --> pdb=" O HIS B 637 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 269 through 275 removed outlier: 6.692A pdb=" N SER B 270 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE B 21 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS B 272 " --> pdb=" O GLU B 19 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU B 17 " --> pdb=" O GLN B 274 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 14 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN B 507 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 10.106A pdb=" N ILE B 18 " --> pdb=" O GLY B 505 " (cutoff:3.500A) removed outlier: 13.675A pdb=" N GLY B 505 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 19.772A pdb=" N GLN B 20 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 23.155A pdb=" N ASP B 503 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 30.471A pdb=" N SER B 22 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 33.943A pdb=" N PHE B 501 " --> pdb=" O SER B 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 66 through 69 removed outlier: 3.557A pdb=" N CYS B 66 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 34 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 171 through 174 removed outlier: 3.559A pdb=" N ASP B 160 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 171 through 174 removed outlier: 3.559A pdb=" N ASP B 160 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU B 139 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE B 159 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR B 137 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR B 137 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 236 through 237 Processing sheet with id=AC1, first strand: chain 'B' and resid 333 through 335 734 hydrogen bonds defined for protein. 2037 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 7.74 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4711 1.34 - 1.45: 2626 1.45 - 1.57: 8488 1.57 - 1.69: 101 1.69 - 1.81: 55 Bond restraints: 15981 Sorted by residual: bond pdb=" N VAL B 212 " pdb=" CA VAL B 212 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.10e+01 bond pdb=" N PHE A 362 " pdb=" CA PHE A 362 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.67e+00 bond pdb=" N GLN B 204 " pdb=" CA GLN B 204 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.25e-02 6.40e+03 8.71e+00 bond pdb=" N LYS A 980 " pdb=" CA LYS A 980 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.57e+00 bond pdb=" N VAL B 208 " pdb=" CA VAL B 208 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.22e+00 ... (remaining 15976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 21171 1.55 - 3.10: 523 3.10 - 4.64: 118 4.64 - 6.19: 8 6.19 - 7.74: 5 Bond angle restraints: 21825 Sorted by residual: angle pdb=" CA TYR A 982 " pdb=" C TYR A 982 " pdb=" O TYR A 982 " ideal model delta sigma weight residual 121.38 114.98 6.40 1.06e+00 8.90e-01 3.65e+01 angle pdb=" C PHE A 362 " pdb=" CA PHE A 362 " pdb=" CB PHE A 362 " ideal model delta sigma weight residual 110.06 117.44 -7.38 1.44e+00 4.82e-01 2.62e+01 angle pdb=" C4' DT C 2 " pdb=" C3' DT C 2 " pdb=" O3' DT C 2 " ideal model delta sigma weight residual 110.00 103.00 7.00 1.50e+00 4.44e-01 2.18e+01 angle pdb=" CA SER A 361 " pdb=" C SER A 361 " pdb=" O SER A 361 " ideal model delta sigma weight residual 120.09 116.15 3.94 1.01e+00 9.80e-01 1.52e+01 angle pdb=" CA PHE A 362 " pdb=" CB PHE A 362 " pdb=" CG PHE A 362 " ideal model delta sigma weight residual 113.80 117.44 -3.64 1.00e+00 1.00e+00 1.33e+01 ... (remaining 21820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.73: 8929 32.73 - 65.45: 521 65.45 - 98.18: 28 98.18 - 130.91: 0 130.91 - 163.63: 2 Dihedral angle restraints: 9480 sinusoidal: 4229 harmonic: 5251 Sorted by residual: dihedral pdb=" C PHE A 362 " pdb=" N PHE A 362 " pdb=" CA PHE A 362 " pdb=" CB PHE A 362 " ideal model delta harmonic sigma weight residual -122.60 -136.22 13.62 0 2.50e+00 1.60e-01 2.97e+01 dihedral pdb=" N PHE A 362 " pdb=" C PHE A 362 " pdb=" CA PHE A 362 " pdb=" CB PHE A 362 " ideal model delta harmonic sigma weight residual 122.80 133.95 -11.15 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" CA TYR B 226 " pdb=" C TYR B 226 " pdb=" N SER B 227 " pdb=" CA SER B 227 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 9477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2262 0.087 - 0.175: 128 0.175 - 0.262: 3 0.262 - 0.350: 0 0.350 - 0.437: 1 Chirality restraints: 2394 Sorted by residual: chirality pdb=" CA PHE A 362 " pdb=" N PHE A 362 " pdb=" C PHE A 362 " pdb=" CB PHE A 362 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" C3' DG D 5 " pdb=" C4' DG D 5 " pdb=" O3' DG D 5 " pdb=" C2' DG D 5 " both_signs ideal model delta sigma weight residual False -2.66 -2.41 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA VAL B 212 " pdb=" N VAL B 212 " pdb=" C VAL B 212 " pdb=" CB VAL B 212 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2391 not shown) Planarity restraints: 2633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 423 " -0.267 9.50e-02 1.11e+02 1.20e-01 9.73e+00 pdb=" NE ARG B 423 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B 423 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 423 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 423 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 466 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C SER A 466 " 0.042 2.00e-02 2.50e+03 pdb=" O SER A 466 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 467 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 979 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C THR A 979 " -0.035 2.00e-02 2.50e+03 pdb=" O THR A 979 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 980 " 0.012 2.00e-02 2.50e+03 ... (remaining 2630 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 78 2.52 - 3.11: 11772 3.11 - 3.71: 24277 3.71 - 4.30: 36502 4.30 - 4.90: 59408 Nonbonded interactions: 132037 Sorted by model distance: nonbonded pdb=" OP1 DA C 4 " pdb="MG MG C 101 " model vdw 1.919 2.170 nonbonded pdb=" N GLU A 7 " pdb=" OE1 GLU A 7 " model vdw 2.187 3.120 nonbonded pdb=" C4' DT D 1 " pdb=" OP1 DC D 2 " model vdw 2.204 3.470 nonbonded pdb=" N GLU B 513 " pdb=" OE1 GLU B 513 " model vdw 2.204 3.120 nonbonded pdb=" N GLU A 618 " pdb=" OE1 GLU A 618 " model vdw 2.208 3.120 ... (remaining 132032 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: 10.550 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: 0.030 Extract box with map and model: 0.810 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 45.580 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15981 Z= 0.186 Angle : 0.606 7.740 21825 Z= 0.371 Chirality : 0.041 0.437 2394 Planarity : 0.004 0.120 2633 Dihedral : 18.042 163.632 6080 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.69 % Allowed : 10.21 % Favored : 89.10 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.21), residues: 1764 helix: 2.20 (0.19), residues: 794 sheet: 0.26 (0.31), residues: 283 loop : 0.52 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 643 HIS 0.003 0.001 HIS A 799 PHE 0.017 0.001 PHE A 607 TYR 0.020 0.001 TYR B 226 ARG 0.017 0.000 ARG B 423 Details of bonding type rmsd hydrogen bonds : bond 0.15142 ( 771) hydrogen bonds : angle 6.59055 ( 2125) covalent geometry : bond 0.00341 (15981) covalent geometry : angle 0.60626 (21825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 1.641 Fit side-chains revert: symmetry clash REVERT: A 1148 ASN cc_start: 0.8353 (p0) cc_final: 0.7277 (p0) outliers start: 11 outliers final: 3 residues processed: 93 average time/residue: 1.4098 time to fit residues: 145.2907 Evaluate side-chains 55 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 228 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 163 optimal weight: 0.0670 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 HIS A 807 ASN B 149 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.090516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.061190 restraints weight = 37677.279| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.90 r_work: 0.2889 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15981 Z= 0.175 Angle : 0.556 6.858 21825 Z= 0.301 Chirality : 0.041 0.196 2394 Planarity : 0.004 0.044 2633 Dihedral : 17.844 172.201 2516 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.45 % Allowed : 10.40 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.21), residues: 1764 helix: 2.19 (0.18), residues: 803 sheet: 0.33 (0.33), residues: 255 loop : 0.39 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 643 HIS 0.004 0.001 HIS A 307 PHE 0.030 0.001 PHE A 362 TYR 0.018 0.001 TYR B 366 ARG 0.007 0.001 ARG B 423 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 771) hydrogen bonds : angle 4.55120 ( 2125) covalent geometry : bond 0.00402 (15981) covalent geometry : angle 0.55564 (21825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 1.648 Fit side-chains REVERT: A 214 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8983 (tm) REVERT: A 288 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8112 (pp30) REVERT: A 1148 ASN cc_start: 0.9039 (p0) cc_final: 0.8290 (p0) REVERT: B 389 GLN cc_start: 0.9128 (mp10) cc_final: 0.8904 (pm20) outliers start: 23 outliers final: 4 residues processed: 84 average time/residue: 1.3006 time to fit residues: 122.2382 Evaluate side-chains 55 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 199 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 146 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 59 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 204 GLN A 252 HIS A 288 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN B 256 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.090538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.061390 restraints weight = 37686.088| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.89 r_work: 0.2898 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15981 Z= 0.139 Angle : 0.513 6.854 21825 Z= 0.277 Chirality : 0.039 0.189 2394 Planarity : 0.004 0.039 2633 Dihedral : 17.542 171.347 2509 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.58 % Allowed : 10.71 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.21), residues: 1764 helix: 2.25 (0.18), residues: 804 sheet: 0.36 (0.32), residues: 258 loop : 0.35 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 643 HIS 0.004 0.001 HIS A 799 PHE 0.023 0.001 PHE A 362 TYR 0.023 0.001 TYR B 226 ARG 0.008 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 771) hydrogen bonds : angle 4.33477 ( 2125) covalent geometry : bond 0.00316 (15981) covalent geometry : angle 0.51342 (21825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 1.730 Fit side-chains revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8978 (tm) REVERT: A 1148 ASN cc_start: 0.9033 (p0) cc_final: 0.8336 (p0) REVERT: B 389 GLN cc_start: 0.9159 (mp10) cc_final: 0.8895 (mp10) REVERT: B 502 ILE cc_start: 0.8545 (mt) cc_final: 0.8341 (pt) REVERT: B 677 ARG cc_start: 0.8376 (tpp80) cc_final: 0.7626 (tpp-160) outliers start: 25 outliers final: 5 residues processed: 81 average time/residue: 1.3631 time to fit residues: 123.4780 Evaluate side-chains 56 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 87 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 175 optimal weight: 0.0020 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 22 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 165 optimal weight: 0.0270 chunk 16 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.4246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN B 549 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.091687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.062876 restraints weight = 37456.266| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.87 r_work: 0.2928 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15981 Z= 0.111 Angle : 0.492 8.777 21825 Z= 0.263 Chirality : 0.039 0.269 2394 Planarity : 0.003 0.037 2633 Dihedral : 17.278 170.964 2509 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.64 % Allowed : 10.65 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.21), residues: 1764 helix: 2.31 (0.18), residues: 814 sheet: 0.38 (0.32), residues: 262 loop : 0.32 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 428 HIS 0.003 0.001 HIS A 799 PHE 0.027 0.001 PHE A 425 TYR 0.011 0.001 TYR A 258 ARG 0.005 0.000 ARG A1145 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 771) hydrogen bonds : angle 4.09640 ( 2125) covalent geometry : bond 0.00246 (15981) covalent geometry : angle 0.49198 (21825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 1.643 Fit side-chains revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8965 (tm) REVERT: A 1148 ASN cc_start: 0.9061 (p0) cc_final: 0.8390 (p0) REVERT: A 1157 GLN cc_start: 0.8432 (mm-40) cc_final: 0.7873 (mp10) REVERT: B 199 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.7166 (t80) REVERT: B 389 GLN cc_start: 0.9225 (mp10) cc_final: 0.8951 (mp10) REVERT: B 677 ARG cc_start: 0.8348 (tpp80) cc_final: 0.7696 (tpp-160) outliers start: 26 outliers final: 7 residues processed: 89 average time/residue: 1.2708 time to fit residues: 126.6057 Evaluate side-chains 63 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 317 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 72 optimal weight: 0.0370 chunk 113 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 20 optimal weight: 0.0070 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 GLN B 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.091310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.062430 restraints weight = 37927.388| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.89 r_work: 0.2921 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15981 Z= 0.117 Angle : 0.488 8.896 21825 Z= 0.261 Chirality : 0.039 0.289 2394 Planarity : 0.003 0.037 2633 Dihedral : 17.163 171.000 2509 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.58 % Allowed : 11.22 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.21), residues: 1764 helix: 2.33 (0.18), residues: 815 sheet: 0.39 (0.32), residues: 263 loop : 0.36 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 643 HIS 0.003 0.001 HIS A 799 PHE 0.022 0.001 PHE A 362 TYR 0.027 0.001 TYR B 226 ARG 0.003 0.000 ARG A1145 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 771) hydrogen bonds : angle 4.04222 ( 2125) covalent geometry : bond 0.00263 (15981) covalent geometry : angle 0.48815 (21825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8971 (tm) REVERT: A 1148 ASN cc_start: 0.9054 (p0) cc_final: 0.8395 (p0) REVERT: A 1157 GLN cc_start: 0.8404 (mm110) cc_final: 0.7913 (mp10) REVERT: B 199 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7201 (t80) REVERT: B 366 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.7065 (t80) REVERT: B 389 GLN cc_start: 0.9226 (mp10) cc_final: 0.8938 (mp10) REVERT: B 677 ARG cc_start: 0.8339 (tpp80) cc_final: 0.7712 (tpp-160) outliers start: 25 outliers final: 10 residues processed: 79 average time/residue: 1.3759 time to fit residues: 121.4970 Evaluate side-chains 69 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 633 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.088827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.059456 restraints weight = 37689.922| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.86 r_work: 0.2880 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15981 Z= 0.209 Angle : 0.544 7.680 21825 Z= 0.290 Chirality : 0.041 0.194 2394 Planarity : 0.004 0.038 2633 Dihedral : 17.316 173.315 2509 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.83 % Allowed : 11.53 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.21), residues: 1764 helix: 2.20 (0.18), residues: 809 sheet: 0.23 (0.31), residues: 283 loop : 0.43 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 643 HIS 0.004 0.001 HIS A 458 PHE 0.027 0.002 PHE A 362 TYR 0.013 0.001 TYR B 370 ARG 0.002 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 771) hydrogen bonds : angle 4.24272 ( 2125) covalent geometry : bond 0.00487 (15981) covalent geometry : angle 0.54388 (21825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 1.898 Fit side-chains revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8966 (tm) REVERT: A 1157 GLN cc_start: 0.8457 (mm110) cc_final: 0.7920 (mp10) REVERT: B 199 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7415 (t80) REVERT: B 366 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.7099 (t80) REVERT: B 387 GLN cc_start: 0.9025 (mp10) cc_final: 0.8767 (mp10) REVERT: B 389 GLN cc_start: 0.9274 (mp10) cc_final: 0.8993 (mp10) outliers start: 29 outliers final: 8 residues processed: 84 average time/residue: 1.2620 time to fit residues: 119.7667 Evaluate side-chains 66 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 159 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 157 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.089957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.061039 restraints weight = 37719.153| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.86 r_work: 0.2887 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15981 Z= 0.137 Angle : 0.505 8.805 21825 Z= 0.269 Chirality : 0.039 0.350 2394 Planarity : 0.003 0.037 2633 Dihedral : 17.130 171.863 2509 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.32 % Allowed : 12.60 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.21), residues: 1764 helix: 2.28 (0.18), residues: 807 sheet: 0.41 (0.33), residues: 263 loop : 0.35 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 428 HIS 0.003 0.001 HIS A 458 PHE 0.023 0.001 PHE A 362 TYR 0.027 0.001 TYR B 226 ARG 0.008 0.000 ARG B 386 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 771) hydrogen bonds : angle 4.09496 ( 2125) covalent geometry : bond 0.00315 (15981) covalent geometry : angle 0.50526 (21825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 1.942 Fit side-chains revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8970 (tm) REVERT: A 288 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8208 (pp30) REVERT: A 1094 GLU cc_start: 0.8814 (pm20) cc_final: 0.8571 (pp20) REVERT: A 1148 ASN cc_start: 0.9101 (p0) cc_final: 0.8307 (p0) REVERT: A 1157 GLN cc_start: 0.8427 (mm110) cc_final: 0.7931 (mp10) REVERT: B 366 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.7105 (t80) REVERT: B 387 GLN cc_start: 0.9014 (mp10) cc_final: 0.8766 (mp10) REVERT: B 389 GLN cc_start: 0.9280 (mp10) cc_final: 0.9002 (pm20) REVERT: B 677 ARG cc_start: 0.8352 (tpp80) cc_final: 0.7761 (tpp-160) outliers start: 21 outliers final: 11 residues processed: 77 average time/residue: 1.2987 time to fit residues: 112.3485 Evaluate side-chains 71 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 633 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 116 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 60 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.089061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.059710 restraints weight = 37531.808| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.86 r_work: 0.2884 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15981 Z= 0.189 Angle : 0.532 8.414 21825 Z= 0.283 Chirality : 0.040 0.190 2394 Planarity : 0.004 0.038 2633 Dihedral : 17.167 172.117 2509 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.39 % Allowed : 12.79 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.21), residues: 1764 helix: 2.21 (0.18), residues: 809 sheet: 0.32 (0.32), residues: 276 loop : 0.37 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 428 HIS 0.004 0.001 HIS A 458 PHE 0.026 0.001 PHE A 425 TYR 0.013 0.001 TYR B 370 ARG 0.006 0.000 ARG B 386 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 771) hydrogen bonds : angle 4.15992 ( 2125) covalent geometry : bond 0.00440 (15981) covalent geometry : angle 0.53244 (21825) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8959 (tm) REVERT: A 1094 GLU cc_start: 0.8829 (pm20) cc_final: 0.8596 (pp20) REVERT: A 1148 ASN cc_start: 0.9118 (p0) cc_final: 0.8370 (p0) REVERT: A 1157 GLN cc_start: 0.8434 (mm110) cc_final: 0.7943 (mp10) REVERT: B 366 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.7081 (t80) REVERT: B 389 GLN cc_start: 0.9281 (mp10) cc_final: 0.9007 (mp10) outliers start: 22 outliers final: 11 residues processed: 76 average time/residue: 1.2762 time to fit residues: 109.5545 Evaluate side-chains 67 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 29 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 120 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 124 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.088832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.059493 restraints weight = 37696.787| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.87 r_work: 0.2883 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15981 Z= 0.190 Angle : 0.545 8.230 21825 Z= 0.291 Chirality : 0.041 0.391 2394 Planarity : 0.004 0.046 2633 Dihedral : 17.173 172.577 2509 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.13 % Allowed : 13.55 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.21), residues: 1764 helix: 2.20 (0.18), residues: 809 sheet: 0.34 (0.32), residues: 276 loop : 0.36 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 428 HIS 0.004 0.001 HIS A 458 PHE 0.025 0.001 PHE A 362 TYR 0.031 0.001 TYR B 226 ARG 0.005 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 771) hydrogen bonds : angle 4.19154 ( 2125) covalent geometry : bond 0.00442 (15981) covalent geometry : angle 0.54549 (21825) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8957 (tm) REVERT: A 1094 GLU cc_start: 0.8828 (pm20) cc_final: 0.8602 (pp20) REVERT: A 1148 ASN cc_start: 0.9106 (p0) cc_final: 0.8347 (p0) REVERT: A 1157 GLN cc_start: 0.8437 (mm110) cc_final: 0.7949 (mp10) REVERT: B 366 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.7084 (t80) REVERT: B 389 GLN cc_start: 0.9284 (mp10) cc_final: 0.9004 (mp10) outliers start: 18 outliers final: 11 residues processed: 74 average time/residue: 1.3643 time to fit residues: 113.1887 Evaluate side-chains 67 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 45 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.089478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.060450 restraints weight = 37891.058| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.87 r_work: 0.2875 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15981 Z= 0.152 Angle : 0.523 8.200 21825 Z= 0.279 Chirality : 0.039 0.184 2394 Planarity : 0.004 0.042 2633 Dihedral : 17.093 171.777 2509 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.20 % Allowed : 13.67 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.21), residues: 1764 helix: 2.27 (0.18), residues: 808 sheet: 0.34 (0.32), residues: 278 loop : 0.41 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 428 HIS 0.003 0.001 HIS A 458 PHE 0.023 0.001 PHE A 362 TYR 0.021 0.001 TYR B 39 ARG 0.009 0.000 ARG B 386 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 771) hydrogen bonds : angle 4.10430 ( 2125) covalent geometry : bond 0.00352 (15981) covalent geometry : angle 0.52305 (21825) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8976 (tm) REVERT: A 1094 GLU cc_start: 0.8825 (pm20) cc_final: 0.8620 (pp20) REVERT: A 1148 ASN cc_start: 0.9099 (p0) cc_final: 0.8332 (p0) REVERT: A 1157 GLN cc_start: 0.8438 (mm110) cc_final: 0.7988 (mp10) REVERT: B 366 TYR cc_start: 0.7594 (OUTLIER) cc_final: 0.7050 (t80) REVERT: B 389 GLN cc_start: 0.9302 (mp10) cc_final: 0.9036 (pm20) outliers start: 19 outliers final: 11 residues processed: 70 average time/residue: 1.3580 time to fit residues: 106.6389 Evaluate side-chains 67 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 633 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 171 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 163 optimal weight: 0.2980 chunk 32 optimal weight: 0.0870 chunk 159 optimal weight: 0.7980 chunk 72 optimal weight: 0.2980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.090912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.062209 restraints weight = 37533.019| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.84 r_work: 0.2918 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15981 Z= 0.112 Angle : 0.500 8.645 21825 Z= 0.267 Chirality : 0.039 0.364 2394 Planarity : 0.003 0.037 2633 Dihedral : 16.932 171.209 2509 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.88 % Allowed : 14.05 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.21), residues: 1764 helix: 2.34 (0.18), residues: 816 sheet: 0.37 (0.32), residues: 277 loop : 0.48 (0.26), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 428 HIS 0.003 0.001 HIS A 799 PHE 0.021 0.001 PHE A 362 TYR 0.028 0.001 TYR B 226 ARG 0.006 0.000 ARG B 386 Details of bonding type rmsd hydrogen bonds : bond 0.02999 ( 771) hydrogen bonds : angle 3.98612 ( 2125) covalent geometry : bond 0.00253 (15981) covalent geometry : angle 0.49986 (21825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10505.50 seconds wall clock time: 182 minutes 27.77 seconds (10947.77 seconds total)