Starting phenix.real_space_refine on Thu Aug 6 13:59:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ezy_50091/08_2026/9ezy_50091.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ezy_50091/08_2026/9ezy_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ezy_50091/08_2026/9ezy_50091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ezy_50091/08_2026/9ezy_50091.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ezy_50091/08_2026/9ezy_50091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ezy_50091/08_2026/9ezy_50091.map" } resolution = 2.56 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= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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:plan': 1, ' DA%5*END:plan2': 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: 3.00, per 1000 atoms: 0.19 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: 1.49 Conformation dependent library (CDL) restraints added in 747.5 milliseconds 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: 2.42 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: 3.50 Time building geometry restraints manager: 2.01 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=" O3' DA C 1 " pdb=" P DT C 2 " ideal model delta sigma weight residual 1.607 1.565 0.042 1.20e-02 6.94e+03 1.22e+01 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 ... (remaining 15976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 21219 1.55 - 3.10: 476 3.10 - 4.64: 117 4.64 - 6.19: 7 6.19 - 7.74: 6 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=" N3 DT C 5 " pdb=" C4 DT C 5 " pdb=" O4 DT C 5 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 angle pdb=" N3 DT C 6 " pdb=" C4 DT C 6 " pdb=" O4 DT C 6 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+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 ... (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: 2259 0.087 - 0.175: 131 0.175 - 0.262: 2 0.262 - 0.350: 1 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 -2.73 -2.41 -0.32 2.00e-01 2.50e+01 2.61e+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: 17.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.930 Find NCS groups from input model: 0.080 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 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= 0.201 Angle : 0.591 7.740 21825 Z= 0.375 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 : 4.49 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 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: 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 ARG 0.017 0.000 ARG B 423 TYR 0.020 0.001 TYR B 226 PHE 0.017 0.001 PHE A 607 TRP 0.017 0.001 TRP A 643 HIS 0.003 0.001 HIS A 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.20 (15981) covalent geometry : angle 0.59092 / 0.37 (21825) hydrogen bonds : bond 0.15142 / 10.08 ( 771) hydrogen bonds : angle 6.59055 / 4.77 ( 2125) *********************** 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 : 0.674 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: 0.6364 time to fit residues: 65.4791 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 : 0.552 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0010 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN A 204 GLN A 252 HIS A 288 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 HIS A 584 HIS A 807 ASN A1086 ASN B 149 HIS B 256 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.091987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.062601 restraints weight = 37185.486| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.90 r_work: 0.2953 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15981 Z= 0.134 Angle : 0.578 6.767 21825 Z= 0.313 Chirality : 0.043 0.245 2394 Planarity : 0.004 0.041 2633 Dihedral : 18.030 171.582 2516 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.32 % Allowed : 10.46 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.74 (0.21), residues: 1764 helix: 2.18 (0.18), residues: 799 sheet: 0.34 (0.32), residues: 257 loop : 0.38 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 423 TYR 0.027 0.001 TYR B 366 PHE 0.025 0.001 PHE A 362 TRP 0.021 0.001 TRP A 643 HIS 0.009 0.001 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (15981) covalent geometry : angle 0.57750 / 0.31 (21825) hydrogen bonds : bond 0.04496 / 2.95 ( 771) hydrogen bonds : angle 4.85031 / 3.44 ( 2125) *********************** 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 78 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.608 Fit side-chains REVERT: A 214 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9008 (tm) REVERT: A 1148 ASN cc_start: 0.9028 (p0) cc_final: 0.8232 (p0) REVERT: B 389 GLN cc_start: 0.9067 (mp10) cc_final: 0.8859 (mp10) outliers start: 21 outliers final: 3 residues processed: 72 average time/residue: 0.5961 time to fit residues: 47.9625 Evaluate side-chains 55 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU 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 48 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 chunk 45 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 GLN ** A 460 ASN ** 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 = 0.3638 r_free = 0.3638 target = 0.090815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.061188 restraints weight = 37909.454| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.94 r_work: 0.2920 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15981 Z= 0.163 Angle : 0.553 7.811 21825 Z= 0.297 Chirality : 0.042 0.229 2394 Planarity : 0.004 0.045 2633 Dihedral : 17.920 171.898 2509 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.64 % Allowed : 10.21 % 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 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: 1.66 (0.21), residues: 1764 helix: 2.17 (0.18), residues: 807 sheet: 0.25 (0.33), residues: 254 loop : 0.27 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 386 TYR 0.024 0.001 TYR B 226 PHE 0.026 0.001 PHE A 362 TRP 0.021 0.001 TRP A 643 HIS 0.005 0.001 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (15981) covalent geometry : angle 0.55296 / 0.30 (21825) hydrogen bonds : bond 0.04128 / 2.73 ( 771) hydrogen bonds : angle 4.51831 / 3.20 ( 2125) *********************** 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 82 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.414 Fit side-chains REVERT: A 214 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8980 (tm) REVERT: A 1007 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8600 (tpp) REVERT: A 1148 ASN cc_start: 0.9037 (p0) cc_final: 0.8297 (p0) REVERT: B 389 GLN cc_start: 0.9083 (mp10) cc_final: 0.8823 (mp10) outliers start: 26 outliers final: 8 residues processed: 77 average time/residue: 0.5365 time to fit residues: 46.2805 Evaluate side-chains 57 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU 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 550 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1007 MET Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 199 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 69 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3599 r_free = 0.3599 target = 0.088845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.059436 restraints weight = 37678.229| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.86 r_work: 0.2842 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15981 Z= 0.248 Angle : 0.586 7.824 21825 Z= 0.311 Chirality : 0.044 0.263 2394 Planarity : 0.004 0.045 2633 Dihedral : 17.901 172.891 2509 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.45 % Allowed : 11.59 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.52 (0.20), residues: 1764 helix: 2.03 (0.18), residues: 803 sheet: 0.09 (0.32), residues: 266 loop : 0.27 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 386 TYR 0.014 0.002 TYR B 226 PHE 0.026 0.002 PHE A 362 TRP 0.022 0.001 TRP A 643 HIS 0.006 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.25 (15981) covalent geometry : angle 0.58594 / 0.31 (21825) hydrogen bonds : bond 0.04214 / 2.81 ( 771) hydrogen bonds : angle 4.50719 / 3.21 ( 2125) *********************** 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 76 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.445 Fit side-chains REVERT: A 168 GLU cc_start: 0.8619 (tp30) cc_final: 0.8368 (tp30) REVERT: A 214 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8976 (tm) REVERT: A 1007 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8520 (tpp) REVERT: A 1148 ASN cc_start: 0.9061 (p0) cc_final: 0.8377 (p0) REVERT: B 389 GLN cc_start: 0.9158 (mp10) cc_final: 0.8889 (mp10) outliers start: 23 outliers final: 11 residues processed: 71 average time/residue: 0.5149 time to fit residues: 41.0325 Evaluate side-chains 59 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU 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 710 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1007 MET Chi-restraints excluded: chain B residue 87 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 123 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.089795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.060388 restraints weight = 37862.401| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.89 r_work: 0.2902 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15981 Z= 0.148 Angle : 0.535 7.745 21825 Z= 0.285 Chirality : 0.041 0.233 2394 Planarity : 0.004 0.044 2633 Dihedral : 17.749 172.317 2509 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.32 % Allowed : 11.59 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.57 (0.21), residues: 1764 helix: 2.08 (0.18), residues: 811 sheet: 0.19 (0.33), residues: 255 loop : 0.23 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 386 TYR 0.025 0.001 TYR B 226 PHE 0.025 0.001 PHE A 362 TRP 0.022 0.001 TRP A 643 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (15981) covalent geometry : angle 0.53454 / 0.29 (21825) hydrogen bonds : bond 0.03766 / 2.50 ( 771) hydrogen bonds : angle 4.34720 / 3.09 ( 2125) *********************** 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 74 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.530 Fit side-chains REVERT: A 168 GLU cc_start: 0.8597 (tp30) cc_final: 0.8344 (tp30) REVERT: A 214 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8976 (tm) REVERT: A 1007 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.7887 (tpt) REVERT: A 1148 ASN cc_start: 0.9048 (p0) cc_final: 0.8355 (p0) REVERT: B 389 GLN cc_start: 0.9182 (mp10) cc_final: 0.8903 (mp10) REVERT: B 677 ARG cc_start: 0.8422 (tpp80) cc_final: 0.8007 (tpp-160) outliers start: 21 outliers final: 8 residues processed: 70 average time/residue: 0.5626 time to fit residues: 44.5501 Evaluate side-chains 57 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 550 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1007 MET Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain B residue 87 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 148 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 120 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS B 234 GLN B 549 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.088509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.059074 restraints weight = 37615.505| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.85 r_work: 0.2835 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15981 Z= 0.245 Angle : 0.581 7.638 21825 Z= 0.307 Chirality : 0.044 0.280 2394 Planarity : 0.004 0.045 2633 Dihedral : 17.723 172.468 2509 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.70 % Allowed : 11.97 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.50 (0.20), residues: 1764 helix: 1.99 (0.18), residues: 810 sheet: 0.13 (0.31), residues: 268 loop : 0.25 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 386 TYR 0.013 0.002 TYR A 427 PHE 0.026 0.002 PHE A 362 TRP 0.022 0.002 TRP A 643 HIS 0.006 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.24 (15981) covalent geometry : angle 0.58131 / 0.31 (21825) hydrogen bonds : bond 0.04101 / 2.74 ( 771) hydrogen bonds : angle 4.41826 / 3.15 ( 2125) *********************** 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 78 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 51 time to evaluate : 0.414 Fit side-chains REVERT: A 168 GLU cc_start: 0.8622 (tp30) cc_final: 0.8373 (tp30) REVERT: A 214 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8971 (tm) REVERT: A 1007 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.7970 (tpt) REVERT: A 1148 ASN cc_start: 0.9076 (p0) cc_final: 0.8440 (p0) REVERT: B 366 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.6971 (t80) REVERT: B 389 GLN cc_start: 0.9196 (mp10) cc_final: 0.8916 (mp10) REVERT: B 677 ARG cc_start: 0.8412 (tpp80) cc_final: 0.7663 (tpp-160) outliers start: 27 outliers final: 11 residues processed: 74 average time/residue: 0.6119 time to fit residues: 50.7876 Evaluate side-chains 63 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 447 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1007 MET Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain B residue 87 LEU 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 34 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 GLN B 234 GLN B 303 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.089287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.059877 restraints weight = 37280.003| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.87 r_work: 0.2894 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15981 Z= 0.150 Angle : 0.536 7.535 21825 Z= 0.286 Chirality : 0.041 0.252 2394 Planarity : 0.004 0.044 2633 Dihedral : 17.604 172.710 2509 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.39 % Allowed : 12.41 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.59 (0.21), residues: 1764 helix: 2.09 (0.18), residues: 810 sheet: 0.22 (0.32), residues: 268 loop : 0.24 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 573 TYR 0.029 0.001 TYR B 226 PHE 0.029 0.001 PHE A 425 TRP 0.022 0.001 TRP A 643 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (15981) covalent geometry : angle 0.53590 / 0.29 (21825) hydrogen bonds : bond 0.03667 / 2.43 ( 771) hydrogen bonds : angle 4.30093 / 3.06 ( 2125) *********************** 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 77 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.613 Fit side-chains REVERT: A 168 GLU cc_start: 0.8597 (tp30) cc_final: 0.8346 (tp30) REVERT: A 214 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8988 (tm) REVERT: A 517 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8150 (mmtm) REVERT: A 1007 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.7907 (tpt) REVERT: A 1072 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8834 (p) REVERT: A 1157 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7836 (mp10) REVERT: B 366 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6960 (t80) REVERT: B 389 GLN cc_start: 0.9205 (mp10) cc_final: 0.8924 (mp10) REVERT: B 677 ARG cc_start: 0.8380 (tpp80) cc_final: 0.7645 (tpp-160) outliers start: 22 outliers final: 11 residues processed: 72 average time/residue: 0.6045 time to fit residues: 49.1424 Evaluate side-chains 67 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 504 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1007 MET Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1148 ASN Chi-restraints excluded: chain A residue 1157 GLN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 10 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 78 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3605 r_free = 0.3605 target = 0.089161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.059831 restraints weight = 37550.443| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.87 r_work: 0.2891 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15981 Z= 0.162 Angle : 0.543 7.486 21825 Z= 0.290 Chirality : 0.042 0.387 2394 Planarity : 0.004 0.044 2633 Dihedral : 17.554 172.367 2509 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.20 % Allowed : 12.98 % 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 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: 1.62 (0.21), residues: 1764 helix: 2.11 (0.18), residues: 810 sheet: 0.25 (0.32), residues: 267 loop : 0.26 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 386 TYR 0.011 0.001 TYR B 293 PHE 0.026 0.001 PHE A 472 TRP 0.021 0.001 TRP A 643 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (15981) covalent geometry : angle 0.54264 / 0.29 (21825) hydrogen bonds : bond 0.03646 / 2.42 ( 771) hydrogen bonds : angle 4.29823 / 3.06 ( 2125) *********************** 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 69 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.606 Fit side-chains REVERT: A 168 GLU cc_start: 0.8604 (tp30) cc_final: 0.8356 (tp30) REVERT: A 214 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8983 (tm) REVERT: A 288 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8124 (pp30) REVERT: A 517 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8175 (mmtm) REVERT: A 1007 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.7926 (tpt) REVERT: A 1072 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8838 (p) REVERT: A 1157 GLN cc_start: 0.8450 (mm110) cc_final: 0.7864 (mp10) REVERT: B 366 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6965 (t80) REVERT: B 389 GLN cc_start: 0.9208 (mp10) cc_final: 0.8924 (mp10) REVERT: B 677 ARG cc_start: 0.8361 (tpp80) cc_final: 0.7662 (tpp-160) outliers start: 19 outliers final: 11 residues processed: 65 average time/residue: 0.5558 time to fit residues: 40.6642 Evaluate side-chains 65 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 338 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1007 MET Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1148 ASN Chi-restraints excluded: chain B residue 226 TYR 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 136 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 173 optimal weight: 0.0020 chunk 127 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 5 optimal weight: 0.0970 chunk 98 optimal weight: 0.3980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3618 r_free = 0.3618 target = 0.089732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.060741 restraints weight = 37684.676| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.87 r_work: 0.2880 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15981 Z= 0.118 Angle : 0.523 8.025 21825 Z= 0.280 Chirality : 0.040 0.249 2394 Planarity : 0.004 0.044 2633 Dihedral : 17.473 171.774 2509 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.20 % Allowed : 13.04 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.70 (0.21), residues: 1764 helix: 2.19 (0.18), residues: 809 sheet: 0.36 (0.33), residues: 254 loop : 0.25 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 386 TYR 0.011 0.001 TYR B 293 PHE 0.030 0.001 PHE A 425 TRP 0.022 0.001 TRP A 643 HIS 0.002 0.001 HIS B 663 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (15981) covalent geometry : angle 0.52292 / 0.28 (21825) hydrogen bonds : bond 0.03451 / 2.28 ( 771) hydrogen bonds : angle 4.22855 / 3.01 ( 2125) *********************** 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 74 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.528 Fit side-chains REVERT: A 168 GLU cc_start: 0.8599 (tp30) cc_final: 0.8351 (tp30) REVERT: A 214 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8989 (tm) REVERT: A 517 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8159 (mmtm) REVERT: A 1072 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8829 (p) REVERT: A 1157 GLN cc_start: 0.8494 (mm110) cc_final: 0.7857 (mp10) REVERT: B 366 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.6929 (t80) REVERT: B 389 GLN cc_start: 0.9214 (mp10) cc_final: 0.8929 (mp10) REVERT: B 677 ARG cc_start: 0.8357 (tpp80) cc_final: 0.7692 (tpp-160) outliers start: 19 outliers final: 10 residues processed: 70 average time/residue: 0.5672 time to fit residues: 44.6263 Evaluate side-chains 64 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 504 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1148 ASN 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 142 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 171 optimal weight: 0.0670 chunk 160 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3591 r_free = 0.3591 target = 0.088374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.059024 restraints weight = 37704.280| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.87 r_work: 0.2872 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15981 Z= 0.221 Angle : 0.574 8.467 21825 Z= 0.303 Chirality : 0.043 0.369 2394 Planarity : 0.004 0.044 2633 Dihedral : 17.514 172.240 2509 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.20 % Allowed : 13.23 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.21), residues: 1764 helix: 2.13 (0.18), residues: 809 sheet: 0.19 (0.31), residues: 267 loop : 0.29 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 386 TYR 0.032 0.001 TYR B 226 PHE 0.026 0.002 PHE A 362 TRP 0.021 0.001 TRP A 643 HIS 0.005 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (15981) covalent geometry : angle 0.57360 / 0.30 (21825) hydrogen bonds : bond 0.03839 / 2.57 ( 771) hydrogen bonds : angle 4.32910 / 3.09 ( 2125) ********************** 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 72 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.599 Fit side-chains REVERT: A 168 GLU cc_start: 0.8632 (tp30) cc_final: 0.8384 (tp30) REVERT: A 214 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8960 (tm) REVERT: A 517 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8183 (mmtm) REVERT: A 1157 GLN cc_start: 0.8490 (mm110) cc_final: 0.8072 (tp-100) REVERT: B 366 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6975 (t80) REVERT: B 389 GLN cc_start: 0.9223 (mp10) cc_final: 0.8944 (mp10) REVERT: B 677 ARG cc_start: 0.8370 (tpp80) cc_final: 0.7662 (tpp-160) outliers start: 19 outliers final: 10 residues processed: 69 average time/residue: 0.5559 time to fit residues: 43.0167 Evaluate side-chains 65 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 447 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1148 ASN 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 178 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 83 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 106 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 GLN A 303 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.089562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.060612 restraints weight = 37675.192| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.86 r_work: 0.2876 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15981 Z= 0.124 Angle : 0.531 8.610 21825 Z= 0.283 Chirality : 0.040 0.254 2394 Planarity : 0.003 0.040 2633 Dihedral : 17.372 171.942 2509 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.95 % Allowed : 13.74 % 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 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: 1.70 (0.21), residues: 1764 helix: 2.21 (0.18), residues: 809 sheet: 0.20 (0.32), residues: 267 loop : 0.30 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 386 TYR 0.011 0.001 TYR B 293 PHE 0.029 0.001 PHE A 425 TRP 0.022 0.001 TRP A 643 HIS 0.002 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15981) covalent geometry : angle 0.53074 / 0.28 (21825) hydrogen bonds : bond 0.03422 / 2.27 ( 771) hydrogen bonds : angle 4.21279 / 3.00 ( 2125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4522.47 seconds wall clock time: 78 minutes 2.39 seconds (4682.39 seconds total)