Starting phenix.real_space_refine on Tue Nov 18 16:38:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ezy_50091/11_2025/9ezy_50091.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ezy_50091/11_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ezy_50091/11_2025/9ezy_50091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ezy_50091/11_2025/9ezy_50091.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ezy_50091/11_2025/9ezy_50091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ezy_50091/11_2025/9ezy_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-2.0-5881/lib/python3.9/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: 3.77, per 1000 atoms: 0.24 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: 1.47 Conformation dependent library (CDL) restraints added in 520.6 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: 2.20 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: 3.71 Time building geometry restraints manager: 1.97 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: 16.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.570 Find NCS groups from input model: 0.180 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.320 ------------------------------------------------------------------------------- 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 : 4.49 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 covalent geometry : bond 0.00341 (15981) covalent geometry : angle 0.60626 (21825) hydrogen bonds : bond 0.15142 ( 771) hydrogen bonds : angle 6.59055 ( 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 : 0.571 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: 0.7205 time to fit residues: 73.9445 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 : 0.659 ------------------------------------------------------------------------------- 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: 0.8980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- 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 B 256 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.092290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.062954 restraints weight = 37322.851| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.92 r_work: 0.2963 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1410 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= 0.130 Angle : 0.527 6.733 21825 Z= 0.287 Chirality : 0.040 0.188 2394 Planarity : 0.004 0.041 2633 Dihedral : 17.770 172.178 2516 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.39 % Allowed : 10.27 % Favored : 88.34 % 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: 1.87 (0.21), residues: 1764 helix: 2.29 (0.19), residues: 803 sheet: 0.40 (0.33), residues: 253 loop : 0.43 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 386 TYR 0.017 0.001 TYR B 366 PHE 0.030 0.001 PHE A 362 TRP 0.021 0.001 TRP A 643 HIS 0.004 0.001 HIS A 799 Details of bonding type rmsd covalent geometry : bond 0.00277 (15981) covalent geometry : angle 0.52703 (21825) hydrogen bonds : bond 0.03848 ( 771) hydrogen bonds : angle 4.50419 ( 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 91 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.777 Fit side-chains REVERT: A 214 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8979 (tm) REVERT: A 1148 ASN cc_start: 0.9023 (p0) cc_final: 0.8255 (p0) REVERT: B 389 GLN cc_start: 0.9089 (mp10) cc_final: 0.8866 (pm20) outliers start: 22 outliers final: 3 residues processed: 87 average time/residue: 0.7039 time to fit residues: 68.2050 Evaluate side-chains 56 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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: 2.9990 chunk 101 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 45 optimal weight: 1.9990 chunk 145 optimal weight: 0.3980 chunk 105 optimal weight: 6.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- 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** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.089746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.060486 restraints weight = 38171.812| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.89 r_work: 0.2875 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15981 Z= 0.178 Angle : 0.537 6.938 21825 Z= 0.289 Chirality : 0.040 0.189 2394 Planarity : 0.004 0.043 2633 Dihedral : 17.564 171.739 2509 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.64 % Allowed : 10.90 % Favored : 87.46 % 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: 1.81 (0.21), residues: 1764 helix: 2.25 (0.18), residues: 799 sheet: 0.23 (0.32), residues: 270 loop : 0.47 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 163 TYR 0.023 0.001 TYR B 226 PHE 0.024 0.001 PHE A 362 TRP 0.022 0.001 TRP A 643 HIS 0.004 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00412 (15981) covalent geometry : angle 0.53710 (21825) hydrogen bonds : bond 0.03825 ( 771) hydrogen bonds : angle 4.36149 ( 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 84 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8969 (tm) REVERT: A 1148 ASN cc_start: 0.9034 (p0) cc_final: 0.8348 (p0) REVERT: A 1157 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7818 (mp10) REVERT: B 389 GLN cc_start: 0.9169 (mp10) cc_final: 0.8892 (pm20) REVERT: B 677 ARG cc_start: 0.8391 (tpp80) cc_final: 0.7659 (tpp-160) outliers start: 26 outliers final: 4 residues processed: 78 average time/residue: 0.7089 time to fit residues: 61.4762 Evaluate side-chains 56 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 550 THR Chi-restraints excluded: chain A residue 870 VAL 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: 0.6980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 96 optimal weight: 0.0470 chunk 134 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 ** 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 = 0.3639 r_free = 0.3639 target = 0.090839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.061948 restraints weight = 37633.633| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.87 r_work: 0.2912 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2021 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= 0.123 Angle : 0.499 10.609 21825 Z= 0.266 Chirality : 0.039 0.264 2394 Planarity : 0.003 0.038 2633 Dihedral : 17.345 171.387 2509 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.89 % Allowed : 10.52 % Favored : 87.59 % 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: 1.84 (0.21), residues: 1764 helix: 2.27 (0.18), residues: 813 sheet: 0.38 (0.33), residues: 259 loop : 0.38 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 386 TYR 0.011 0.001 TYR B 366 PHE 0.025 0.001 PHE A 425 TRP 0.025 0.001 TRP A 428 HIS 0.003 0.001 HIS A 799 Details of bonding type rmsd covalent geometry : bond 0.00278 (15981) covalent geometry : angle 0.49905 (21825) hydrogen bonds : bond 0.03309 ( 771) hydrogen bonds : angle 4.16511 ( 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 94 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8967 (tm) REVERT: A 1148 ASN cc_start: 0.9062 (p0) cc_final: 0.8417 (p0) REVERT: A 1157 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7899 (mp10) REVERT: A 1160 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7462 (ptmt) REVERT: B 199 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7243 (t80) REVERT: B 366 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.6998 (t80) REVERT: B 389 GLN cc_start: 0.9212 (mp10) cc_final: 0.8925 (mp10) REVERT: B 677 ARG cc_start: 0.8338 (tpp80) cc_final: 0.7693 (tpp-160) outliers start: 30 outliers final: 7 residues processed: 87 average time/residue: 0.6629 time to fit residues: 64.2311 Evaluate side-chains 65 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 504 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 123 optimal weight: 0.9980 chunk 131 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.089930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.060828 restraints weight = 38045.767| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.89 r_work: 0.2883 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15981 Z= 0.156 Angle : 0.508 9.674 21825 Z= 0.271 Chirality : 0.039 0.226 2394 Planarity : 0.003 0.038 2633 Dihedral : 17.283 171.792 2509 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.58 % Allowed : 11.47 % 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: 1.81 (0.21), residues: 1764 helix: 2.27 (0.18), residues: 805 sheet: 0.35 (0.33), residues: 261 loop : 0.37 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 573 TYR 0.029 0.001 TYR B 226 PHE 0.024 0.001 PHE A 362 TRP 0.021 0.001 TRP A 643 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00361 (15981) covalent geometry : angle 0.50758 (21825) hydrogen bonds : bond 0.03420 ( 771) hydrogen bonds : angle 4.16507 ( 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 84 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8971 (tm) REVERT: A 288 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8119 (pp30) REVERT: A 421 ARG cc_start: 0.8028 (ttt180) cc_final: 0.7731 (ttt180) REVERT: A 1148 ASN cc_start: 0.9053 (p0) cc_final: 0.8425 (p0) REVERT: A 1157 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7937 (mp10) REVERT: A 1160 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7532 (ptmt) REVERT: B 199 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7362 (t80) REVERT: B 366 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.6980 (t80) REVERT: B 389 GLN cc_start: 0.9238 (mp10) cc_final: 0.8954 (mp10) REVERT: B 677 ARG cc_start: 0.8346 (tpp80) cc_final: 0.7713 (tpp-160) outliers start: 25 outliers final: 11 residues processed: 82 average time/residue: 0.6787 time to fit residues: 62.0701 Evaluate side-chains 70 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 550 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1160 LYS 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=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: 0.5980 chunk 59 optimal weight: 0.0670 chunk 120 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.088871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.059479 restraints weight = 37560.727| |-----------------------------------------------------------------------------| 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: 0.8379 moved from start: 0.2261 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= 0.204 Angle : 0.537 8.295 21825 Z= 0.286 Chirality : 0.041 0.325 2394 Planarity : 0.004 0.038 2633 Dihedral : 17.283 172.320 2509 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.58 % Allowed : 11.78 % 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 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: 2.17 (0.18), residues: 809 sheet: 0.23 (0.32), residues: 274 loop : 0.35 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 386 TYR 0.013 0.001 TYR B 370 PHE 0.028 0.002 PHE A 425 TRP 0.021 0.001 TRP A 643 HIS 0.004 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00476 (15981) covalent geometry : angle 0.53741 (21825) hydrogen bonds : bond 0.03644 ( 771) hydrogen bonds : angle 4.24327 ( 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: 25 poor density : 53 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8962 (tm) REVERT: A 421 ARG cc_start: 0.8043 (ttt180) cc_final: 0.7767 (ttt180) REVERT: A 1157 GLN cc_start: 0.8492 (mm-40) cc_final: 0.7969 (mp10) REVERT: B 366 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.7019 (t80) REVERT: B 389 GLN cc_start: 0.9261 (mp10) cc_final: 0.8967 (mp10) outliers start: 25 outliers final: 12 residues processed: 76 average time/residue: 0.6364 time to fit residues: 54.2558 Evaluate side-chains 66 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 550 THR Chi-restraints excluded: chain A residue 780 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 120 optimal weight: 0.0470 chunk 108 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 168 optimal weight: 0.0170 chunk 83 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.090521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.061613 restraints weight = 37442.164| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.86 r_work: 0.2903 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2427 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= 0.121 Angle : 0.494 8.891 21825 Z= 0.263 Chirality : 0.039 0.193 2394 Planarity : 0.003 0.037 2633 Dihedral : 17.056 171.175 2509 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.01 % Allowed : 12.60 % Favored : 86.39 % 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: 1.82 (0.21), residues: 1764 helix: 2.29 (0.18), residues: 810 sheet: 0.38 (0.33), residues: 261 loop : 0.33 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 573 TYR 0.026 0.001 TYR B 226 PHE 0.022 0.001 PHE A 362 TRP 0.023 0.001 TRP A 428 HIS 0.003 0.001 HIS A 799 Details of bonding type rmsd covalent geometry : bond 0.00273 (15981) covalent geometry : angle 0.49358 (21825) hydrogen bonds : bond 0.03130 ( 771) hydrogen bonds : angle 4.06139 ( 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 74 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.653 Fit side-chains REVERT: A 214 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8988 (tm) REVERT: A 288 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8176 (pp30) REVERT: A 1148 ASN cc_start: 0.9090 (p0) cc_final: 0.8300 (p0) REVERT: A 1157 GLN cc_start: 0.8440 (mm-40) cc_final: 0.7969 (mp10) REVERT: B 366 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.6991 (t80) REVERT: B 387 GLN cc_start: 0.9004 (mp10) cc_final: 0.8730 (mp10) REVERT: B 389 GLN cc_start: 0.9276 (mp10) cc_final: 0.8988 (mp10) REVERT: B 677 ARG cc_start: 0.8341 (tpp80) cc_final: 0.7742 (tpp-160) outliers start: 16 outliers final: 4 residues processed: 72 average time/residue: 0.6958 time to fit residues: 55.6409 Evaluate side-chains 60 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 288 GLN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 550 THR 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: 1.9990 chunk 175 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 111 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1021 ASN 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 = 0.088837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.059412 restraints weight = 37644.003| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.87 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: 0.8398 moved from start: 0.2446 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= 0.204 Angle : 0.535 7.946 21825 Z= 0.286 Chirality : 0.041 0.394 2394 Planarity : 0.004 0.038 2633 Dihedral : 17.165 172.125 2509 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.88 % Allowed : 13.11 % Favored : 86.01 % 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: 1.77 (0.21), residues: 1764 helix: 2.22 (0.18), residues: 806 sheet: 0.29 (0.32), residues: 275 loop : 0.38 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 386 TYR 0.013 0.001 TYR B 370 PHE 0.026 0.002 PHE A 362 TRP 0.037 0.001 TRP A 428 HIS 0.004 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00475 (15981) covalent geometry : angle 0.53550 (21825) hydrogen bonds : bond 0.03599 ( 771) hydrogen bonds : angle 4.18365 ( 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 68 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8952 (tm) REVERT: A 517 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8262 (mmtm) REVERT: A 1148 ASN cc_start: 0.9110 (p0) cc_final: 0.8392 (p0) REVERT: A 1157 GLN cc_start: 0.8406 (mm-40) cc_final: 0.7936 (mp10) REVERT: B 366 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6956 (t80) REVERT: B 387 GLN cc_start: 0.9018 (mp10) cc_final: 0.8779 (mp10) REVERT: B 389 GLN cc_start: 0.9273 (mp10) cc_final: 0.8982 (mp10) outliers start: 14 outliers final: 10 residues processed: 67 average time/residue: 0.7082 time to fit residues: 52.7669 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 : 0.649 ------------------------------------------------------------------------------- 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 517 LYS Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 633 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 136 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 98 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.090160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.061181 restraints weight = 37711.916| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.87 r_work: 0.2888 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2546 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= 0.130 Angle : 0.497 8.068 21825 Z= 0.266 Chirality : 0.039 0.180 2394 Planarity : 0.003 0.037 2633 Dihedral : 17.028 171.296 2509 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.95 % Allowed : 13.42 % Favored : 85.63 % 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: 1.85 (0.21), residues: 1764 helix: 2.29 (0.18), residues: 811 sheet: 0.42 (0.33), residues: 263 loop : 0.37 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 573 TYR 0.026 0.001 TYR B 226 PHE 0.022 0.001 PHE A 362 TRP 0.030 0.001 TRP A 428 HIS 0.003 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00298 (15981) covalent geometry : angle 0.49711 (21825) hydrogen bonds : bond 0.03171 ( 771) hydrogen bonds : angle 4.04022 ( 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 73 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8978 (tm) REVERT: A 288 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8192 (pp30) REVERT: A 1072 THR cc_start: 0.9055 (m) cc_final: 0.8644 (p) REVERT: A 1148 ASN cc_start: 0.9095 (p0) cc_final: 0.8357 (p0) REVERT: A 1157 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7959 (mp10) REVERT: B 366 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6942 (t80) REVERT: B 387 GLN cc_start: 0.9022 (mp10) cc_final: 0.8788 (mp10) REVERT: B 389 GLN cc_start: 0.9283 (mp10) cc_final: 0.9015 (mp10) REVERT: B 677 ARG cc_start: 0.8348 (tpp80) cc_final: 0.7768 (tpp-160) outliers start: 15 outliers final: 10 residues processed: 72 average time/residue: 0.6991 time to fit residues: 56.2587 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 : 0.664 ------------------------------------------------------------------------------- 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 504 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1024 VAL 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 142 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.089579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.060487 restraints weight = 37668.316| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.87 r_work: 0.2877 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15981 Z= 0.152 Angle : 0.511 8.704 21825 Z= 0.272 Chirality : 0.040 0.417 2394 Planarity : 0.004 0.062 2633 Dihedral : 17.034 171.516 2509 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.95 % Allowed : 13.48 % 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: 1.87 (0.21), residues: 1764 helix: 2.30 (0.18), residues: 809 sheet: 0.32 (0.32), residues: 276 loop : 0.44 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 386 TYR 0.019 0.001 TYR B 39 PHE 0.026 0.001 PHE A 425 TRP 0.028 0.001 TRP A 428 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00353 (15981) covalent geometry : angle 0.51063 (21825) hydrogen bonds : bond 0.03282 ( 771) hydrogen bonds : angle 4.10625 ( 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 75 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8976 (tm) REVERT: A 517 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8174 (mmtm) REVERT: A 1072 THR cc_start: 0.9050 (m) cc_final: 0.8632 (p) REVERT: A 1148 ASN cc_start: 0.9102 (p0) cc_final: 0.8384 (p0) REVERT: A 1157 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7950 (mp10) REVERT: B 366 TYR cc_start: 0.7458 (OUTLIER) cc_final: 0.6931 (t80) REVERT: B 387 GLN cc_start: 0.9032 (mp10) cc_final: 0.8795 (mp10) REVERT: B 389 GLN cc_start: 0.9287 (mp10) cc_final: 0.9013 (mp10) outliers start: 15 outliers final: 10 residues processed: 74 average time/residue: 0.7295 time to fit residues: 59.8152 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 : 0.664 ------------------------------------------------------------------------------- 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 780 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1024 VAL 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 178 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 106 optimal weight: 0.0770 chunk 96 optimal weight: 2.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.089602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.060570 restraints weight = 37558.679| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.86 r_work: 0.2881 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15981 Z= 0.149 Angle : 0.521 8.626 21825 Z= 0.277 Chirality : 0.039 0.184 2394 Planarity : 0.003 0.037 2633 Dihedral : 17.013 171.631 2509 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.01 % Allowed : 13.74 % Favored : 85.26 % 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: 1.88 (0.21), residues: 1764 helix: 2.31 (0.18), residues: 809 sheet: 0.29 (0.32), residues: 278 loop : 0.46 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 386 TYR 0.029 0.001 TYR B 226 PHE 0.024 0.001 PHE A 362 TRP 0.025 0.001 TRP A 428 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00344 (15981) covalent geometry : angle 0.52058 (21825) hydrogen bonds : bond 0.03280 ( 771) hydrogen bonds : angle 4.09737 ( 2125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5768.76 seconds wall clock time: 99 minutes 15.22 seconds (5955.22 seconds total)