Starting phenix.real_space_refine on Tue Sep 15 05:12:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6d73_7822/09_2026/6d73_7822.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d73_7822/09_2026/6d73_7822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6d73_7822/09_2026/6d73_7822.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6d73_7822/09_2026/6d73_7822.cif" model { file = "/net/cci-nas-00/data/ceres_data/6d73_7822/09_2026/6d73_7822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d73_7822/09_2026/6d73_7822.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6d73_7822/09_2026/6d73_7822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d73_7822/09_2026/6d73_7822.map" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 148 5.16 5 C 22892 2.51 5 N 6182 2.21 5 O 6114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35340 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 7490 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 246} Link IDs: {'PTRANS': 34, 'TRANS': 995} Chain breaks: 7 Unresolved non-hydrogen bonds: 872 Unresolved non-hydrogen angles: 1077 Unresolved non-hydrogen dihedrals: 690 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLU:plan': 50, 'GLN:plan1': 16, 'ASP:plan': 32, 'ARG:plan': 18, 'HIS:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 10, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 542 Chain: "B" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1402 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 14, 'TRANS': 211} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 535 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'UNK:plan-1': 22, 'GLU:plan': 14, 'HIS:plan': 6, 'ASP:plan': 7, 'ARG:plan': 11, 'ASN:plan1': 3, 'GLN:plan1': 8, 'PHE:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 247 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7470 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 238} Link IDs: {'PTRANS': 32, 'TRANS': 993} Chain breaks: 5 Unresolved non-hydrogen bonds: 861 Unresolved non-hydrogen angles: 1063 Unresolved non-hydrogen dihedrals: 686 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLU:plan': 49, 'TRP:plan': 1, 'ASP:plan': 30, 'ARG:plan': 18, 'HIS:plan': 3, 'GLN:plan1': 20, 'ASN:plan1': 14, 'TYR:plan': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 560 Chain: "A" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1306 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 8 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'UNK:plan-1': 22, 'ASP:plan': 5, 'GLU:plan': 6, 'HIS:plan': 3, 'ARG:plan': 11, 'GLN:plan1': 6, 'ASN:plan1': 6, 'TYR:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 205 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, C Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N GLU B1272 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU B1272 " occ=0.50 residue: pdb=" N VAL B1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL B1400 " occ=0.50 residue: pdb=" N ARG B1447 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG B1447 " occ=0.50 residue: pdb=" N GLU A1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU A1272 " occ=0.50 residue: pdb=" N VAL A1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL A1287 " occ=0.50 residue: pdb=" N VAL A1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL A1400 " occ=0.50 residue: pdb=" N GLU C1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU C1272 " occ=0.50 residue: pdb=" N VAL C1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL C1287 " occ=0.50 residue: pdb=" N VAL C1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL C1400 " occ=0.50 residue: pdb=" N GLU D1272 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU D1272 " occ=0.50 residue: pdb=" N VAL D1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL D1400 " occ=0.50 residue: pdb=" N ARG D1447 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG D1447 " occ=0.50 Time building chain proxies: 23.11, per 1000 atoms: 0.65 Number of scatterers: 35340 At special positions: 0 Unit cell: (161, 154.1, 175.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 148 16.00 O 6114 8.00 N 6182 7.00 C 22892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B1012 " - pdb=" SG CYS B1024 " distance=2.04 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A1012 " - pdb=" SG CYS A1024 " distance=2.02 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D 326 " distance=2.03 Simple disulfide: pdb=" SG CYS D1012 " - pdb=" SG CYS D1024 " distance=2.03 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C 326 " distance=2.03 Simple disulfide: pdb=" SG CYS C1012 " - pdb=" SG CYS C1024 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.7 seconds 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9412 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 14 sheets defined 61.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'B' and resid 40 through 48 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 159 through 176 removed outlier: 4.044A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.644A pdb=" N HIS B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.611A pdb=" N LEU B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ARG B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 321 Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 371 through 387 Processing helix chain 'B' and resid 404 through 419 removed outlier: 3.672A pdb=" N ALA B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 439 removed outlier: 4.457A pdb=" N TRP B 428 " --> pdb=" O GLY B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 448 removed outlier: 3.971A pdb=" N ALA B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 459 Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.555A pdb=" N GLY B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 482 removed outlier: 3.616A pdb=" N VAL B 476 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 Processing helix chain 'B' and resid 492 through 502 removed outlier: 3.987A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 535 through 548 removed outlier: 3.984A pdb=" N VAL B 539 " --> pdb=" O CYS B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 605 Processing helix chain 'B' and resid 607 through 618 Processing helix chain 'B' and resid 620 through 638 Processing helix chain 'B' and resid 644 through 672 removed outlier: 3.703A pdb=" N ASP B 672 " --> pdb=" O CYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 681 Processing helix chain 'B' and resid 692 through 699 Processing helix chain 'B' and resid 707 through 720 Processing helix chain 'B' and resid 727 through 737 removed outlier: 3.619A pdb=" N PHE B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 745 Processing helix chain 'B' and resid 748 through 765 removed outlier: 3.635A pdb=" N GLU B 752 " --> pdb=" O PHE B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 807 Processing helix chain 'B' and resid 808 through 833 Processing helix chain 'B' and resid 840 through 864 removed outlier: 3.839A pdb=" N ASP B 864 " --> pdb=" O GLN B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 879 Processing helix chain 'B' and resid 881 through 901 Processing helix chain 'B' and resid 904 through 931 Processing helix chain 'B' and resid 936 through 973 removed outlier: 3.688A pdb=" N ILE B 941 " --> pdb=" O GLY B 937 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE B 942 " --> pdb=" O PRO B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 996 removed outlier: 5.794A pdb=" N GLU B 989 " --> pdb=" O GLY B 985 " (cutoff:3.500A) Proline residue: B 990 - end of helix removed outlier: 3.898A pdb=" N GLY B 996 " --> pdb=" O ILE B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1071 Processing helix chain 'B' and resid 1073 through 1092 removed outlier: 3.575A pdb=" N ILE B1077 " --> pdb=" O ASN B1073 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B1079 " --> pdb=" O ASP B1075 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B1091 " --> pdb=" O LYS B1087 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B1092 " --> pdb=" O GLU B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1114 removed outlier: 4.460A pdb=" N LEU B1102 " --> pdb=" O PRO B1098 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B1112 " --> pdb=" O PHE B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1157 Processing helix chain 'B' and resid 1158 through 1184 Processing helix chain 'B' and resid 1189 through 1209 Processing helix chain 'B' and resid 1252 through 1256 removed outlier: 3.567A pdb=" N GLN B1256 " --> pdb=" O PHE B1253 " (cutoff:3.500A) Processing helix chain 'B' and resid 1370 through 1381 Processing helix chain 'B' and resid 1427 through 1433 removed outlier: 3.794A pdb=" N MET B1433 " --> pdb=" O ASP B1429 " (cutoff:3.500A) Processing helix chain 'B' and resid 1437 through 1441 removed outlier: 3.574A pdb=" N SER B1440 " --> pdb=" O SER B1437 " (cutoff:3.500A) Processing helix chain 'B' and resid 1456 through 1470 removed outlier: 3.641A pdb=" N ILE B1466 " --> pdb=" O ALA B1462 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B1467 " --> pdb=" O LEU B1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 48 removed outlier: 3.663A pdb=" N ASN A 47 " --> pdb=" O TRP A 43 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 159 through 177 Processing helix chain 'A' and resid 189 through 202 removed outlier: 3.877A pdb=" N HIS A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.819A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 344 removed outlier: 3.928A pdb=" N SER A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 363 through 371 removed outlier: 5.058A pdb=" N ASN A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 371 " --> pdb=" O TYR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 387 Processing helix chain 'A' and resid 404 through 421 removed outlier: 4.164A pdb=" N ALA A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 439 removed outlier: 4.305A pdb=" N ARG A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 448 removed outlier: 3.894A pdb=" N ALA A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 removed outlier: 3.582A pdb=" N LEU A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) Proline residue: A 462 - end of helix removed outlier: 3.780A pdb=" N GLY A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 481 Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.804A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 removed outlier: 3.537A pdb=" N ARG A 510 " --> pdb=" O CYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 548 Processing helix chain 'A' and resid 593 through 606 removed outlier: 3.634A pdb=" N ASP A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 598 " --> pdb=" O PRO A 594 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 599 " --> pdb=" O GLY A 595 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 Processing helix chain 'A' and resid 620 through 638 Processing helix chain 'A' and resid 643 through 672 Processing helix chain 'A' and resid 673 through 682 removed outlier: 3.551A pdb=" N ARG A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 699 removed outlier: 3.534A pdb=" N LEU A 695 " --> pdb=" O THR A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.584A pdb=" N ILE A 705 " --> pdb=" O ASP A 701 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 701 through 706' Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 727 through 737 removed outlier: 3.521A pdb=" N PHE A 737 " --> pdb=" O LEU A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 removed outlier: 3.749A pdb=" N ILE A 741 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 742 " --> pdb=" O PRO A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 763 Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 808 through 833 Processing helix chain 'A' and resid 840 through 863 Processing helix chain 'A' and resid 868 through 876 removed outlier: 4.012A pdb=" N ARG A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 901 removed outlier: 3.874A pdb=" N LEU A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 926 removed outlier: 3.616A pdb=" N ILE A 920 " --> pdb=" O CYS A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 929 No H-bonds generated for 'chain 'A' and resid 927 through 929' Processing helix chain 'A' and resid 936 through 973 removed outlier: 3.587A pdb=" N ARG A 945 " --> pdb=" O ILE A 941 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU A 948 " --> pdb=" O ARG A 944 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP A 949 " --> pdb=" O ARG A 945 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 953 " --> pdb=" O ASP A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 996 removed outlier: 4.956A pdb=" N GLU A 989 " --> pdb=" O GLY A 985 " (cutoff:3.500A) Proline residue: A 990 - end of helix removed outlier: 3.538A pdb=" N ILE A 994 " --> pdb=" O PRO A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1002 Processing helix chain 'A' and resid 1036 through 1068 removed outlier: 4.047A pdb=" N TYR A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A1066 " --> pdb=" O ILE A1062 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A1068 " --> pdb=" O ASN A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1092 removed outlier: 4.485A pdb=" N TYR A1083 " --> pdb=" O LYS A1079 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU A1084 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1114 removed outlier: 5.175A pdb=" N LEU A1102 " --> pdb=" O PRO A1098 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A1103 " --> pdb=" O PHE A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1157 Processing helix chain 'A' and resid 1158 through 1182 Processing helix chain 'A' and resid 1189 through 1208 Processing helix chain 'A' and resid 1270 through 1275 removed outlier: 3.704A pdb=" N SER A1275 " --> pdb=" O GLU A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1381 Processing helix chain 'A' and resid 1456 through 1467 Processing helix chain 'C' and resid 41 through 48 removed outlier: 3.663A pdb=" N ASN C 47 " --> pdb=" O TRP C 43 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE C 48 " --> pdb=" O ILE C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 159 through 177 Processing helix chain 'C' and resid 189 through 202 removed outlier: 3.877A pdb=" N HIS C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.819A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 344 removed outlier: 3.929A pdb=" N SER C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 363 through 371 removed outlier: 5.058A pdb=" N ASN C 369 " --> pdb=" O GLN C 365 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 387 Processing helix chain 'C' and resid 404 through 421 removed outlier: 4.165A pdb=" N ALA C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 439 removed outlier: 4.305A pdb=" N ARG C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 448 removed outlier: 3.893A pdb=" N ALA C 444 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.583A pdb=" N LEU C 460 " --> pdb=" O THR C 456 " (cutoff:3.500A) Proline residue: C 462 - end of helix removed outlier: 3.781A pdb=" N GLY C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 481 Processing helix chain 'C' and resid 485 through 490 Processing helix chain 'C' and resid 492 through 501 removed outlier: 3.804A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 517 removed outlier: 3.537A pdb=" N ARG C 510 " --> pdb=" O CYS C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 548 Processing helix chain 'C' and resid 593 through 606 removed outlier: 3.634A pdb=" N ASP C 597 " --> pdb=" O ASP C 593 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 599 " --> pdb=" O GLY C 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 618 Processing helix chain 'C' and resid 620 through 638 Processing helix chain 'C' and resid 643 through 672 Processing helix chain 'C' and resid 673 through 682 removed outlier: 3.551A pdb=" N ARG C 682 " --> pdb=" O LYS C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 699 removed outlier: 3.534A pdb=" N LEU C 695 " --> pdb=" O THR C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 706 removed outlier: 3.585A pdb=" N ILE C 705 " --> pdb=" O ASP C 701 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 706 " --> pdb=" O LYS C 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 701 through 706' Processing helix chain 'C' and resid 707 through 719 Processing helix chain 'C' and resid 727 through 737 removed outlier: 3.521A pdb=" N PHE C 737 " --> pdb=" O LEU C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 removed outlier: 3.749A pdb=" N ILE C 741 " --> pdb=" O PHE C 738 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR C 742 " --> pdb=" O PRO C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 Processing helix chain 'C' and resid 799 through 807 Processing helix chain 'C' and resid 808 through 833 Processing helix chain 'C' and resid 840 through 863 Processing helix chain 'C' and resid 868 through 876 removed outlier: 4.012A pdb=" N ARG C 872 " --> pdb=" O SER C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 901 removed outlier: 3.875A pdb=" N LEU C 885 " --> pdb=" O LEU C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 926 removed outlier: 3.615A pdb=" N ILE C 920 " --> pdb=" O CYS C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 929 No H-bonds generated for 'chain 'C' and resid 927 through 929' Processing helix chain 'C' and resid 936 through 973 removed outlier: 3.586A pdb=" N ARG C 945 " --> pdb=" O ILE C 941 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP C 949 " --> pdb=" O ARG C 945 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 953 " --> pdb=" O ASP C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 996 removed outlier: 4.955A pdb=" N GLU C 989 " --> pdb=" O GLY C 985 " (cutoff:3.500A) Proline residue: C 990 - end of helix removed outlier: 3.538A pdb=" N ILE C 994 " --> pdb=" O PRO C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1002 Processing helix chain 'C' and resid 1036 through 1068 removed outlier: 4.048A pdb=" N TYR C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR C1066 " --> pdb=" O ILE C1062 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN C1068 " --> pdb=" O ASN C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1092 removed outlier: 4.485A pdb=" N TYR C1083 " --> pdb=" O LYS C1079 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU C1084 " --> pdb=" O PHE C1080 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG C1092 " --> pdb=" O GLU C1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 1096 through 1114 removed outlier: 5.176A pdb=" N LEU C1102 " --> pdb=" O PRO C1098 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER C1103 " --> pdb=" O PHE C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1157 Processing helix chain 'C' and resid 1158 through 1182 Processing helix chain 'C' and resid 1189 through 1208 Processing helix chain 'C' and resid 1270 through 1275 removed outlier: 3.703A pdb=" N SER C1275 " --> pdb=" O GLU C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1370 through 1381 Processing helix chain 'C' and resid 1456 through 1467 Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 159 through 176 removed outlier: 4.044A pdb=" N THR D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.646A pdb=" N HIS D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'D' and resid 273 through 287 removed outlier: 3.611A pdb=" N LEU D 277 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARG D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 321 Processing helix chain 'D' and resid 334 through 341 Processing helix chain 'D' and resid 351 through 363 Processing helix chain 'D' and resid 366 through 370 Processing helix chain 'D' and resid 371 through 387 Processing helix chain 'D' and resid 404 through 419 removed outlier: 3.670A pdb=" N ALA D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 439 removed outlier: 4.457A pdb=" N TRP D 428 " --> pdb=" O GLY D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 448 removed outlier: 3.972A pdb=" N ALA D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 459 Processing helix chain 'D' and resid 460 through 470 removed outlier: 3.554A pdb=" N GLY D 470 " --> pdb=" O SER D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 482 removed outlier: 3.617A pdb=" N VAL D 476 " --> pdb=" O LYS D 472 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 490 Processing helix chain 'D' and resid 492 through 502 removed outlier: 3.987A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 517 Processing helix chain 'D' and resid 535 through 548 removed outlier: 3.984A pdb=" N VAL D 539 " --> pdb=" O CYS D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 605 Processing helix chain 'D' and resid 607 through 618 Processing helix chain 'D' and resid 620 through 638 Processing helix chain 'D' and resid 644 through 672 removed outlier: 3.702A pdb=" N ASP D 672 " --> pdb=" O CYS D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 681 Processing helix chain 'D' and resid 692 through 699 Processing helix chain 'D' and resid 707 through 720 Processing helix chain 'D' and resid 727 through 737 removed outlier: 3.619A pdb=" N PHE D 737 " --> pdb=" O LEU D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 745 Processing helix chain 'D' and resid 748 through 765 removed outlier: 3.636A pdb=" N GLU D 752 " --> pdb=" O PHE D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 807 Processing helix chain 'D' and resid 808 through 833 Processing helix chain 'D' and resid 840 through 864 removed outlier: 3.839A pdb=" N ASP D 864 " --> pdb=" O GLN D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 879 Processing helix chain 'D' and resid 881 through 901 Processing helix chain 'D' and resid 904 through 931 Processing helix chain 'D' and resid 936 through 973 removed outlier: 3.688A pdb=" N ILE D 941 " --> pdb=" O GLY D 937 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE D 942 " --> pdb=" O PRO D 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 996 removed outlier: 5.795A pdb=" N GLU D 989 " --> pdb=" O GLY D 985 " (cutoff:3.500A) Proline residue: D 990 - end of helix removed outlier: 3.897A pdb=" N GLY D 996 " --> pdb=" O ILE D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1036 through 1071 Processing helix chain 'D' and resid 1073 through 1092 removed outlier: 3.575A pdb=" N ILE D1077 " --> pdb=" O ASN D1073 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS D1079 " --> pdb=" O ASP D1075 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER D1091 " --> pdb=" O LYS D1087 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D1092 " --> pdb=" O GLU D1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 1096 through 1114 removed outlier: 4.460A pdb=" N LEU D1102 " --> pdb=" O PRO D1098 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D1112 " --> pdb=" O PHE D1108 " (cutoff:3.500A) Processing helix chain 'D' and resid 1129 through 1157 Processing helix chain 'D' and resid 1158 through 1184 Processing helix chain 'D' and resid 1189 through 1209 Processing helix chain 'D' and resid 1252 through 1256 removed outlier: 3.568A pdb=" N GLN D1256 " --> pdb=" O PHE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1370 through 1381 Processing helix chain 'D' and resid 1427 through 1433 removed outlier: 3.795A pdb=" N MET D1433 " --> pdb=" O ASP D1429 " (cutoff:3.500A) Processing helix chain 'D' and resid 1437 through 1441 removed outlier: 3.573A pdb=" N SER D1440 " --> pdb=" O SER D1437 " (cutoff:3.500A) Processing helix chain 'D' and resid 1456 through 1470 removed outlier: 3.641A pdb=" N ILE D1466 " --> pdb=" O ALA D1462 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D1467 " --> pdb=" O LEU D1463 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 49 through 52 Processing sheet with id=AA2, first strand: chain 'B' and resid 237 through 240 removed outlier: 6.117A pdb=" N ILE B 181 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 217 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR B 183 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE B 147 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N GLY B 184 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N VAL B 149 " --> pdb=" O GLY B 184 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N CYS B 326 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE B 395 " --> pdb=" O CYS B 326 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL B 328 " --> pdb=" O PHE B 395 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1324 through 1329 removed outlier: 3.578A pdb=" N HIS B1329 " --> pdb=" O SER B1414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1357 through 1358 removed outlier: 3.663A pdb=" N ALA B1357 " --> pdb=" O VAL B1348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.877A pdb=" N TYR A 240 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS A 117 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU A 262 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 119 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ASP A 264 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A 121 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A 214 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU A 261 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY A 216 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL A 263 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA A 218 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A 181 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 217 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR A 183 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE A 147 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLY A 184 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N VAL A 149 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU A 146 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL A 304 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A 148 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N VAL A 327 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS A 326 " --> pdb=" O THR A 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1361 through 1362 removed outlier: 5.610A pdb=" N GLY A1323 " --> pdb=" O TRP A1410 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU A1412 " --> pdb=" O GLY A1323 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASN A1325 " --> pdb=" O GLU A1412 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N SER A1414 " --> pdb=" O ASN A1325 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE A1327 " --> pdb=" O SER A1414 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE A1416 " --> pdb=" O ILE A1327 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N HIS A1329 " --> pdb=" O ILE A1416 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU A1418 " --> pdb=" O HIS A1329 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE A1331 " --> pdb=" O LEU A1418 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL A1411 " --> pdb=" O TYR A1399 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TYR A1399 " --> pdb=" O VAL A1411 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR A1413 " --> pdb=" O LYS A1397 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS A1397 " --> pdb=" O THR A1413 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A1415 " --> pdb=" O VAL A1395 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1361 through 1362 removed outlier: 5.990A pdb=" N PHE A1332 " --> pdb=" O LEU A1346 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A1346 " --> pdb=" O PHE A1332 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 237 through 240 removed outlier: 3.877A pdb=" N TYR C 240 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS C 117 " --> pdb=" O PHE C 260 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU C 262 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C 119 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASP C 264 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 121 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 214 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU C 261 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY C 216 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL C 263 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA C 218 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE C 181 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL C 217 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR C 183 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE C 147 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLY C 184 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N VAL C 149 " --> pdb=" O GLY C 184 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C 146 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL C 304 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER C 148 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N VAL C 327 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS C 326 " --> pdb=" O THR C 393 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1361 through 1362 removed outlier: 5.610A pdb=" N GLY C1323 " --> pdb=" O TRP C1410 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLU C1412 " --> pdb=" O GLY C1323 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASN C1325 " --> pdb=" O GLU C1412 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N SER C1414 " --> pdb=" O ASN C1325 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C1327 " --> pdb=" O SER C1414 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE C1416 " --> pdb=" O ILE C1327 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N HIS C1329 " --> pdb=" O ILE C1416 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU C1418 " --> pdb=" O HIS C1329 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE C1331 " --> pdb=" O LEU C1418 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL C1411 " --> pdb=" O TYR C1399 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TYR C1399 " --> pdb=" O VAL C1411 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR C1413 " --> pdb=" O LYS C1397 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS C1397 " --> pdb=" O THR C1413 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE C1415 " --> pdb=" O VAL C1395 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 1361 through 1362 removed outlier: 5.991A pdb=" N PHE C1332 " --> pdb=" O LEU C1346 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C1346 " --> pdb=" O PHE C1332 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 49 through 52 Processing sheet with id=AB3, first strand: chain 'D' and resid 237 through 240 removed outlier: 6.117A pdb=" N ILE D 181 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL D 217 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR D 183 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE D 147 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N GLY D 184 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N VAL D 149 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N CYS D 326 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE D 395 " --> pdb=" O CYS D 326 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL D 328 " --> pdb=" O PHE D 395 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 1324 through 1329 removed outlier: 3.578A pdb=" N HIS D1329 " --> pdb=" O SER D1414 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 1357 through 1358 removed outlier: 3.663A pdb=" N ALA D1357 " --> pdb=" O VAL D1348 " (cutoff:3.500A) 2165 hydrogen bonds defined for protein. 6369 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.42 Time building geometry restraints manager: 4.15 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: 11415 1.34 - 1.46: 8917 1.46 - 1.58: 15624 1.58 - 1.70: 0 1.70 - 1.82: 212 Bond restraints: 36168 Sorted by residual: bond pdb=" C SER A1281 " pdb=" N PRO A1282 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.62e+00 bond pdb=" C SER C1281 " pdb=" N PRO C1282 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.54e+00 bond pdb=" CB VAL C 604 " pdb=" CG1 VAL C 604 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 4.99e+00 bond pdb=" CB VAL A 604 " pdb=" CG1 VAL A 604 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.94e+00 bond pdb=" CG LEU A 926 " pdb=" CD1 LEU A 926 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.20e+00 ... (remaining 36163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 48664 3.25 - 6.50: 732 6.50 - 9.75: 116 9.75 - 13.00: 16 13.00 - 16.24: 4 Bond angle restraints: 49532 Sorted by residual: angle pdb=" N GLY D 272 " pdb=" CA GLY D 272 " pdb=" C GLY D 272 " ideal model delta sigma weight residual 113.24 129.48 -16.24 1.31e+00 5.83e-01 1.54e+02 angle pdb=" N GLY B 272 " pdb=" CA GLY B 272 " pdb=" C GLY B 272 " ideal model delta sigma weight residual 113.24 129.42 -16.18 1.31e+00 5.83e-01 1.53e+02 angle pdb=" N HIS B 502 " pdb=" CA HIS B 502 " pdb=" C HIS B 502 " ideal model delta sigma weight residual 112.92 123.83 -10.91 1.23e+00 6.61e-01 7.86e+01 angle pdb=" N HIS D 502 " pdb=" CA HIS D 502 " pdb=" C HIS D 502 " ideal model delta sigma weight residual 112.92 123.80 -10.88 1.23e+00 6.61e-01 7.83e+01 angle pdb=" N VAL D 273 " pdb=" CA VAL D 273 " pdb=" C VAL D 273 " ideal model delta sigma weight residual 110.62 118.08 -7.46 1.02e+00 9.61e-01 5.36e+01 ... (remaining 49527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.64: 19521 14.64 - 29.27: 1083 29.27 - 43.91: 278 43.91 - 58.54: 34 58.54 - 73.18: 6 Dihedral angle restraints: 20922 sinusoidal: 6470 harmonic: 14452 Sorted by residual: dihedral pdb=" CA SER C1013 " pdb=" C SER C1013 " pdb=" N VAL C1014 " pdb=" CA VAL C1014 " ideal model delta harmonic sigma weight residual -180.00 -122.19 -57.81 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA SER A1013 " pdb=" C SER A1013 " pdb=" N VAL A1014 " pdb=" CA VAL A1014 " ideal model delta harmonic sigma weight residual -180.00 -122.19 -57.81 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA LYS C1021 " pdb=" C LYS C1021 " pdb=" N PRO C1022 " pdb=" CA PRO C1022 " ideal model delta harmonic sigma weight residual -180.00 -138.99 -41.01 0 5.00e+00 4.00e-02 6.73e+01 ... (remaining 20919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 4949 0.075 - 0.150: 809 0.150 - 0.225: 100 0.225 - 0.301: 18 0.301 - 0.376: 4 Chirality restraints: 5880 Sorted by residual: chirality pdb=" CA HIS D 502 " pdb=" N HIS D 502 " pdb=" C HIS D 502 " pdb=" CB HIS D 502 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA HIS B 502 " pdb=" N HIS B 502 " pdb=" C HIS B 502 " pdb=" CB HIS B 502 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA LYS B 154 " pdb=" N LYS B 154 " pdb=" C LYS B 154 " pdb=" CB LYS B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 5877 not shown) Planarity restraints: 6272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B1084 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C GLU B1084 " 0.056 2.00e-02 2.50e+03 pdb=" O GLU B1084 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B1085 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D1084 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C GLU D1084 " 0.056 2.00e-02 2.50e+03 pdb=" O GLU D1084 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU D1085 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B1087 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C LYS B1087 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS B1087 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU B1088 " -0.018 2.00e-02 2.50e+03 ... (remaining 6269 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 2 2.12 - 2.81: 10123 2.81 - 3.51: 48347 3.51 - 4.20: 78096 4.20 - 4.90: 132713 Nonbonded interactions: 269281 Sorted by model distance: nonbonded pdb=" OG SER C 348 " pdb=" OE1 GLU C1271 " model vdw 1.420 3.040 nonbonded pdb=" OG SER A 348 " pdb=" OE1 GLU A1271 " model vdw 1.421 3.040 nonbonded pdb=" O TYR C 367 " pdb=" CG2 THR C 371 " model vdw 2.179 3.460 nonbonded pdb=" O TYR A 367 " pdb=" CG2 THR A 371 " model vdw 2.180 3.460 nonbonded pdb=" O VAL C 301 " pdb=" OG1 THR C 324 " model vdw 2.221 3.040 ... (remaining 269276 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: 0.05 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 2.920 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 48.480 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 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 : 0.007 0.083 36176 Z= 0.295 Angle : 1.043 16.245 49548 Z= 0.577 Chirality : 0.057 0.376 5880 Planarity : 0.007 0.062 6272 Dihedral : 10.450 73.176 11486 Min Nonbonded Distance : 1.420 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.42 % Favored : 93.50 % Rotamer: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.04 % 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: -3.78 (0.10), residues: 4770 helix: -2.25 (0.07), residues: 2734 sheet: -1.36 (0.29), residues: 346 loop : -2.93 (0.13), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1092 TYR 0.035 0.003 TYR B 847 PHE 0.033 0.003 PHE A 827 TRP 0.047 0.003 TRP B 815 HIS 0.028 0.002 HIS D 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.30 (36168) covalent geometry : angle 1.04158 / 0.58 (49532) SS BOND : bond 0.00466 / 0.30 ( 8) SS BOND : angle 3.23238 / 2.10 ( 16) hydrogen bonds : bond 0.13014 / 8.79 ( 2161) hydrogen bonds : angle 6.35622 / 4.64 ( 6369) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 497 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 394 VAL cc_start: 0.8546 (t) cc_final: 0.8251 (m) REVERT: B 1176 LEU cc_start: 0.8778 (tt) cc_final: 0.8252 (mm) REVERT: D 394 VAL cc_start: 0.8598 (t) cc_final: 0.8321 (m) outliers start: 2 outliers final: 0 residues processed: 498 average time/residue: 0.2095 time to fit residues: 173.7005 Evaluate side-chains 235 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 7.9990 chunk 470 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 187 HIS B 256 ASN B 259 HIS B 268 GLN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 HIS B 707 HIS B 716 GLN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1001 ASN B1090 HIS ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1146 ASN B1161 HIS A 129 ASN A 187 HIS A 224 HIS A 256 ASN A 259 HIS A 268 GLN A 314 ASN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 655 ASN A 707 HIS A1073 ASN A1081 GLN A1121 HIS A1146 ASN A1157 GLN C 129 ASN C 187 HIS C 256 ASN C 259 HIS C 268 GLN C 314 ASN ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 816 ASN C1073 ASN C1081 GLN C1121 HIS C1146 ASN C1157 GLN ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN D 187 HIS D 256 ASN D 259 HIS D 268 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 HIS D 707 HIS D 716 GLN ** D 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1001 ASN D1090 HIS ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1146 ASN D1161 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.081731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.065457 restraints weight = 186000.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.066931 restraints weight = 100227.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.067896 restraints weight = 65675.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.068459 restraints weight = 49179.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.068901 restraints weight = 40864.951| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 36176 Z= 0.220 Angle : 0.694 10.049 49548 Z= 0.365 Chirality : 0.042 0.180 5880 Planarity : 0.005 0.056 6272 Dihedral : 5.410 36.199 5224 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.62 % Favored : 94.34 % Rotamer: Outliers : 3.06 % Allowed : 10.94 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.04 % 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 (0.12), residues: 4770 helix: -0.05 (0.09), residues: 2742 sheet: -1.67 (0.27), residues: 358 loop : -2.65 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 477 TYR 0.025 0.002 TYR D 555 PHE 0.025 0.002 PHE C 930 TRP 0.030 0.002 TRP C 981 HIS 0.009 0.002 HIS B1104 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 (36168) covalent geometry : angle 0.69407 / 0.37 (49532) SS BOND : bond 0.00388 / 0.25 ( 8) SS BOND : angle 1.31591 / 0.83 ( 16) hydrogen bonds : bond 0.04539 / 3.18 ( 2161) hydrogen bonds : angle 4.53350 / 3.31 ( 6369) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 245 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 394 VAL cc_start: 0.8978 (t) cc_final: 0.8707 (m) REVERT: B 475 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.8482 (t80) REVERT: B 1326 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.7940 (m-70) REVERT: A 191 MET cc_start: 0.8950 (mpp) cc_final: 0.8597 (mpp) REVERT: A 324 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8536 (t) REVERT: A 946 MET cc_start: 0.8233 (tmm) cc_final: 0.7679 (tmm) REVERT: A 1053 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9225 (tt) REVERT: A 1153 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7774 (tm-30) REVERT: A 1165 ASP cc_start: 0.9220 (t0) cc_final: 0.8939 (t0) REVERT: A 1177 LEU cc_start: 0.9022 (tp) cc_final: 0.8802 (tp) REVERT: C 183 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8991 (p) REVERT: C 191 MET cc_start: 0.9146 (mpp) cc_final: 0.8195 (mpp) REVERT: C 324 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8718 (t) REVERT: C 930 PHE cc_start: 0.8816 (m-80) cc_final: 0.8603 (m-80) REVERT: C 946 MET cc_start: 0.7969 (tmm) cc_final: 0.7291 (tmm) REVERT: D 394 VAL cc_start: 0.8922 (t) cc_final: 0.8645 (m) REVERT: D 475 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8569 (t80) REVERT: D 612 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8090 (tm-30) REVERT: D 1052 ASN cc_start: 0.9236 (OUTLIER) cc_final: 0.8979 (m-40) REVERT: D 1055 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9137 (tt) outliers start: 92 outliers final: 33 residues processed: 327 average time/residue: 0.1850 time to fit residues: 107.7615 Evaluate side-chains 252 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1163 ILE Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1326 HIS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1329 HIS Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1163 ILE Chi-restraints excluded: chain C residue 1329 HIS Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 1052 ASN Chi-restraints excluded: chain D residue 1055 LEU Chi-restraints excluded: chain D residue 1060 ILE Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1304 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 207 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 272 optimal weight: 2.9990 chunk 438 optimal weight: 2.9990 chunk 300 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 294 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN B1052 ASN ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 816 ASN ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 816 ASN ** D1104 HIS ** 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 = 0.3768 r_free = 0.3768 target = 0.081431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.065311 restraints weight = 186495.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.066748 restraints weight = 100474.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.067707 restraints weight = 66110.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.068306 restraints weight = 49626.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.068721 restraints weight = 40847.036| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36176 Z= 0.172 Angle : 0.621 18.242 49548 Z= 0.322 Chirality : 0.040 0.176 5880 Planarity : 0.004 0.058 6272 Dihedral : 4.916 31.329 5224 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.75 % Rotamer: Outliers : 3.43 % Allowed : 12.48 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.12), residues: 4770 helix: 0.88 (0.10), residues: 2726 sheet: -1.62 (0.27), residues: 364 loop : -2.44 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1404 TYR 0.023 0.002 TYR D 555 PHE 0.018 0.002 PHE A 919 TRP 0.037 0.001 TRP C 981 HIS 0.008 0.001 HIS B1104 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (36168) covalent geometry : angle 0.62100 / 0.32 (49532) SS BOND : bond 0.00421 / 0.27 ( 8) SS BOND : angle 1.02340 / 0.65 ( 16) hydrogen bonds : bond 0.04083 / 2.86 ( 2161) hydrogen bonds : angle 4.16138 / 3.04 ( 6369) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 232 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 394 VAL cc_start: 0.8896 (t) cc_final: 0.8610 (m) REVERT: B 475 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8437 (t80) REVERT: B 1100 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8355 (tp) REVERT: B 1418 LEU cc_start: 0.5228 (OUTLIER) cc_final: 0.4864 (pt) REVERT: A 946 MET cc_start: 0.8046 (tmm) cc_final: 0.7565 (tmm) REVERT: A 1153 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 1165 ASP cc_start: 0.9103 (t0) cc_final: 0.8883 (t0) REVERT: C 191 MET cc_start: 0.9108 (mpp) cc_final: 0.8170 (mpp) REVERT: C 946 MET cc_start: 0.7990 (tmm) cc_final: 0.7430 (tmm) REVERT: D 394 VAL cc_start: 0.8811 (t) cc_final: 0.8533 (m) REVERT: D 475 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8466 (t80) REVERT: D 612 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8079 (tm-30) REVERT: D 1418 LEU cc_start: 0.5142 (OUTLIER) cc_final: 0.4779 (pt) outliers start: 103 outliers final: 53 residues processed: 323 average time/residue: 0.1840 time to fit residues: 106.8972 Evaluate side-chains 261 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1326 HIS Chi-restraints excluded: chain B residue 1418 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 ILE Chi-restraints excluded: chain C residue 1163 ILE Chi-restraints excluded: chain C residue 1329 HIS Chi-restraints excluded: chain C residue 1358 LEU Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1304 HIS Chi-restraints excluded: chain D residue 1418 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 420 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 221 optimal weight: 8.9990 chunk 424 optimal weight: 5.9990 chunk 450 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 chunk 324 optimal weight: 0.9990 chunk 474 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN A 231 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.081095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.064886 restraints weight = 185700.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.066330 restraints weight = 100142.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.067303 restraints weight = 65743.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.067904 restraints weight = 49107.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.068339 restraints weight = 40557.517| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36176 Z= 0.162 Angle : 0.594 13.133 49548 Z= 0.308 Chirality : 0.039 0.171 5880 Planarity : 0.004 0.057 6272 Dihedral : 4.703 30.542 5224 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.04 % Favored : 93.92 % Rotamer: Outliers : 3.16 % Allowed : 14.14 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.12), residues: 4770 helix: 1.30 (0.10), residues: 2732 sheet: -1.62 (0.27), residues: 364 loop : -2.28 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 477 TYR 0.023 0.002 TYR D 555 PHE 0.016 0.002 PHE A 919 TRP 0.036 0.001 TRP C 981 HIS 0.008 0.001 HIS D1104 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (36168) covalent geometry : angle 0.59385 / 0.31 (49532) SS BOND : bond 0.00497 / 0.32 ( 8) SS BOND : angle 0.89033 / 0.58 ( 16) hydrogen bonds : bond 0.03901 / 2.72 ( 2161) hydrogen bonds : angle 4.02590 / 2.94 ( 6369) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 215 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 156 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8489 (p90) REVERT: B 394 VAL cc_start: 0.8880 (t) cc_final: 0.8587 (m) REVERT: B 475 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8543 (t80) REVERT: B 1100 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8374 (tp) REVERT: B 1418 LEU cc_start: 0.5311 (OUTLIER) cc_final: 0.4973 (pt) REVERT: A 946 MET cc_start: 0.8132 (tmm) cc_final: 0.7125 (tmm) REVERT: A 953 PHE cc_start: 0.8443 (m-80) cc_final: 0.8205 (m-80) REVERT: A 1165 ASP cc_start: 0.9245 (t0) cc_final: 0.9010 (t0) REVERT: C 191 MET cc_start: 0.9130 (mpp) cc_final: 0.8913 (mpp) REVERT: C 946 MET cc_start: 0.8026 (tmm) cc_final: 0.7404 (tmm) REVERT: C 995 PHE cc_start: 0.6165 (t80) cc_final: 0.5958 (t80) REVERT: C 1165 ASP cc_start: 0.9254 (t0) cc_final: 0.9034 (t0) REVERT: D 156 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8485 (p90) REVERT: D 394 VAL cc_start: 0.8868 (t) cc_final: 0.8572 (m) REVERT: D 475 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8581 (t80) REVERT: D 612 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8193 (tm-30) REVERT: D 1418 LEU cc_start: 0.5146 (OUTLIER) cc_final: 0.4685 (pt) outliers start: 95 outliers final: 54 residues processed: 302 average time/residue: 0.1784 time to fit residues: 96.7408 Evaluate side-chains 257 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1326 HIS Chi-restraints excluded: chain B residue 1418 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 ILE Chi-restraints excluded: chain C residue 1163 ILE Chi-restraints excluded: chain C residue 1329 HIS Chi-restraints excluded: chain C residue 1358 LEU Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 863 HIS Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1304 HIS Chi-restraints excluded: chain D residue 1418 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 469 optimal weight: 1.9990 chunk 399 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 chunk 324 optimal weight: 3.9990 chunk 444 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 325 optimal weight: 0.9990 chunk 270 optimal weight: 0.0050 chunk 341 optimal weight: 3.9990 chunk 409 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 GLN ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 HIS ** 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 = 0.3772 r_free = 0.3772 target = 0.081422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.065213 restraints weight = 185300.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.066693 restraints weight = 100599.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.067636 restraints weight = 65745.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.068185 restraints weight = 49227.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.068642 restraints weight = 41111.736| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36176 Z= 0.136 Angle : 0.566 13.107 49548 Z= 0.291 Chirality : 0.039 0.168 5880 Planarity : 0.004 0.057 6272 Dihedral : 4.512 32.553 5224 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.10 % Favored : 93.88 % Rotamer: Outliers : 3.46 % Allowed : 14.70 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.13), residues: 4770 helix: 1.57 (0.10), residues: 2738 sheet: -1.56 (0.27), residues: 362 loop : -2.21 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 477 TYR 0.021 0.001 TYR D 555 PHE 0.015 0.001 PHE C 919 TRP 0.014 0.001 TRP D 729 HIS 0.005 0.001 HIS C 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (36168) covalent geometry : angle 0.56570 / 0.29 (49532) SS BOND : bond 0.00697 / 0.39 ( 8) SS BOND : angle 0.83589 / 0.56 ( 16) hydrogen bonds : bond 0.03651 / 2.55 ( 2161) hydrogen bonds : angle 3.88824 / 2.84 ( 6369) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 210 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 394 VAL cc_start: 0.8910 (t) cc_final: 0.8627 (m) REVERT: B 475 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8542 (t80) REVERT: B 1100 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8334 (tp) REVERT: B 1418 LEU cc_start: 0.5332 (OUTLIER) cc_final: 0.4992 (pt) REVERT: A 637 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8648 (tm-30) REVERT: A 946 MET cc_start: 0.8121 (tmm) cc_final: 0.7140 (tmm) REVERT: A 953 PHE cc_start: 0.8417 (m-80) cc_final: 0.8206 (m-80) REVERT: A 991 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7989 (t80) REVERT: C 946 MET cc_start: 0.8135 (tmm) cc_final: 0.7225 (tmm) REVERT: C 991 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7989 (t80) REVERT: C 995 PHE cc_start: 0.6047 (t80) cc_final: 0.5840 (t80) REVERT: D 475 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8543 (t80) REVERT: D 1418 LEU cc_start: 0.5016 (OUTLIER) cc_final: 0.4575 (pt) outliers start: 104 outliers final: 62 residues processed: 305 average time/residue: 0.1871 time to fit residues: 101.6754 Evaluate side-chains 266 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 197 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1326 HIS Chi-restraints excluded: chain B residue 1418 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 ILE Chi-restraints excluded: chain C residue 1163 ILE Chi-restraints excluded: chain C residue 1329 HIS Chi-restraints excluded: chain C residue 1358 LEU Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 863 HIS Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 1055 LEU Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1304 HIS Chi-restraints excluded: chain D residue 1418 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 467 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 471 optimal weight: 6.9990 chunk 455 optimal weight: 0.0870 chunk 488 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 158 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 246 optimal weight: 9.9990 overall best weight: 3.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A1081 GLN C 47 ASN ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.079927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.063799 restraints weight = 186161.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.065199 restraints weight = 102393.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066022 restraints weight = 68079.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.066671 restraints weight = 52209.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.067021 restraints weight = 43240.342| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36176 Z= 0.196 Angle : 0.629 12.074 49548 Z= 0.325 Chirality : 0.040 0.171 5880 Planarity : 0.004 0.055 6272 Dihedral : 4.679 32.619 5224 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.67 % Favored : 93.29 % Rotamer: Outliers : 3.83 % Allowed : 15.60 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.13), residues: 4770 helix: 1.52 (0.10), residues: 2738 sheet: -1.59 (0.27), residues: 364 loop : -2.16 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1179 TYR 0.025 0.002 TYR D 555 PHE 0.017 0.002 PHE C 953 TRP 0.035 0.001 TRP C 981 HIS 0.006 0.001 HIS C 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (36168) covalent geometry : angle 0.62823 / 0.33 (49532) SS BOND : bond 0.00379 / 0.22 ( 8) SS BOND : angle 1.56151 / 1.08 ( 16) hydrogen bonds : bond 0.04043 / 2.84 ( 2161) hydrogen bonds : angle 4.09874 / 2.99 ( 6369) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 192 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 475 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8513 (t80) REVERT: B 1100 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8402 (tp) REVERT: A 191 MET cc_start: 0.9108 (mpp) cc_final: 0.8553 (mpp) REVERT: A 946 MET cc_start: 0.8062 (tmm) cc_final: 0.7413 (tmm) REVERT: A 991 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7951 (t80) REVERT: C 196 MET cc_start: 0.8960 (mmm) cc_final: 0.8745 (mmm) REVERT: C 946 MET cc_start: 0.8074 (tmm) cc_final: 0.7552 (tmm) REVERT: C 991 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7959 (t80) REVERT: C 995 PHE cc_start: 0.6064 (t80) cc_final: 0.5847 (t80) REVERT: D 475 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.8542 (t80) REVERT: D 1418 LEU cc_start: 0.5145 (OUTLIER) cc_final: 0.4701 (pt) outliers start: 115 outliers final: 74 residues processed: 302 average time/residue: 0.1782 time to fit residues: 97.7192 Evaluate side-chains 269 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 189 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 995 PHE Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1326 HIS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 ILE Chi-restraints excluded: chain C residue 1163 ILE Chi-restraints excluded: chain C residue 1358 LEU Chi-restraints excluded: chain C residue 1415 ILE Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 863 HIS Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 995 PHE Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1418 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 180 optimal weight: 8.9990 chunk 398 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 295 optimal weight: 0.9980 chunk 489 optimal weight: 20.0000 chunk 376 optimal weight: 2.9990 chunk 316 optimal weight: 6.9990 chunk 482 optimal weight: 40.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.078917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.062735 restraints weight = 187239.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.064123 restraints weight = 103017.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.065039 restraints weight = 68560.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.065567 restraints weight = 52059.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.065977 restraints weight = 43630.637| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 36176 Z= 0.236 Angle : 0.673 12.772 49548 Z= 0.348 Chirality : 0.041 0.174 5880 Planarity : 0.004 0.060 6272 Dihedral : 4.833 35.974 5224 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.11 % Favored : 92.83 % Rotamer: Outliers : 3.73 % Allowed : 16.63 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.13), residues: 4770 helix: 1.39 (0.10), residues: 2740 sheet: -1.71 (0.28), residues: 354 loop : -2.21 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 859 TYR 0.028 0.002 TYR D 555 PHE 0.028 0.002 PHE D 395 TRP 0.027 0.002 TRP C 981 HIS 0.005 0.001 HIS C 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.24 (36168) covalent geometry : angle 0.67300 / 0.35 (49532) SS BOND : bond 0.00459 / 0.30 ( 8) SS BOND : angle 1.58688 / 1.05 ( 16) hydrogen bonds : bond 0.04281 / 3.01 ( 2161) hydrogen bonds : angle 4.30901 / 3.14 ( 6369) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 190 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 475 PHE cc_start: 0.9223 (OUTLIER) cc_final: 0.8532 (t80) REVERT: B 1143 MET cc_start: 0.8998 (mmt) cc_final: 0.8635 (mmt) REVERT: B 1418 LEU cc_start: 0.5340 (OUTLIER) cc_final: 0.4960 (pt) REVERT: A 191 MET cc_start: 0.9132 (mpp) cc_final: 0.8543 (mpp) REVERT: A 946 MET cc_start: 0.8202 (tmm) cc_final: 0.7537 (tmm) REVERT: A 947 MET cc_start: 0.7528 (mmm) cc_final: 0.7284 (ttp) REVERT: A 991 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7996 (t80) REVERT: A 1358 LEU cc_start: -0.2451 (OUTLIER) cc_final: -0.2874 (mt) REVERT: C 191 MET cc_start: 0.9111 (mpp) cc_final: 0.8634 (mpp) REVERT: C 946 MET cc_start: 0.8118 (tmm) cc_final: 0.7480 (tmm) REVERT: C 991 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.8034 (t80) REVERT: D 475 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8516 (t80) REVERT: D 1418 LEU cc_start: 0.5283 (OUTLIER) cc_final: 0.4919 (pt) outliers start: 112 outliers final: 85 residues processed: 295 average time/residue: 0.1781 time to fit residues: 94.7312 Evaluate side-chains 277 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 185 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 995 PHE Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1173 MET Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1326 HIS Chi-restraints excluded: chain B residue 1418 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1012 CYS Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 821 PHE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1024 CYS Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 ILE Chi-restraints excluded: chain C residue 1163 ILE Chi-restraints excluded: chain C residue 1359 LEU Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 890 ILE Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 995 PHE Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1304 HIS Chi-restraints excluded: chain D residue 1418 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 135 optimal weight: 0.9980 chunk 278 optimal weight: 0.0570 chunk 58 optimal weight: 3.9990 chunk 419 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 225 optimal weight: 1.9990 chunk 369 optimal weight: 10.0000 chunk 284 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1081 GLN ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 HIS ** 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 = 0.3775 r_free = 0.3775 target = 0.081662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.065664 restraints weight = 185149.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.067078 restraints weight = 100185.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.068098 restraints weight = 66157.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.068687 restraints weight = 49462.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.069130 restraints weight = 40769.863| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36176 Z= 0.110 Angle : 0.558 12.447 49548 Z= 0.284 Chirality : 0.038 0.194 5880 Planarity : 0.004 0.053 6272 Dihedral : 4.404 28.826 5224 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.50 % Allowed : 17.70 % Favored : 79.81 % 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: 0.35 (0.13), residues: 4770 helix: 1.79 (0.10), residues: 2718 sheet: -1.63 (0.28), residues: 356 loop : -2.04 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1179 TYR 0.019 0.001 TYR D 555 PHE 0.035 0.001 PHE D 395 TRP 0.015 0.001 TRP C 981 HIS 0.005 0.001 HIS D1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (36168) covalent geometry : angle 0.55740 / 0.28 (49532) SS BOND : bond 0.00280 / 0.17 ( 8) SS BOND : angle 1.61661 / 1.08 ( 16) hydrogen bonds : bond 0.03466 / 2.41 ( 2161) hydrogen bonds : angle 3.83097 / 2.80 ( 6369) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 220 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 475 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8490 (t80) REVERT: B 1143 MET cc_start: 0.8986 (mmt) cc_final: 0.8442 (mmt) REVERT: B 1418 LEU cc_start: 0.5456 (OUTLIER) cc_final: 0.5129 (pt) REVERT: A 637 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8576 (tm-30) REVERT: A 946 MET cc_start: 0.8039 (tmm) cc_final: 0.7408 (tmm) REVERT: A 991 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7958 (t80) REVERT: A 1358 LEU cc_start: -0.2557 (OUTLIER) cc_final: -0.2948 (mt) REVERT: C 946 MET cc_start: 0.8037 (tmm) cc_final: 0.7413 (tmm) REVERT: C 991 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.8021 (t80) REVERT: C 1140 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8114 (tm-30) REVERT: D 475 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8410 (t80) REVERT: D 1418 LEU cc_start: 0.5246 (OUTLIER) cc_final: 0.4826 (pt) outliers start: 75 outliers final: 52 residues processed: 286 average time/residue: 0.1796 time to fit residues: 92.6582 Evaluate side-chains 265 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 995 PHE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1173 MET Chi-restraints excluded: chain B residue 1418 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1062 ILE Chi-restraints excluded: chain C residue 1359 LEU Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 995 PHE Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1418 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 384 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 274 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 464 optimal weight: 5.9990 chunk 371 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 chunk 212 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 259 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 47 ASN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.080046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.063881 restraints weight = 186989.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.065332 restraints weight = 101627.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.066179 restraints weight = 66967.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.066833 restraints weight = 51061.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.067257 restraints weight = 41907.860| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 36176 Z= 0.170 Angle : 0.606 13.172 49548 Z= 0.309 Chirality : 0.040 0.179 5880 Planarity : 0.004 0.057 6272 Dihedral : 4.431 29.938 5224 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.67 % Favored : 93.31 % Rotamer: Outliers : 2.69 % Allowed : 18.00 % Favored : 79.31 % 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: 0.32 (0.13), residues: 4770 helix: 1.75 (0.10), residues: 2732 sheet: -1.66 (0.28), residues: 356 loop : -2.04 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1092 TYR 0.024 0.002 TYR D 555 PHE 0.035 0.002 PHE D 395 TRP 0.018 0.001 TRP A 981 HIS 0.005 0.001 HIS A 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (36168) covalent geometry : angle 0.60548 / 0.31 (49532) SS BOND : bond 0.00689 / 0.46 ( 8) SS BOND : angle 1.76946 / 1.19 ( 16) hydrogen bonds : bond 0.03788 / 2.65 ( 2161) hydrogen bonds : angle 3.99000 / 2.91 ( 6369) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 201 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 475 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8449 (t80) REVERT: B 1418 LEU cc_start: 0.5416 (OUTLIER) cc_final: 0.5049 (pt) REVERT: A 946 MET cc_start: 0.8061 (tmm) cc_final: 0.7428 (tmm) REVERT: A 991 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7936 (t80) REVERT: A 1358 LEU cc_start: -0.2370 (OUTLIER) cc_final: -0.2772 (mt) REVERT: C 946 MET cc_start: 0.8035 (tmm) cc_final: 0.7395 (tmm) REVERT: C 991 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.8028 (t80) REVERT: D 475 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8494 (t80) REVERT: D 1418 LEU cc_start: 0.5200 (OUTLIER) cc_final: 0.4754 (pt) outliers start: 81 outliers final: 60 residues processed: 274 average time/residue: 0.1815 time to fit residues: 89.4893 Evaluate side-chains 263 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 196 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 995 PHE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1418 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 821 PHE Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1062 ILE Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 995 PHE Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1418 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 315 optimal weight: 8.9990 chunk 117 optimal weight: 50.0000 chunk 266 optimal weight: 9.9990 chunk 387 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 244 optimal weight: 30.0000 chunk 180 optimal weight: 9.9990 chunk 371 optimal weight: 5.9990 chunk 398 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 GLN ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 HIS D 656 HIS ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.077096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.061033 restraints weight = 191512.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.062353 restraints weight = 106763.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.063173 restraints weight = 71933.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.063760 restraints weight = 55253.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.064179 restraints weight = 46162.426| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 36176 Z= 0.349 Angle : 0.809 13.311 49548 Z= 0.419 Chirality : 0.045 0.226 5880 Planarity : 0.005 0.060 6272 Dihedral : 5.236 36.248 5224 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.11 % Favored : 91.84 % Rotamer: Outliers : 3.06 % Allowed : 17.53 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.12), residues: 4770 helix: 1.06 (0.10), residues: 2746 sheet: -1.71 (0.29), residues: 322 loop : -2.23 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1092 TYR 0.033 0.003 TYR D 555 PHE 0.039 0.003 PHE D 395 TRP 0.029 0.002 TRP C 981 HIS 0.008 0.002 HIS C1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.35 (36168) covalent geometry : angle 0.80796 / 0.42 (49532) SS BOND : bond 0.00673 / 0.47 ( 8) SS BOND : angle 2.14803 / 1.44 ( 16) hydrogen bonds : bond 0.05005 / 3.53 ( 2161) hydrogen bonds : angle 4.82026 / 3.50 ( 6369) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 182 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 475 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8481 (t80) REVERT: B 991 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8467 (m-10) REVERT: B 1143 MET cc_start: 0.8988 (mmt) cc_final: 0.8590 (mmt) REVERT: A 191 MET cc_start: 0.9178 (mpp) cc_final: 0.8933 (mpp) REVERT: A 946 MET cc_start: 0.8277 (tmm) cc_final: 0.7571 (tmm) REVERT: A 991 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.8030 (t80) REVERT: A 1043 MET cc_start: 0.9260 (ttp) cc_final: 0.9044 (mtp) REVERT: C 191 MET cc_start: 0.9211 (mpp) cc_final: 0.8944 (mpp) REVERT: C 946 MET cc_start: 0.8308 (tmm) cc_final: 0.7627 (tmm) REVERT: C 991 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.8063 (t80) REVERT: C 995 PHE cc_start: 0.6261 (t80) cc_final: 0.5992 (t80) REVERT: D 475 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8499 (t80) REVERT: D 991 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.8375 (m-10) REVERT: D 1418 LEU cc_start: 0.5418 (OUTLIER) cc_final: 0.5029 (pt) outliers start: 92 outliers final: 70 residues processed: 267 average time/residue: 0.1843 time to fit residues: 88.6219 Evaluate side-chains 254 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 177 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 995 PHE Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1024 CYS Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1400 VAL Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 821 PHE Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 ILE Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 890 ILE Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 995 PHE Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1304 HIS Chi-restraints excluded: chain D residue 1418 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 408 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 255 optimal weight: 8.9990 chunk 169 optimal weight: 0.5980 chunk 197 optimal weight: 6.9990 chunk 430 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 chunk 403 optimal weight: 5.9990 chunk 458 optimal weight: 1.9990 chunk 406 optimal weight: 0.0070 chunk 230 optimal weight: 30.0000 overall best weight: 1.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.079918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.064000 restraints weight = 185723.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.065420 restraints weight = 100741.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.066370 restraints weight = 66519.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.066913 restraints weight = 50036.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.067374 restraints weight = 41818.977| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 36176 Z= 0.139 Angle : 0.602 14.050 49548 Z= 0.307 Chirality : 0.039 0.191 5880 Planarity : 0.004 0.056 6272 Dihedral : 4.621 30.964 5224 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.89 % Favored : 94.07 % Rotamer: Outliers : 2.26 % Allowed : 18.36 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.13), residues: 4770 helix: 1.70 (0.10), residues: 2688 sheet: -1.62 (0.29), residues: 312 loop : -2.08 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1092 TYR 0.021 0.001 TYR C1089 PHE 0.040 0.001 PHE D 395 TRP 0.017 0.001 TRP C 981 HIS 0.006 0.001 HIS A 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (36168) covalent geometry : angle 0.60091 / 0.31 (49532) SS BOND : bond 0.00396 / 0.26 ( 8) SS BOND : angle 1.69799 / 1.13 ( 16) hydrogen bonds : bond 0.03807 / 2.66 ( 2161) hydrogen bonds : angle 4.08818 / 2.98 ( 6369) =============================================================================== Job complete usr+sys time: 5784.22 seconds wall clock time: 100 minutes 37.28 seconds (6037.28 seconds total)