Starting phenix.real_space_refine on Fri Sep 11 15:34:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ppu_20447/09_2026/6ppu_20447.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ppu_20447/09_2026/6ppu_20447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ppu_20447/09_2026/6ppu_20447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ppu_20447/09_2026/6ppu_20447.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ppu_20447/09_2026/6ppu_20447.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ppu_20447/09_2026/6ppu_20447.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ppu_20447/09_2026/6ppu_20447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ppu_20447/09_2026/6ppu_20447.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 29 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 6299 2.51 5 N 1867 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s 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: 10104 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 5359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5359 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 705} Chain breaks: 17 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 508 Unresolved non-hydrogen dihedrals: 320 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 22, 'GLU:plan': 29, 'ARG:plan': 13, 'GLN:plan1': 4, 'ASN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 301 Chain: "A" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 1932 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 280} Chain breaks: 15 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'UNK:plan-1': 38, 'ASP:plan': 9, 'GLN:plan1': 6, 'ARG:plan': 13, 'HIS:plan': 3, 'GLU:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 204 Chain: "A" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2212 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 22, 'TRANS': 286} Chain breaks: 7 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'UNK:plan-1': 13, 'ARG:plan': 4, 'ASP:plan': 5, 'GLU:plan': 14} Unresolved non-hydrogen planarities: 104 Chain: "X" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 592 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MG': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.35, per 1000 atoms: 0.23 Number of scatterers: 10104 At special positions: 0 Unit cell: (123.166, 95.6043, 112.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 32 16.00 P 29 15.00 Mg 1 11.99 O 1872 8.00 N 1867 7.00 C 6299 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 438.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1102 " pdb="FE4 SF4 A1102 " - pdb=" SG CYS A 807 " pdb="FE1 SF4 A1102 " - pdb=" SG CYS A1030 " pdb="FE2 SF4 A1102 " - pdb=" SG CYS A1036 " Number of angles added : 9 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 6 sheets defined 48.4% alpha, 5.8% beta 4 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 52 through 55 Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.617A pdb=" N VAL B 60 " --> pdb=" O MET B 56 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 98 removed outlier: 3.710A pdb=" N GLY B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 removed outlier: 4.124A pdb=" N GLY B 124 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 157 removed outlier: 3.751A pdb=" N LEU B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 200 through 206 removed outlier: 3.736A pdb=" N VAL B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 200 through 206' Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.941A pdb=" N ARG B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET B 225 " --> pdb=" O TRP B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.732A pdb=" N ARG B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR B 233 " --> pdb=" O GLN B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 233' Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.953A pdb=" N MET B 258 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 4.023A pdb=" N GLY B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.930A pdb=" N ASP B 289 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 290 " --> pdb=" O TYR B 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 286 through 290' Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.736A pdb=" N LEU B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 402 through 416 removed outlier: 3.690A pdb=" N ALA B 411 " --> pdb=" O ARG B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 452 removed outlier: 3.874A pdb=" N MET B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 466 removed outlier: 3.830A pdb=" N ALA B 465 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 481 removed outlier: 3.811A pdb=" N LEU B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.620A pdb=" N ALA B 487 " --> pdb=" O ALA B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 514 removed outlier: 3.616A pdb=" N ALA B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 513 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 530 removed outlier: 4.029A pdb=" N GLN B 530 " --> pdb=" O ASP B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 543 removed outlier: 4.048A pdb=" N ASP B 542 " --> pdb=" O CYS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 573 removed outlier: 3.722A pdb=" N ILE B 561 " --> pdb=" O GLY B 557 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET B 570 " --> pdb=" O ARG B 566 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 590 removed outlier: 3.773A pdb=" N ARG B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.575A pdb=" N ALA B 604 " --> pdb=" O PRO B 601 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 605 " --> pdb=" O VAL B 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 601 through 605' Processing helix chain 'B' and resid 610 through 623 removed outlier: 3.668A pdb=" N PHE B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP B 617 " --> pdb=" O ASP B 613 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.765A pdb=" N GLU B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 748 removed outlier: 3.519A pdb=" N LYS B 740 " --> pdb=" O SER B 736 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 745 " --> pdb=" O SER B 741 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 747 " --> pdb=" O ASP B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 759 removed outlier: 3.944A pdb=" N THR B 759 " --> pdb=" O TYR B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 removed outlier: 3.649A pdb=" N THR B 791 " --> pdb=" O CYS B 787 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 851 removed outlier: 3.612A pdb=" N GLN B 845 " --> pdb=" O HIS B 841 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 846 " --> pdb=" O ARG B 842 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL B 847 " --> pdb=" O GLY B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 876 removed outlier: 3.546A pdb=" N ASP B 867 " --> pdb=" O GLY B 863 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 868 " --> pdb=" O TRP B 864 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 869 " --> pdb=" O ALA B 865 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 873 " --> pdb=" O ASP B 869 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU B 874 " --> pdb=" O ALA B 870 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.531A pdb=" N UNK A 185 " --> pdb=" O UNK A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 removed outlier: 4.147A pdb=" N UNK A 191 " --> pdb=" O UNK A 187 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N UNK A 193 " --> pdb=" O UNK A 189 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N UNK A 194 " --> pdb=" O UNK A 190 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N UNK A 196 " --> pdb=" O UNK A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 356 through 374 removed outlier: 3.892A pdb=" N ILE A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.530A pdb=" N ALA A 403 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 433 removed outlier: 3.598A pdb=" N ALA A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 447 removed outlier: 3.965A pdb=" N ALA A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 removed outlier: 3.684A pdb=" N ARG A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.656A pdb=" N VAL A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 508 removed outlier: 3.682A pdb=" N THR A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 500 " --> pdb=" O HIS A 496 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 506 " --> pdb=" O ARG A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.508A pdb=" N TRP A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 547 through 569 removed outlier: 3.639A pdb=" N ALA A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 586 removed outlier: 4.165A pdb=" N ASP A 582 " --> pdb=" O ARG A 578 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 Processing helix chain 'A' and resid 701 through 707 removed outlier: 3.714A pdb=" N UNK A 707 " --> pdb=" O UNK A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 removed outlier: 3.512A pdb=" N VAL A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 736 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 737 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 763 removed outlier: 3.609A pdb=" N GLN A 757 " --> pdb=" O CYS A 753 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 803 removed outlier: 3.671A pdb=" N GLN A 802 " --> pdb=" O PRO A 798 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 798 through 803' Processing helix chain 'A' and resid 809 through 815 removed outlier: 3.524A pdb=" N ARG A 815 " --> pdb=" O TRP A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 827 Processing helix chain 'A' and resid 828 through 838 removed outlier: 3.696A pdb=" N HIS A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 834 " --> pdb=" O SER A 830 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 837 " --> pdb=" O HIS A 833 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 854 removed outlier: 3.614A pdb=" N VAL A 847 " --> pdb=" O GLU A 843 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 873 removed outlier: 4.570A pdb=" N LEU A 869 " --> pdb=" O SER A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 884 removed outlier: 4.145A pdb=" N THR A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 961 removed outlier: 3.856A pdb=" N TYR A 956 " --> pdb=" O GLN A 952 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1001 removed outlier: 3.899A pdb=" N ALA A1001 " --> pdb=" O PRO A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1012 removed outlier: 3.836A pdb=" N VAL A1007 " --> pdb=" O TRP A1003 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A1012 " --> pdb=" O GLY A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1015 No H-bonds generated for 'chain 'A' and resid 1013 through 1015' Processing sheet with id=AA1, first strand: chain 'B' and resid 116 through 118 removed outlier: 7.614A pdb=" N SER B 117 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLY B 76 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 75 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.635A pdb=" N ARG B 141 " --> pdb=" O MET B 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 395 through 397 removed outlier: 6.004A pdb=" N ARG B 396 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 675 " --> pdb=" O LEU B 766 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 676 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 829 through 830 Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 354 removed outlier: 6.744A pdb=" N THR A 350 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ALA A 688 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG A 352 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 619 " --> pdb=" O MET A 685 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N THR A 687 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 621 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N VAL A 689 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 383 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ALA A 622 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE A 385 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 384 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 891 through 897 removed outlier: 7.308A pdb=" N LEU A 922 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR A 895 " --> pdb=" O ASP A 920 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASP A 920 " --> pdb=" O THR A 895 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 921 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 930 " --> pdb=" O GLY A 973 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS A 975 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL A 932 " --> pdb=" O LYS A 975 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL A 977 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 992 " --> pdb=" O GLY A 974 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 978 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR A 988 " --> pdb=" O TYR A 978 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 4180 1.43 - 1.64: 6087 1.64 - 1.85: 45 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 10324 Sorted by residual: bond pdb=" N THR A 795 " pdb=" CA THR A 795 " ideal model delta sigma weight residual 1.457 1.508 -0.051 1.29e-02 6.01e+03 1.56e+01 bond pdb=" C3' DG X 57 " pdb=" O3' DG X 57 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.49e+01 bond pdb=" N VAL A 794 " pdb=" CA VAL A 794 " ideal model delta sigma weight residual 1.460 1.506 -0.046 1.19e-02 7.06e+03 1.48e+01 bond pdb=" C3' DC X 5 " pdb=" O3' DC X 5 " ideal model delta sigma weight residual 1.435 1.485 -0.050 1.30e-02 5.92e+03 1.45e+01 bond pdb=" N VAL A 793 " pdb=" CA VAL A 793 " ideal model delta sigma weight residual 1.459 1.504 -0.044 1.29e-02 6.01e+03 1.19e+01 ... (remaining 10319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 13144 2.05 - 4.10: 927 4.10 - 6.15: 113 6.15 - 8.21: 36 8.21 - 10.26: 18 Bond angle restraints: 14238 Sorted by residual: angle pdb=" N VAL B 488 " pdb=" CA VAL B 488 " pdb=" C VAL B 488 " ideal model delta sigma weight residual 111.90 105.31 6.59 8.10e-01 1.52e+00 6.62e+01 angle pdb=" N VAL A 794 " pdb=" CA VAL A 794 " pdb=" C VAL A 794 " ideal model delta sigma weight residual 110.53 117.95 -7.42 9.40e-01 1.13e+00 6.23e+01 angle pdb=" N LEU B 476 " pdb=" CA LEU B 476 " pdb=" C LEU B 476 " ideal model delta sigma weight residual 113.12 104.52 8.60 1.25e+00 6.40e-01 4.73e+01 angle pdb=" N THR B 338 " pdb=" CA THR B 338 " pdb=" C THR B 338 " ideal model delta sigma weight residual 114.56 106.74 7.82 1.27e+00 6.20e-01 3.79e+01 angle pdb=" C THR B 449 " pdb=" N ALA B 450 " pdb=" CA ALA B 450 " ideal model delta sigma weight residual 120.28 127.80 -7.52 1.34e+00 5.57e-01 3.15e+01 ... (remaining 14233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 5884 35.58 - 71.16: 148 71.16 - 106.73: 5 106.73 - 142.31: 3 142.31 - 177.89: 2 Dihedral angle restraints: 6042 sinusoidal: 2182 harmonic: 3860 Sorted by residual: dihedral pdb=" CA ASP B 189 " pdb=" C ASP B 189 " pdb=" N THR B 190 " pdb=" CA THR B 190 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA SER B 362 " pdb=" C SER B 362 " pdb=" N THR B 363 " pdb=" CA THR B 363 " ideal model delta harmonic sigma weight residual 180.00 152.26 27.74 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA TYR A 859 " pdb=" C TYR A 859 " pdb=" N ASP A 860 " pdb=" CA ASP A 860 " ideal model delta harmonic sigma weight residual 180.00 154.24 25.76 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 6039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1453 0.083 - 0.166: 276 0.166 - 0.249: 29 0.249 - 0.332: 3 0.332 - 0.415: 2 Chirality restraints: 1763 Sorted by residual: chirality pdb=" C3' DT X 2 " pdb=" C4' DT X 2 " pdb=" O3' DT X 2 " pdb=" C2' DT X 2 " both_signs ideal model delta sigma weight residual False -2.73 -2.32 -0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CA THR A 795 " pdb=" N THR A 795 " pdb=" C THR A 795 " pdb=" CB THR A 795 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C3' DC X 5 " pdb=" C4' DC X 5 " pdb=" O3' DC X 5 " pdb=" C2' DC X 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.46 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1760 not shown) Planarity restraints: 1715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 532 " -0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO B 533 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 533 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 533 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 217 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO B 218 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 218 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 218 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 435 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C VAL B 435 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL B 435 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG B 436 " -0.016 2.00e-02 2.50e+03 ... (remaining 1712 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 21 2.46 - 3.07: 5729 3.07 - 3.68: 14376 3.68 - 4.29: 19869 4.29 - 4.90: 33108 Nonbonded interactions: 73103 Sorted by model distance: nonbonded pdb=" O PHE B 336 " pdb=" OG1 THR B 337 " model vdw 1.855 3.040 nonbonded pdb=" O LEU B 522 " pdb=" OD2 ASP B 526 " model vdw 2.263 3.040 nonbonded pdb=" CG2 THR A 447 " pdb=" CG2 VAL A 453 " model vdw 2.269 3.880 nonbonded pdb=" CD2 HIS B 130 " pdb=" CG1 VAL B 271 " model vdw 2.310 3.680 nonbonded pdb=" OD2 ASP B 867 " pdb=" NH2 ARG A 724 " model vdw 2.341 3.120 ... (remaining 73098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.000 Normalize map: mean=0, sd=1: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.190 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.016 0.809 10327 Z= 0.627 Angle : 1.436 50.782 14247 Z= 0.732 Chirality : 0.067 0.415 1763 Planarity : 0.008 0.086 1715 Dihedral : 15.183 177.887 3508 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.10 % Allowed : 6.44 % Favored : 90.46 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 2.74 % 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: -5.80 (0.18), residues: 1226 helix: -4.40 (0.12), residues: 621 sheet: -2.73 (0.55), residues: 96 loop : -3.11 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 572 TYR 0.027 0.003 TYR A 956 PHE 0.016 0.003 PHE B 685 TRP 0.033 0.004 TRP B 497 HIS 0.010 0.002 HIS B 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00859 / 0.49 (10324) covalent geometry : angle 1.18656 / 0.73 (14238) hydrogen bonds : bond 0.32193 / 22.52 ( 277) hydrogen bonds : angle 10.20655 / 7.12 ( 787) metal coordination : bond 0.79195 / 39.68 ( 3) metal coordination : angle 32.20525 / 20.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 819 ASP cc_start: 0.8103 (t0) cc_final: 0.7774 (t0) REVERT: A 913 VAL cc_start: 0.7818 (OUTLIER) cc_final: 0.7578 (t) REVERT: A 1025 ASN cc_start: 0.7729 (t0) cc_final: 0.7356 (t0) outliers start: 26 outliers final: 10 residues processed: 212 average time/residue: 0.1156 time to fit residues: 33.0597 Evaluate side-chains 125 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 919 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 ASN B 130 HIS B 294 GLN B 413 HIS B 738 HIS B 770 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.159089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.134341 restraints weight = 14238.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133024 restraints weight = 15104.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.134733 restraints weight = 15354.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134530 restraints weight = 10695.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.134947 restraints weight = 11217.443| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10327 Z= 0.161 Angle : 0.878 33.203 14247 Z= 0.388 Chirality : 0.046 0.444 1763 Planarity : 0.006 0.055 1715 Dihedral : 16.994 176.680 1745 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.93 % Favored : 92.99 % Rotamer: Outliers : 3.69 % Allowed : 12.40 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -4.82 (0.20), residues: 1226 helix: -3.47 (0.15), residues: 624 sheet: -2.66 (0.54), residues: 97 loop : -2.71 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 683 TYR 0.017 0.002 TYR A 859 PHE 0.035 0.002 PHE B 68 TRP 0.026 0.002 TRP B 497 HIS 0.006 0.001 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (10324) covalent geometry : angle 0.74256 / 0.39 (14238) hydrogen bonds : bond 0.06582 / 4.64 ( 277) hydrogen bonds : angle 5.50580 / 3.93 ( 787) metal coordination : bond 0.03455 / 1.72 ( 3) metal coordination : angle 18.68915 / 12.00 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: B 223 LEU cc_start: 0.8432 (mm) cc_final: 0.8212 (mm) REVERT: A 777 MET cc_start: 0.8264 (mmm) cc_final: 0.8016 (mmm) REVERT: A 819 ASP cc_start: 0.7977 (t0) cc_final: 0.7637 (t70) REVERT: A 1025 ASN cc_start: 0.7503 (t0) cc_final: 0.7238 (t0) outliers start: 31 outliers final: 19 residues processed: 152 average time/residue: 0.0894 time to fit residues: 19.5281 Evaluate side-chains 126 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 103 optimal weight: 0.0470 chunk 88 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.160350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134585 restraints weight = 14205.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.133898 restraints weight = 15269.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.135463 restraints weight = 14190.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.134990 restraints weight = 10831.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.135268 restraints weight = 9522.312| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10327 Z= 0.122 Angle : 0.762 28.052 14247 Z= 0.331 Chirality : 0.043 0.415 1763 Planarity : 0.005 0.052 1715 Dihedral : 16.595 175.883 1737 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.29 % Rotamer: Outliers : 3.58 % Allowed : 13.83 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -3.86 (0.21), residues: 1226 helix: -2.62 (0.18), residues: 622 sheet: -2.09 (0.55), residues: 96 loop : -2.37 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 683 TYR 0.013 0.001 TYR A 859 PHE 0.020 0.001 PHE B 68 TRP 0.018 0.001 TRP B 497 HIS 0.007 0.001 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (10324) covalent geometry : angle 0.63524 / 0.33 (14238) hydrogen bonds : bond 0.04141 / 2.89 ( 277) hydrogen bonds : angle 4.37755 / 3.12 ( 787) metal coordination : bond 0.00684 / 0.35 ( 3) metal coordination : angle 16.73070 / 10.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.242 Fit side-chains REVERT: A 577 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6903 (pp) REVERT: A 777 MET cc_start: 0.8246 (mmm) cc_final: 0.8020 (mmm) REVERT: A 1025 ASN cc_start: 0.7446 (t0) cc_final: 0.7137 (t0) outliers start: 30 outliers final: 20 residues processed: 142 average time/residue: 0.0858 time to fit residues: 17.7590 Evaluate side-chains 122 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 946 ASP Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 229 GLN ** A 372 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 = 0.3766 r_free = 0.3766 target = 0.159788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.134647 restraints weight = 14234.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133556 restraints weight = 16639.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.135517 restraints weight = 14881.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.135222 restraints weight = 10973.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.135946 restraints weight = 11994.304| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10327 Z= 0.118 Angle : 0.737 25.209 14247 Z= 0.317 Chirality : 0.043 0.416 1763 Planarity : 0.004 0.052 1715 Dihedral : 16.494 175.587 1730 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.29 % Allowed : 14.66 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -3.33 (0.22), residues: 1226 helix: -2.14 (0.19), residues: 613 sheet: -1.93 (0.54), residues: 104 loop : -2.17 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 97 TYR 0.011 0.001 TYR A 859 PHE 0.018 0.001 PHE B 68 TRP 0.017 0.001 TRP B 497 HIS 0.005 0.001 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (10324) covalent geometry : angle 0.61550 / 0.32 (14238) hydrogen bonds : bond 0.03684 / 2.57 ( 277) hydrogen bonds : angle 4.02355 / 2.87 ( 787) metal coordination : bond 0.00738 / 0.38 ( 3) metal coordination : angle 16.16226 / 9.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.332 Fit side-chains REVERT: A 577 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.6948 (pp) REVERT: A 777 MET cc_start: 0.8268 (mmm) cc_final: 0.8040 (mmm) REVERT: A 1025 ASN cc_start: 0.7404 (t0) cc_final: 0.7069 (t0) outliers start: 36 outliers final: 24 residues processed: 134 average time/residue: 0.0857 time to fit residues: 16.9679 Evaluate side-chains 118 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 53 optimal weight: 0.0170 chunk 57 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.159754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.134621 restraints weight = 14179.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133313 restraints weight = 11807.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134700 restraints weight = 11443.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134758 restraints weight = 9242.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134780 restraints weight = 9024.663| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10327 Z= 0.117 Angle : 0.715 23.329 14247 Z= 0.308 Chirality : 0.043 0.409 1763 Planarity : 0.004 0.052 1715 Dihedral : 16.349 174.949 1727 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.05 % Allowed : 14.78 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -2.87 (0.23), residues: 1226 helix: -1.67 (0.20), residues: 621 sheet: -1.62 (0.56), residues: 98 loop : -2.10 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 97 TYR 0.011 0.001 TYR A 859 PHE 0.013 0.001 PHE B 68 TRP 0.018 0.001 TRP B 497 HIS 0.004 0.001 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (10324) covalent geometry : angle 0.59460 / 0.31 (14238) hydrogen bonds : bond 0.03342 / 2.32 ( 277) hydrogen bonds : angle 3.79910 / 2.72 ( 787) metal coordination : bond 0.00750 / 0.38 ( 3) metal coordination : angle 15.82943 / 9.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.350 Fit side-chains REVERT: B 66 ASN cc_start: 0.8157 (m-40) cc_final: 0.7946 (m-40) REVERT: B 642 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6597 (mt-10) REVERT: B 754 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8631 (tp) REVERT: A 577 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6918 (pp) outliers start: 34 outliers final: 24 residues processed: 131 average time/residue: 0.0878 time to fit residues: 17.1228 Evaluate side-chains 119 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 783 SER Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 0.0970 chunk 128 optimal weight: 0.0070 chunk 57 optimal weight: 0.0060 chunk 60 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 132 optimal weight: 0.0030 chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 HIS A 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.162210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.135494 restraints weight = 14375.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134962 restraints weight = 17618.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.136161 restraints weight = 14958.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.136462 restraints weight = 11639.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.136833 restraints weight = 10059.256| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10327 Z= 0.097 Angle : 0.676 21.837 14247 Z= 0.290 Chirality : 0.040 0.381 1763 Planarity : 0.004 0.049 1715 Dihedral : 16.126 176.000 1726 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.34 % Allowed : 15.97 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -2.15 (0.23), residues: 1226 helix: -1.04 (0.21), residues: 616 sheet: -1.31 (0.62), residues: 81 loop : -1.80 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 97 TYR 0.006 0.001 TYR A 859 PHE 0.010 0.001 PHE B 68 TRP 0.015 0.001 TRP B 497 HIS 0.008 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.10 (10324) covalent geometry : angle 0.56461 / 0.29 (14238) hydrogen bonds : bond 0.02676 / 1.86 ( 277) hydrogen bonds : angle 3.41646 / 2.45 ( 787) metal coordination : bond 0.00504 / 0.26 ( 3) metal coordination : angle 14.77248 / 8.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.358 Fit side-chains REVERT: B 117 SER cc_start: 0.8814 (p) cc_final: 0.8595 (m) REVERT: B 239 ILE cc_start: 0.8550 (pt) cc_final: 0.8302 (mt) REVERT: B 642 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6341 (mt-10) REVERT: B 754 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8692 (tp) REVERT: A 577 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6945 (pp) REVERT: A 819 ASP cc_start: 0.7069 (t0) cc_final: 0.6835 (t0) outliers start: 28 outliers final: 18 residues processed: 135 average time/residue: 0.0869 time to fit residues: 17.6770 Evaluate side-chains 118 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 783 SER Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 94 optimal weight: 0.0670 chunk 86 optimal weight: 9.9990 chunk 83 optimal weight: 0.0570 chunk 12 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 229 GLN A 419 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.160970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135959 restraints weight = 14157.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.136001 restraints weight = 15285.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.136838 restraints weight = 13322.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.136164 restraints weight = 11777.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.136747 restraints weight = 9956.852| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10327 Z= 0.112 Angle : 0.685 21.956 14247 Z= 0.294 Chirality : 0.042 0.408 1763 Planarity : 0.004 0.049 1715 Dihedral : 16.090 174.679 1726 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.46 % Allowed : 16.57 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.24), residues: 1226 helix: -0.78 (0.21), residues: 628 sheet: -1.23 (0.56), residues: 99 loop : -1.74 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 97 TYR 0.009 0.001 TYR A 859 PHE 0.033 0.001 PHE B 68 TRP 0.016 0.001 TRP B 497 HIS 0.004 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10324) covalent geometry : angle 0.57733 / 0.29 (14238) hydrogen bonds : bond 0.02853 / 1.95 ( 277) hydrogen bonds : angle 3.44343 / 2.47 ( 787) metal coordination : bond 0.00754 / 0.38 ( 3) metal coordination : angle 14.66504 / 8.43 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.342 Fit side-chains REVERT: B 117 SER cc_start: 0.8832 (p) cc_final: 0.8599 (m) REVERT: B 642 GLU cc_start: 0.6655 (mt-10) cc_final: 0.6354 (mt-10) REVERT: A 577 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6900 (pp) REVERT: A 819 ASP cc_start: 0.7135 (t0) cc_final: 0.6930 (t0) outliers start: 29 outliers final: 19 residues processed: 114 average time/residue: 0.0829 time to fit residues: 14.1584 Evaluate side-chains 112 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 68 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 93 optimal weight: 0.0370 chunk 26 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.160484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.135489 restraints weight = 14188.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.135876 restraints weight = 15834.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.136676 restraints weight = 14961.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.136671 restraints weight = 10611.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.137146 restraints weight = 10897.587| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10327 Z= 0.112 Angle : 0.685 22.175 14247 Z= 0.291 Chirality : 0.042 0.405 1763 Planarity : 0.004 0.050 1715 Dihedral : 16.050 174.275 1726 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.62 % Allowed : 17.40 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.24), residues: 1226 helix: -0.49 (0.22), residues: 628 sheet: -1.10 (0.56), residues: 99 loop : -1.71 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 97 TYR 0.010 0.001 TYR A 859 PHE 0.023 0.001 PHE B 68 TRP 0.020 0.001 TRP B 497 HIS 0.005 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10324) covalent geometry : angle 0.57241 / 0.29 (14238) hydrogen bonds : bond 0.02883 / 1.98 ( 277) hydrogen bonds : angle 3.43936 / 2.46 ( 787) metal coordination : bond 0.00667 / 0.34 ( 3) metal coordination : angle 14.95294 / 8.54 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.355 Fit side-chains REVERT: B 117 SER cc_start: 0.8827 (p) cc_final: 0.8616 (m) REVERT: B 642 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6507 (mt-10) REVERT: A 577 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6890 (pp) outliers start: 22 outliers final: 20 residues processed: 107 average time/residue: 0.0850 time to fit residues: 13.4732 Evaluate side-chains 108 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 96 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.0870 chunk 119 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.160557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134790 restraints weight = 14140.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.134350 restraints weight = 14739.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.135508 restraints weight = 13511.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.134726 restraints weight = 12507.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.135420 restraints weight = 9902.311| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10327 Z= 0.108 Angle : 0.691 22.320 14247 Z= 0.295 Chirality : 0.042 0.402 1763 Planarity : 0.004 0.049 1715 Dihedral : 15.988 174.113 1726 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.62 % Allowed : 17.76 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.24), residues: 1226 helix: -0.30 (0.22), residues: 629 sheet: -1.04 (0.55), residues: 99 loop : -1.66 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 97 TYR 0.009 0.001 TYR A 859 PHE 0.024 0.001 PHE B 68 TRP 0.022 0.001 TRP A 379 HIS 0.005 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (10324) covalent geometry : angle 0.58200 / 0.29 (14238) hydrogen bonds : bond 0.02774 / 1.89 ( 277) hydrogen bonds : angle 3.38877 / 2.43 ( 787) metal coordination : bond 0.00700 / 0.35 ( 3) metal coordination : angle 14.84363 / 8.46 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.354 Fit side-chains REVERT: B 117 SER cc_start: 0.8820 (p) cc_final: 0.8611 (m) REVERT: B 642 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6391 (mt-10) REVERT: A 577 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6898 (pp) outliers start: 22 outliers final: 20 residues processed: 109 average time/residue: 0.0956 time to fit residues: 15.2563 Evaluate side-chains 106 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.158020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.132444 restraints weight = 14074.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.132047 restraints weight = 14444.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133499 restraints weight = 14994.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.133260 restraints weight = 11107.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133618 restraints weight = 10072.497| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10327 Z= 0.126 Angle : 0.705 22.736 14247 Z= 0.303 Chirality : 0.043 0.414 1763 Planarity : 0.004 0.049 1715 Dihedral : 15.975 173.046 1726 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.50 % Allowed : 18.24 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.25), residues: 1226 helix: -0.21 (0.22), residues: 637 sheet: -0.96 (0.56), residues: 99 loop : -1.70 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 97 TYR 0.011 0.001 TYR A 859 PHE 0.021 0.001 PHE B 68 TRP 0.020 0.001 TRP B 497 HIS 0.005 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (10324) covalent geometry : angle 0.59715 / 0.30 (14238) hydrogen bonds : bond 0.02935 / 2.00 ( 277) hydrogen bonds : angle 3.47246 / 2.50 ( 787) metal coordination : bond 0.00782 / 0.39 ( 3) metal coordination : angle 14.92952 / 8.45 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.289 Fit side-chains REVERT: B 117 SER cc_start: 0.8799 (p) cc_final: 0.8579 (m) REVERT: B 642 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6503 (mt-10) REVERT: A 577 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6912 (pp) REVERT: A 820 ASP cc_start: 0.7274 (m-30) cc_final: 0.6784 (m-30) outliers start: 21 outliers final: 18 residues processed: 103 average time/residue: 0.0903 time to fit residues: 13.8802 Evaluate side-chains 105 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 65 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 51 optimal weight: 0.0470 chunk 63 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.152272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126582 restraints weight = 14323.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.125979 restraints weight = 16479.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127172 restraints weight = 15681.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.126913 restraints weight = 11628.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.127369 restraints weight = 11199.878| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10327 Z= 0.220 Angle : 0.801 23.740 14247 Z= 0.348 Chirality : 0.047 0.457 1763 Planarity : 0.005 0.049 1715 Dihedral : 16.164 170.390 1726 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.86 % Allowed : 17.88 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.24), residues: 1226 helix: -0.55 (0.21), residues: 633 sheet: -0.91 (0.57), residues: 98 loop : -1.91 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 97 TYR 0.015 0.002 TYR A 864 PHE 0.021 0.002 PHE B 68 TRP 0.022 0.002 TRP B 497 HIS 0.010 0.002 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (10324) covalent geometry : angle 0.68877 / 0.35 (14238) hydrogen bonds : bond 0.03835 / 2.63 ( 277) hydrogen bonds : angle 3.90030 / 2.80 ( 787) metal coordination : bond 0.01229 / 0.61 ( 3) metal coordination : angle 16.30946 / 9.13 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1595.14 seconds wall clock time: 28 minutes 4.67 seconds (1684.67 seconds total)