Starting phenix.real_space_refine on Mon Jul 28 06:19:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ppu_20447/07_2025/6ppu_20447.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ppu_20447/07_2025/6ppu_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_20447/07_2025/6ppu_20447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ppu_20447/07_2025/6ppu_20447.map" model { file = "/net/cci-nas-00/data/ceres_data/6ppu_20447/07_2025/6ppu_20447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ppu_20447/07_2025/6ppu_20447.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 22, 'PHE:plan': 1, 'GLU:plan': 29, 'ARG:plan': 13} 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: {'GLN:plan1': 6, 'ASP:plan': 9, 'TYR:plan': 1, 'UNK:plan-1': 38, 'HIS:plan': 3, 'GLU:plan': 7, 'ARG:plan': 13} 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: {'GLU:plan': 14, 'UNK:plan-1': 13, 'ASP:plan': 5, 'ARG:plan': 4} 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: 7.17, per 1000 atoms: 0.71 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: 2.88 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 3.30 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: 3.07 Time building geometry restraints manager: 3.38 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=" 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=" 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 bond pdb=" N VAL A 904 " pdb=" CA VAL A 904 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.10e+01 bond pdb=" N VAL A 915 " pdb=" CA VAL A 915 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.00e+01 ... (remaining 10319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 13174 2.05 - 4.10: 897 4.10 - 6.15: 113 6.15 - 8.21: 37 8.21 - 10.26: 17 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 - 0.071: 1366 0.071 - 0.143: 324 0.143 - 0.214: 65 0.214 - 0.286: 6 0.286 - 0.357: 2 Chirality restraints: 1763 Sorted by residual: 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' 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 -2.66 -2.32 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA ARG A 914 " pdb=" N ARG A 914 " pdb=" C ARG A 914 " pdb=" CB ARG A 914 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+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: 1.770 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.890 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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= 0.599 Angle : 1.428 50.782 14247 Z= 0.698 Chirality : 0.065 0.357 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.033 0.004 TRP B 497 HIS 0.010 0.002 HIS B 577 PHE 0.016 0.003 PHE B 685 TYR 0.027 0.003 TYR A 956 ARG 0.015 0.001 ARG B 572 Details of bonding type rmsd hydrogen bonds : bond 0.32193 ( 277) hydrogen bonds : angle 10.20655 ( 787) metal coordination : bond 0.79195 ( 3) metal coordination : angle 32.20525 ( 9) covalent geometry : bond 0.00853 (10324) covalent geometry : angle 1.17651 (14238) *********************** 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 : 1.120 Fit side-chains revert: symmetry clash REVERT: A 819 ASP cc_start: 0.8103 (t0) cc_final: 0.7776 (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: 0.2935 time to fit residues: 84.4250 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 : 1.039 ------------------------------------------------------------------------------- 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 114 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 106 optimal weight: 0.0040 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3783 r_free = 0.3783 target = 0.160698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135866 restraints weight = 14172.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.133892 restraints weight = 12454.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.135080 restraints weight = 11515.494| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10327 Z= 0.123 Angle : 0.771 28.143 14247 Z= 0.339 Chirality : 0.041 0.239 1763 Planarity : 0.005 0.052 1715 Dihedral : 16.664 175.242 1745 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 2.98 % Allowed : 13.23 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.20), residues: 1226 helix: -3.38 (0.15), residues: 622 sheet: -2.72 (0.54), residues: 92 loop : -2.48 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 497 HIS 0.009 0.001 HIS A 372 PHE 0.037 0.002 PHE B 68 TYR 0.012 0.001 TYR A 859 ARG 0.006 0.001 ARG B 683 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 277) hydrogen bonds : angle 4.70181 ( 787) metal coordination : bond 0.00951 ( 3) metal coordination : angle 16.45269 ( 9) covalent geometry : bond 0.00270 (10324) covalent geometry : angle 0.65105 (14238) *********************** 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 166 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.969 Fit side-chains REVERT: A 1025 ASN cc_start: 0.7410 (t0) cc_final: 0.7109 (t0) outliers start: 25 outliers final: 12 residues processed: 160 average time/residue: 0.2417 time to fit residues: 52.8519 Evaluate side-chains 106 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR 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 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 914 ARG 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 HIS ** 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 = 0.3737 r_free = 0.3737 target = 0.156960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.131588 restraints weight = 14123.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.130000 restraints weight = 13053.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130672 restraints weight = 12240.992| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10327 Z= 0.175 Angle : 0.787 23.087 14247 Z= 0.344 Chirality : 0.043 0.162 1763 Planarity : 0.005 0.056 1715 Dihedral : 16.661 172.385 1734 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.85 % Favored : 93.07 % Rotamer: Outliers : 4.41 % Allowed : 13.35 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.21), residues: 1226 helix: -2.67 (0.17), residues: 625 sheet: -2.13 (0.54), residues: 104 loop : -2.38 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 497 HIS 0.008 0.001 HIS B 243 PHE 0.018 0.002 PHE B 68 TYR 0.015 0.002 TYR A 864 ARG 0.005 0.000 ARG B 178 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 277) hydrogen bonds : angle 4.28695 ( 787) metal coordination : bond 0.00857 ( 3) metal coordination : angle 16.65138 ( 9) covalent geometry : bond 0.00419 (10324) covalent geometry : angle 0.66686 (14238) *********************** 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 139 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 1.065 Fit side-chains REVERT: A 577 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6893 (pp) REVERT: A 1025 ASN cc_start: 0.7459 (t0) cc_final: 0.7118 (t0) outliers start: 37 outliers final: 27 residues processed: 128 average time/residue: 0.2100 time to fit residues: 39.2124 Evaluate side-chains 123 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 252 MET Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 537 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 754 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 931 VAL 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 17 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 679 HIS B 771 HIS ** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.150084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.123914 restraints weight = 14192.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122853 restraints weight = 14460.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.124396 restraints weight = 13903.266| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 10327 Z= 0.369 Angle : 0.976 30.437 14247 Z= 0.434 Chirality : 0.052 0.212 1763 Planarity : 0.007 0.056 1715 Dihedral : 17.035 164.058 1726 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 6.79 % Allowed : 14.30 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.21), residues: 1226 helix: -2.61 (0.18), residues: 621 sheet: -1.97 (0.59), residues: 90 loop : -2.50 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A1003 HIS 0.017 0.002 HIS A 775 PHE 0.022 0.003 PHE B 340 TYR 0.021 0.003 TYR A 864 ARG 0.005 0.001 ARG A 990 Details of bonding type rmsd hydrogen bonds : bond 0.05289 ( 277) hydrogen bonds : angle 4.99074 ( 787) metal coordination : bond 0.01875 ( 3) metal coordination : angle 19.15101 ( 9) covalent geometry : bond 0.00900 (10324) covalent geometry : angle 0.84925 (14238) *********************** 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 152 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 95 time to evaluate : 1.128 Fit side-chains REVERT: B 66 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8103 (t0) REVERT: B 68 PHE cc_start: 0.8480 (m-80) cc_final: 0.8197 (m-80) REVERT: B 223 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8261 (mm) REVERT: B 430 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.7141 (p) REVERT: B 497 TRP cc_start: 0.8940 (OUTLIER) cc_final: 0.8354 (p90) REVERT: B 754 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8851 (tp) REVERT: A 577 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6618 (pp) REVERT: A 777 MET cc_start: 0.8299 (mmm) cc_final: 0.8066 (mmm) outliers start: 57 outliers final: 32 residues processed: 139 average time/residue: 0.2224 time to fit residues: 44.9372 Evaluate side-chains 129 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 91 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ASN 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 155 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 539 CYS 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 754 LEU Chi-restraints excluded: chain B residue 756 VAL 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 407 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 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 920 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 946 ASP Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.0570 chunk 75 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.157630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.131426 restraints weight = 14138.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.130244 restraints weight = 16047.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132251 restraints weight = 14415.927| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10327 Z= 0.105 Angle : 0.712 23.721 14247 Z= 0.302 Chirality : 0.040 0.143 1763 Planarity : 0.004 0.049 1715 Dihedral : 16.561 173.931 1726 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.81 % Allowed : 16.81 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.22), residues: 1226 helix: -1.82 (0.20), residues: 620 sheet: -1.80 (0.55), residues: 101 loop : -2.10 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 497 HIS 0.005 0.001 HIS A 372 PHE 0.008 0.001 PHE B 340 TYR 0.008 0.001 TYR A 859 ARG 0.004 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.02770 ( 277) hydrogen bonds : angle 3.77205 ( 787) metal coordination : bond 0.00709 ( 3) metal coordination : angle 16.18546 ( 9) covalent geometry : bond 0.00230 (10324) covalent geometry : angle 0.58471 (14238) *********************** 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 136 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.983 Fit side-chains REVERT: B 497 TRP cc_start: 0.8758 (OUTLIER) cc_final: 0.8032 (p90) REVERT: A 577 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6961 (pt) REVERT: A 777 MET cc_start: 0.8206 (mmm) cc_final: 0.7908 (mmm) REVERT: A 812 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8901 (tp) outliers start: 32 outliers final: 17 residues processed: 128 average time/residue: 0.2044 time to fit residues: 38.0833 Evaluate side-chains 106 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 163 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 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 687 THR Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 109 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 HIS B 229 GLN ** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.151865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.125627 restraints weight = 14237.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124749 restraints weight = 15219.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125928 restraints weight = 14969.116| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10327 Z= 0.260 Angle : 0.847 26.687 14247 Z= 0.369 Chirality : 0.047 0.175 1763 Planarity : 0.006 0.053 1715 Dihedral : 16.733 170.539 1726 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 4.77 % Allowed : 16.45 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.22), residues: 1226 helix: -1.85 (0.19), residues: 628 sheet: -1.78 (0.57), residues: 92 loop : -2.24 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 497 HIS 0.011 0.002 HIS A 775 PHE 0.030 0.003 PHE B 68 TYR 0.016 0.002 TYR A 859 ARG 0.005 0.001 ARG B 780 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 277) hydrogen bonds : angle 4.34380 ( 787) metal coordination : bond 0.01532 ( 3) metal coordination : angle 17.55526 ( 9) covalent geometry : bond 0.00636 (10324) covalent geometry : angle 0.72344 (14238) *********************** 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 126 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 86 time to evaluate : 1.014 Fit side-chains REVERT: B 497 TRP cc_start: 0.8877 (OUTLIER) cc_final: 0.8304 (p90) REVERT: A 577 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6668 (pp) REVERT: A 777 MET cc_start: 0.8303 (mmm) cc_final: 0.8014 (mmm) outliers start: 40 outliers final: 31 residues processed: 118 average time/residue: 0.2338 time to fit residues: 39.8162 Evaluate side-chains 116 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 155 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 747 VAL 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 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 786 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.156533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.129982 restraints weight = 14229.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.129637 restraints weight = 16178.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.131263 restraints weight = 12971.756| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10327 Z= 0.127 Angle : 0.718 23.285 14247 Z= 0.306 Chirality : 0.041 0.143 1763 Planarity : 0.004 0.051 1715 Dihedral : 16.453 176.815 1726 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.46 % Allowed : 17.64 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.23), residues: 1226 helix: -1.37 (0.20), residues: 628 sheet: -1.48 (0.56), residues: 101 loop : -2.05 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 497 HIS 0.006 0.001 HIS A 372 PHE 0.020 0.001 PHE B 68 TYR 0.010 0.001 TYR A 859 ARG 0.006 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 277) hydrogen bonds : angle 3.74564 ( 787) metal coordination : bond 0.00791 ( 3) metal coordination : angle 16.01876 ( 9) covalent geometry : bond 0.00296 (10324) covalent geometry : angle 0.59489 (14238) *********************** 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 121 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 1.055 Fit side-chains REVERT: B 497 TRP cc_start: 0.8817 (OUTLIER) cc_final: 0.8115 (p90) REVERT: A 577 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6668 (pp) REVERT: A 777 MET cc_start: 0.8240 (mmm) cc_final: 0.7969 (mmm) REVERT: A 812 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8860 (tp) outliers start: 29 outliers final: 24 residues processed: 113 average time/residue: 0.1928 time to fit residues: 32.2809 Evaluate side-chains 116 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 155 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 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 687 THR 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 903 VAL Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 108 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 101 optimal weight: 0.0030 chunk 9 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.158761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.131933 restraints weight = 14302.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131514 restraints weight = 17502.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133942 restraints weight = 14171.242| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10327 Z= 0.103 Angle : 0.661 20.572 14247 Z= 0.285 Chirality : 0.040 0.143 1763 Planarity : 0.004 0.048 1715 Dihedral : 16.176 178.985 1726 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.98 % Allowed : 19.07 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.24), residues: 1226 helix: -0.92 (0.21), residues: 629 sheet: -1.22 (0.57), residues: 99 loop : -1.92 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 497 HIS 0.004 0.001 HIS B 130 PHE 0.017 0.001 PHE B 68 TYR 0.008 0.001 TYR A 859 ARG 0.006 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.02625 ( 277) hydrogen bonds : angle 3.41153 ( 787) metal coordination : bond 0.00612 ( 3) metal coordination : angle 14.32610 ( 9) covalent geometry : bond 0.00236 (10324) covalent geometry : angle 0.55426 (14238) *********************** 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 121 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 1.051 Fit side-chains REVERT: B 497 TRP cc_start: 0.8785 (OUTLIER) cc_final: 0.8100 (p90) REVERT: A 577 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6666 (pp) REVERT: A 777 MET cc_start: 0.8164 (mmm) cc_final: 0.7875 (mmm) outliers start: 25 outliers final: 18 residues processed: 115 average time/residue: 0.1964 time to fit residues: 33.7940 Evaluate side-chains 117 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 163 LEU Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 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 687 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.154700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.128752 restraints weight = 14183.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127824 restraints weight = 15723.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.129125 restraints weight = 14727.930| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10327 Z= 0.184 Angle : 0.752 22.184 14247 Z= 0.323 Chirality : 0.044 0.222 1763 Planarity : 0.005 0.049 1715 Dihedral : 16.346 177.929 1726 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.69 % Allowed : 18.71 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.24), residues: 1226 helix: -0.97 (0.21), residues: 629 sheet: -1.22 (0.56), residues: 102 loop : -1.95 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 497 HIS 0.007 0.001 HIS A 775 PHE 0.019 0.002 PHE B 68 TYR 0.014 0.002 TYR A 859 ARG 0.006 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 277) hydrogen bonds : angle 3.88485 ( 787) metal coordination : bond 0.01151 ( 3) metal coordination : angle 16.14451 ( 9) covalent geometry : bond 0.00450 (10324) covalent geometry : angle 0.63388 (14238) *********************** 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 121 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 1.068 Fit side-chains REVERT: B 497 TRP cc_start: 0.8824 (OUTLIER) cc_final: 0.8162 (p90) REVERT: A 577 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6838 (pp) REVERT: A 777 MET cc_start: 0.8257 (mmm) cc_final: 0.7982 (mmm) outliers start: 31 outliers final: 24 residues processed: 111 average time/residue: 0.1990 time to fit residues: 33.0076 Evaluate side-chains 110 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 155 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 539 CYS 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 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 687 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 77 optimal weight: 10.0000 chunk 50 optimal weight: 0.0770 chunk 124 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.157888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.131566 restraints weight = 14124.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.130867 restraints weight = 16000.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.131935 restraints weight = 12898.749| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10327 Z= 0.108 Angle : 0.673 20.139 14247 Z= 0.289 Chirality : 0.040 0.163 1763 Planarity : 0.004 0.049 1715 Dihedral : 16.148 178.173 1726 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.10 % Allowed : 19.31 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.24), residues: 1226 helix: -0.68 (0.21), residues: 636 sheet: -1.25 (0.58), residues: 92 loop : -1.76 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 497 HIS 0.007 0.001 HIS B 130 PHE 0.020 0.001 PHE B 68 TYR 0.009 0.001 TYR A 859 ARG 0.007 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.02712 ( 277) hydrogen bonds : angle 3.48027 ( 787) metal coordination : bond 0.00681 ( 3) metal coordination : angle 14.72597 ( 9) covalent geometry : bond 0.00253 (10324) covalent geometry : angle 0.56264 (14238) ********************** 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 114 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 1.106 Fit side-chains REVERT: B 497 TRP cc_start: 0.8785 (OUTLIER) cc_final: 0.8082 (p90) REVERT: A 577 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6745 (pp) REVERT: A 777 MET cc_start: 0.8219 (mmm) cc_final: 0.7907 (mmm) outliers start: 26 outliers final: 23 residues processed: 107 average time/residue: 0.2021 time to fit residues: 32.4021 Evaluate side-chains 109 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 155 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 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 687 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 109 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.158461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.133625 restraints weight = 14135.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.132379 restraints weight = 13427.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.133338 restraints weight = 12189.421| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10327 Z= 0.107 Angle : 0.657 22.582 14247 Z= 0.282 Chirality : 0.040 0.143 1763 Planarity : 0.004 0.048 1715 Dihedral : 16.051 177.425 1726 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.22 % Allowed : 19.55 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.25), residues: 1226 helix: -0.40 (0.22), residues: 641 sheet: -1.13 (0.59), residues: 92 loop : -1.73 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 497 HIS 0.008 0.001 HIS B 130 PHE 0.020 0.001 PHE B 68 TYR 0.010 0.001 TYR A 859 ARG 0.006 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.02642 ( 277) hydrogen bonds : angle 3.38157 ( 787) metal coordination : bond 0.00566 ( 3) metal coordination : angle 14.20209 ( 9) covalent geometry : bond 0.00250 (10324) covalent geometry : angle 0.55127 (14238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3248.42 seconds wall clock time: 57 minutes 23.49 seconds (3443.49 seconds total)