Starting phenix.real_space_refine on Sat Aug 23 05:51:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ppu_20447/08_2025/6ppu_20447.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ppu_20447/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ppu_20447/08_2025/6ppu_20447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ppu_20447/08_2025/6ppu_20447.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ppu_20447/08_2025/6ppu_20447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ppu_20447/08_2025/6ppu_20447.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 29 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 6299 2.51 5 N 1867 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10104 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 5359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5359 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 705} Chain breaks: 17 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 508 Unresolved non-hydrogen dihedrals: 320 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 22, 'GLU:plan': 29, 'ARG:plan': 13, 'GLN:plan1': 4, 'ASN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 301 Chain: "A" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 1932 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 280} Chain breaks: 15 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'UNK:plan-1': 38, 'ASP:plan': 9, 'GLN:plan1': 6, 'ARG:plan': 13, 'HIS:plan': 3, 'GLU:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 204 Chain: "A" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2212 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 22, 'TRANS': 286} Chain breaks: 7 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'UNK:plan-1': 13, 'ARG:plan': 4, 'ASP:plan': 5, 'GLU:plan': 14} Unresolved non-hydrogen planarities: 104 Chain: "X" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 592 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MG': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.74, per 1000 atoms: 0.27 Number of scatterers: 10104 At special positions: 0 Unit cell: (123.166, 95.6043, 112.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 32 16.00 P 29 15.00 Mg 1 11.99 O 1872 8.00 N 1867 7.00 C 6299 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 388.2 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1102 " pdb="FE4 SF4 A1102 " - pdb=" SG CYS A 807 " pdb="FE1 SF4 A1102 " - pdb=" SG CYS A1030 " pdb="FE2 SF4 A1102 " - pdb=" SG CYS A1036 " Number of angles added : 9 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 6 sheets defined 48.4% alpha, 5.8% beta 4 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 52 through 55 Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.617A pdb=" N VAL B 60 " --> pdb=" O MET B 56 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 98 removed outlier: 3.710A pdb=" N GLY B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 removed outlier: 4.124A pdb=" N GLY B 124 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 157 removed outlier: 3.751A pdb=" N LEU B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 200 through 206 removed outlier: 3.736A pdb=" N VAL B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 200 through 206' Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.941A pdb=" N ARG B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET B 225 " --> pdb=" O TRP B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.732A pdb=" N ARG B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR B 233 " --> pdb=" O GLN B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 233' Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.953A pdb=" N MET B 258 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 4.023A pdb=" N GLY B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.930A pdb=" N ASP B 289 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 290 " --> pdb=" O TYR B 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 286 through 290' Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.736A pdb=" N LEU B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 402 through 416 removed outlier: 3.690A pdb=" N ALA B 411 " --> pdb=" O ARG B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 452 removed outlier: 3.874A pdb=" N MET B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 466 removed outlier: 3.830A pdb=" N ALA B 465 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 481 removed outlier: 3.811A pdb=" N LEU B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.620A pdb=" N ALA B 487 " --> pdb=" O ALA B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 514 removed outlier: 3.616A pdb=" N ALA B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 513 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 530 removed outlier: 4.029A pdb=" N GLN B 530 " --> pdb=" O ASP B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 543 removed outlier: 4.048A pdb=" N ASP B 542 " --> pdb=" O CYS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 573 removed outlier: 3.722A pdb=" N ILE B 561 " --> pdb=" O GLY B 557 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET B 570 " --> pdb=" O ARG B 566 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 590 removed outlier: 3.773A pdb=" N ARG B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.575A pdb=" N ALA B 604 " --> pdb=" O PRO B 601 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 605 " --> pdb=" O VAL B 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 601 through 605' Processing helix chain 'B' and resid 610 through 623 removed outlier: 3.668A pdb=" N PHE B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP B 617 " --> pdb=" O ASP B 613 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.765A pdb=" N GLU B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 748 removed outlier: 3.519A pdb=" N LYS B 740 " --> pdb=" O SER B 736 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 745 " --> pdb=" O SER B 741 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 747 " --> pdb=" O ASP B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 759 removed outlier: 3.944A pdb=" N THR B 759 " --> pdb=" O TYR B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 removed outlier: 3.649A pdb=" N THR B 791 " --> pdb=" O CYS B 787 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 851 removed outlier: 3.612A pdb=" N GLN B 845 " --> pdb=" O HIS B 841 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 846 " --> pdb=" O ARG B 842 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL B 847 " --> pdb=" O GLY B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 876 removed outlier: 3.546A pdb=" N ASP B 867 " --> pdb=" O GLY B 863 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 868 " --> pdb=" O TRP B 864 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 869 " --> pdb=" O ALA B 865 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 873 " --> pdb=" O ASP B 869 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU B 874 " --> pdb=" O ALA B 870 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.531A pdb=" N UNK A 185 " --> pdb=" O UNK A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 removed outlier: 4.147A pdb=" N UNK A 191 " --> pdb=" O UNK A 187 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N UNK A 193 " --> pdb=" O UNK A 189 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N UNK A 194 " --> pdb=" O UNK A 190 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N UNK A 196 " --> pdb=" O UNK A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 356 through 374 removed outlier: 3.892A pdb=" N ILE A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.530A pdb=" N ALA A 403 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 433 removed outlier: 3.598A pdb=" N ALA A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 447 removed outlier: 3.965A pdb=" N ALA A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 removed outlier: 3.684A pdb=" N ARG A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.656A pdb=" N VAL A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 508 removed outlier: 3.682A pdb=" N THR A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 500 " --> pdb=" O HIS A 496 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 506 " --> pdb=" O ARG A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.508A pdb=" N TRP A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 547 through 569 removed outlier: 3.639A pdb=" N ALA A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 586 removed outlier: 4.165A pdb=" N ASP A 582 " --> pdb=" O ARG A 578 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 Processing helix chain 'A' and resid 701 through 707 removed outlier: 3.714A pdb=" N UNK A 707 " --> pdb=" O UNK A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 removed outlier: 3.512A pdb=" N VAL A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 736 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 737 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 763 removed outlier: 3.609A pdb=" N GLN A 757 " --> pdb=" O CYS A 753 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 803 removed outlier: 3.671A pdb=" N GLN A 802 " --> pdb=" O PRO A 798 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 798 through 803' Processing helix chain 'A' and resid 809 through 815 removed outlier: 3.524A pdb=" N ARG A 815 " --> pdb=" O TRP A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 827 Processing helix chain 'A' and resid 828 through 838 removed outlier: 3.696A pdb=" N HIS A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 834 " --> pdb=" O SER A 830 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 837 " --> pdb=" O HIS A 833 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 854 removed outlier: 3.614A pdb=" N VAL A 847 " --> pdb=" O GLU A 843 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 873 removed outlier: 4.570A pdb=" N LEU A 869 " --> pdb=" O SER A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 884 removed outlier: 4.145A pdb=" N THR A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 961 removed outlier: 3.856A pdb=" N TYR A 956 " --> pdb=" O GLN A 952 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1001 removed outlier: 3.899A pdb=" N ALA A1001 " --> pdb=" O PRO A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1012 removed outlier: 3.836A pdb=" N VAL A1007 " --> pdb=" O TRP A1003 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A1012 " --> pdb=" O GLY A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1015 No H-bonds generated for 'chain 'A' and resid 1013 through 1015' Processing sheet with id=AA1, first strand: chain 'B' and resid 116 through 118 removed outlier: 7.614A pdb=" N SER B 117 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLY B 76 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 75 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.635A pdb=" N ARG B 141 " --> pdb=" O MET B 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 395 through 397 removed outlier: 6.004A pdb=" N ARG B 396 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 675 " --> pdb=" O LEU B 766 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 676 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 829 through 830 Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 354 removed outlier: 6.744A pdb=" N THR A 350 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ALA A 688 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG A 352 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 619 " --> pdb=" O MET A 685 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N THR A 687 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 621 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N VAL A 689 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 383 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ALA A 622 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE A 385 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 384 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 891 through 897 removed outlier: 7.308A pdb=" N LEU A 922 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR A 895 " --> pdb=" O ASP A 920 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASP A 920 " --> pdb=" O THR A 895 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 921 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 930 " --> pdb=" O GLY A 973 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS A 975 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL A 932 " --> pdb=" O LYS A 975 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL A 977 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 992 " --> pdb=" O GLY A 974 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 978 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR A 988 " --> pdb=" O TYR A 978 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.22 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: 1.690 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.810 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.80 (0.18), residues: 1226 helix: -4.40 (0.12), residues: 621 sheet: -2.73 (0.55), residues: 96 loop : -3.11 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 572 TYR 0.027 0.003 TYR A 956 PHE 0.016 0.003 PHE B 685 TRP 0.033 0.004 TRP B 497 HIS 0.010 0.002 HIS B 577 Details of bonding type rmsd covalent geometry : bond 0.00853 (10324) covalent geometry : angle 1.17651 (14238) hydrogen bonds : bond 0.32193 ( 277) hydrogen bonds : angle 10.20655 ( 787) metal coordination : bond 0.79195 ( 3) metal coordination : angle 32.20525 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.393 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: 0.1247 time to fit residues: 35.1969 Evaluate side-chains 125 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 919 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3770 r_free = 0.3770 target = 0.159961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.134042 restraints weight = 14218.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.133384 restraints weight = 15146.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.134773 restraints weight = 14118.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134316 restraints weight = 10822.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.134672 restraints weight = 9837.104| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2138 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= 0.141 Angle : 0.799 28.492 14247 Z= 0.350 Chirality : 0.042 0.232 1763 Planarity : 0.005 0.054 1715 Dihedral : 16.743 175.151 1745 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.69 % Favored : 93.23 % Rotamer: Outliers : 3.46 % Allowed : 12.51 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.65 (0.20), residues: 1226 helix: -3.37 (0.15), residues: 623 sheet: -2.65 (0.54), residues: 98 loop : -2.55 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 683 TYR 0.014 0.001 TYR A 859 PHE 0.036 0.002 PHE B 68 TRP 0.024 0.002 TRP B 497 HIS 0.008 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00328 (10324) covalent geometry : angle 0.67568 (14238) hydrogen bonds : bond 0.04244 ( 277) hydrogen bonds : angle 4.83274 ( 787) metal coordination : bond 0.01662 ( 3) metal coordination : angle 16.97708 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.370 Fit side-chains REVERT: A 777 MET cc_start: 0.8256 (mmm) cc_final: 0.8026 (mmm) REVERT: A 1025 ASN cc_start: 0.7455 (t0) cc_final: 0.7168 (t0) outliers start: 29 outliers final: 15 residues processed: 157 average time/residue: 0.0997 time to fit residues: 22.2991 Evaluate side-chains 109 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 B residue 829 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 914 ARG 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 1014 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN ** 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 = 0.3733 r_free = 0.3733 target = 0.156354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130330 restraints weight = 14215.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.129203 restraints weight = 15146.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.130315 restraints weight = 13025.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130413 restraints weight = 10781.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130555 restraints weight = 10022.336| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10327 Z= 0.155 Angle : 0.770 22.403 14247 Z= 0.333 Chirality : 0.042 0.158 1763 Planarity : 0.005 0.052 1715 Dihedral : 16.653 172.330 1735 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.53 % Favored : 93.39 % Rotamer: Outliers : 4.41 % Allowed : 14.54 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.81 (0.22), residues: 1226 helix: -2.58 (0.18), residues: 616 sheet: -2.02 (0.57), residues: 96 loop : -2.36 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 871 TYR 0.013 0.002 TYR A 864 PHE 0.018 0.002 PHE B 68 TRP 0.022 0.002 TRP B 497 HIS 0.009 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00368 (10324) covalent geometry : angle 0.64647 (14238) hydrogen bonds : bond 0.03829 ( 277) hydrogen bonds : angle 4.17275 ( 787) metal coordination : bond 0.00659 ( 3) metal coordination : angle 16.64953 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.261 Fit side-chains REVERT: B 754 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8643 (tp) REVERT: A 577 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6951 (pp) REVERT: A 777 MET cc_start: 0.8284 (mmm) cc_final: 0.8059 (mmm) outliers start: 37 outliers final: 24 residues processed: 134 average time/residue: 0.1011 time to fit residues: 19.0587 Evaluate side-chains 119 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 275 LEU 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 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 454 ASP Chi-restraints excluded: chain A residue 577 LEU 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 820 ASP 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 74 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.0030 chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 87 optimal weight: 0.0040 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 770 HIS ** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.160518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.133650 restraints weight = 14269.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.133127 restraints weight = 14805.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.134404 restraints weight = 13564.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.134354 restraints weight = 10036.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.134698 restraints weight = 9398.666| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10327 Z= 0.099 Angle : 0.667 20.783 14247 Z= 0.288 Chirality : 0.039 0.139 1763 Planarity : 0.004 0.047 1715 Dihedral : 16.369 170.812 1727 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.34 % Allowed : 15.61 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.23), residues: 1226 helix: -1.91 (0.19), residues: 624 sheet: -1.84 (0.55), residues: 99 loop : -2.10 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 97 TYR 0.007 0.001 TYR A 859 PHE 0.011 0.001 PHE B 68 TRP 0.015 0.001 TRP B 497 HIS 0.005 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00218 (10324) covalent geometry : angle 0.55590 (14238) hydrogen bonds : bond 0.02636 ( 277) hydrogen bonds : angle 3.55074 ( 787) metal coordination : bond 0.00674 ( 3) metal coordination : angle 14.69876 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.347 Fit side-chains REVERT: B 66 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7954 (t0) REVERT: B 68 PHE cc_start: 0.8268 (m-80) cc_final: 0.7982 (m-80) REVERT: B 117 SER cc_start: 0.8856 (p) cc_final: 0.8604 (m) REVERT: B 642 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6447 (mt-10) REVERT: B 754 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8673 (tp) REVERT: A 577 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6837 (pp) outliers start: 28 outliers final: 16 residues processed: 126 average time/residue: 0.0783 time to fit residues: 14.5523 Evaluate side-chains 111 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 252 MET Chi-restraints excluded: chain B residue 684 VAL 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 454 ASP Chi-restraints excluded: chain A residue 577 LEU 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 931 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 51 optimal weight: 0.0970 chunk 65 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 162 HIS ** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.159458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133905 restraints weight = 14216.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.132565 restraints weight = 14933.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133823 restraints weight = 13281.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.134030 restraints weight = 10044.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134147 restraints weight = 9253.981| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3304 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= 0.106 Angle : 0.667 21.840 14247 Z= 0.287 Chirality : 0.040 0.178 1763 Planarity : 0.004 0.046 1715 Dihedral : 16.261 171.862 1726 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.93 % Allowed : 15.61 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.23), residues: 1226 helix: -1.46 (0.20), residues: 624 sheet: -1.49 (0.56), residues: 99 loop : -1.94 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 97 TYR 0.009 0.001 TYR A 859 PHE 0.009 0.001 PHE B 68 TRP 0.016 0.001 TRP B 497 HIS 0.005 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00243 (10324) covalent geometry : angle 0.55954 (14238) hydrogen bonds : bond 0.02702 ( 277) hydrogen bonds : angle 3.45139 ( 787) metal coordination : bond 0.00616 ( 3) metal coordination : angle 14.47725 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.335 Fit side-chains REVERT: B 66 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7921 (t0) REVERT: B 117 SER cc_start: 0.8839 (p) cc_final: 0.8613 (m) REVERT: B 497 TRP cc_start: 0.8581 (OUTLIER) cc_final: 0.7935 (p90) REVERT: B 642 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6472 (mt-10) REVERT: A 577 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6920 (pp) outliers start: 33 outliers final: 22 residues processed: 122 average time/residue: 0.0894 time to fit residues: 15.7347 Evaluate side-chains 122 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 252 MET Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain 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 996 THR Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 128 optimal weight: 0.0050 chunk 57 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 0.1980 chunk 32 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN ** 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 = 0.3764 r_free = 0.3764 target = 0.159548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.133440 restraints weight = 14274.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.132550 restraints weight = 15574.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.134404 restraints weight = 13889.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133965 restraints weight = 10050.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.134105 restraints weight = 9260.255| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3406 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= 0.119 Angle : 0.677 22.615 14247 Z= 0.290 Chirality : 0.040 0.169 1763 Planarity : 0.004 0.045 1715 Dihedral : 16.224 172.724 1726 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.81 % Allowed : 15.73 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.24), residues: 1226 helix: -1.13 (0.21), residues: 636 sheet: -1.28 (0.56), residues: 99 loop : -1.86 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 97 TYR 0.010 0.001 TYR A 859 PHE 0.028 0.001 PHE B 68 TRP 0.017 0.001 TRP B 497 HIS 0.005 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00278 (10324) covalent geometry : angle 0.56489 (14238) hydrogen bonds : bond 0.02805 ( 277) hydrogen bonds : angle 3.44846 ( 787) metal coordination : bond 0.00697 ( 3) metal coordination : angle 14.83934 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.348 Fit side-chains REVERT: B 117 SER cc_start: 0.8843 (p) cc_final: 0.8621 (m) REVERT: B 497 TRP cc_start: 0.8636 (OUTLIER) cc_final: 0.7981 (p90) REVERT: B 642 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6550 (mt-10) REVERT: A 577 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6903 (pp) outliers start: 32 outliers final: 24 residues processed: 118 average time/residue: 0.0774 time to fit residues: 13.6661 Evaluate side-chains 115 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 252 MET Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain 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 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 996 THR Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 83 optimal weight: 0.0170 chunk 12 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.155163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.129354 restraints weight = 14115.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.128622 restraints weight = 15838.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.130263 restraints weight = 14979.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.129963 restraints weight = 10824.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.130147 restraints weight = 9795.548| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10327 Z= 0.188 Angle : 0.776 22.868 14247 Z= 0.332 Chirality : 0.044 0.186 1763 Planarity : 0.005 0.047 1715 Dihedral : 16.426 171.683 1726 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.93 % Allowed : 16.57 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.23), residues: 1226 helix: -1.10 (0.20), residues: 638 sheet: -1.13 (0.58), residues: 98 loop : -1.97 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 871 TYR 0.015 0.002 TYR A 859 PHE 0.026 0.002 PHE B 68 TRP 0.017 0.002 TRP B 497 HIS 0.008 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00456 (10324) covalent geometry : angle 0.65255 (14238) hydrogen bonds : bond 0.03655 ( 277) hydrogen bonds : angle 3.95570 ( 787) metal coordination : bond 0.01099 ( 3) metal coordination : angle 16.73222 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.342 Fit side-chains REVERT: B 185 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7626 (tp30) REVERT: B 497 TRP cc_start: 0.8778 (OUTLIER) cc_final: 0.8065 (p90) REVERT: A 577 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6884 (pp) REVERT: A 789 GLU cc_start: 0.7379 (pm20) cc_final: 0.7010 (tp30) outliers start: 33 outliers final: 25 residues processed: 116 average time/residue: 0.0735 time to fit residues: 13.0455 Evaluate side-chains 117 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 252 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain 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 738 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 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 55 optimal weight: 2.9990 chunk 24 optimal weight: 0.0270 chunk 19 optimal weight: 0.4980 chunk 68 optimal weight: 10.0000 chunk 111 optimal weight: 0.1980 chunk 122 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 93 optimal weight: 0.0030 chunk 26 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 overall best weight: 0.2048 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.160619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134789 restraints weight = 14203.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.133568 restraints weight = 15356.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.135411 restraints weight = 14452.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.135099 restraints weight = 10095.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.135351 restraints weight = 10383.694| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10327 Z= 0.092 Angle : 0.655 21.079 14247 Z= 0.278 Chirality : 0.039 0.145 1763 Planarity : 0.004 0.045 1715 Dihedral : 16.077 179.433 1726 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.86 % Allowed : 17.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.24), residues: 1226 helix: -0.57 (0.21), residues: 641 sheet: -1.09 (0.55), residues: 99 loop : -1.72 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 97 TYR 0.005 0.001 TYR B 153 PHE 0.020 0.001 PHE B 68 TRP 0.014 0.001 TRP B 497 HIS 0.005 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00201 (10324) covalent geometry : angle 0.54631 (14238) hydrogen bonds : bond 0.02262 ( 277) hydrogen bonds : angle 3.21076 ( 787) metal coordination : bond 0.00640 ( 3) metal coordination : angle 14.41669 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.375 Fit side-chains REVERT: B 497 TRP cc_start: 0.8659 (OUTLIER) cc_final: 0.7941 (p90) REVERT: B 642 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6443 (mt-10) REVERT: A 441 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.7915 (p) REVERT: A 577 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6867 (pp) REVERT: A 820 ASP cc_start: 0.6917 (t70) cc_final: 0.6364 (p0) outliers start: 24 outliers final: 20 residues processed: 118 average time/residue: 0.0865 time to fit residues: 15.2762 Evaluate side-chains 115 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 497 TRP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 441 SER 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 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 996 THR Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.2997 > 50: distance: 9 - 14: 3.116 distance: 14 - 15: 8.086 distance: 15 - 16: 5.977 distance: 15 - 18: 12.585 distance: 16 - 17: 15.475 distance: 16 - 19: 7.088 distance: 19 - 20: 4.507 distance: 20 - 21: 6.416 distance: 20 - 23: 8.785 distance: 21 - 22: 14.238 distance: 24 - 25: 6.505 distance: 25 - 26: 9.193 distance: 25 - 28: 8.990 distance: 26 - 27: 15.899 distance: 26 - 29: 3.502 distance: 29 - 30: 3.754 distance: 30 - 31: 5.092 distance: 31 - 32: 4.921 distance: 31 - 34: 6.317 distance: 34 - 35: 8.107 distance: 35 - 36: 4.496 distance: 35 - 38: 7.723 distance: 36 - 37: 6.861 distance: 36 - 45: 10.305 distance: 38 - 39: 10.773 distance: 39 - 40: 11.729 distance: 40 - 41: 5.439 distance: 42 - 43: 8.505 distance: 42 - 44: 8.649 distance: 46 - 47: 8.631 distance: 46 - 49: 11.379 distance: 47 - 48: 22.273 distance: 47 - 50: 7.485 distance: 50 - 51: 19.621 distance: 51 - 52: 14.060 distance: 51 - 54: 17.844 distance: 52 - 53: 11.683 distance: 52 - 55: 11.606 distance: 55 - 56: 5.270 distance: 56 - 57: 20.289 distance: 56 - 59: 15.790 distance: 57 - 58: 20.004 distance: 57 - 60: 9.860 distance: 60 - 61: 7.685 distance: 60 - 66: 16.770 distance: 61 - 62: 8.969 distance: 61 - 64: 13.100 distance: 62 - 63: 15.051 distance: 62 - 67: 6.656 distance: 64 - 65: 25.260 distance: 65 - 66: 31.050 distance: 67 - 68: 3.009 distance: 68 - 69: 6.336 distance: 68 - 71: 16.090 distance: 69 - 70: 8.016 distance: 69 - 74: 24.758 distance: 71 - 72: 13.949