Starting phenix.real_space_refine on Tue Jun 10 23:59:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ppj_20440/06_2025/6ppj_20440.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ppj_20440/06_2025/6ppj_20440.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/6ppj_20440/06_2025/6ppj_20440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ppj_20440/06_2025/6ppj_20440.map" model { file = "/net/cci-nas-00/data/ceres_data/6ppj_20440/06_2025/6ppj_20440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ppj_20440/06_2025/6ppj_20440.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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 3 5.49 5 S 37 5.16 5 C 7621 2.51 5 N 2230 2.21 5 O 2109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12004 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1102 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 962 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'UNK:plan-1': 11, 'ASP:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2675 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 18, 'TRANS': 375} Chain breaks: 11 Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'UNK:plan-1': 16, 'HIS:plan': 3, 'ARG:plan': 11, 'PHE:plan': 1, 'GLU:plan': 16, 'ASP:plan': 16} Unresolved non-hydrogen planarities: 218 Chain: "B" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 932 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 5 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'UNK:plan-1': 33, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 6209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 6209 Classifications: {'peptide': 901} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 54, 'TRANS': 846} Chain breaks: 25 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 611 Unresolved non-hydrogen angles: 764 Unresolved non-hydrogen dihedrals: 469 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 40, 'TYR:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 34, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 465 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'ANP': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.50, per 1000 atoms: 0.62 Number of scatterers: 12004 At special positions: 0 Unit cell: (144.698, 99.9108, 109.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 37 16.00 P 3 15.00 O 2109 8.00 N 2230 7.00 C 7621 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 Links applied TRANS " UNK B 195 " - " ARG B 194 " " UNK B1063 " - " GLY B1062 " Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1101 " pdb="FE3 SF4 A1101 " - pdb=" SG CYS A1027 " pdb="FE4 SF4 A1101 " - pdb=" SG CYS A 807 " pdb="FE2 SF4 A1101 " - pdb=" SG CYS A1036 " pdb="FE1 SF4 A1101 " - pdb=" SG CYS A1030 " Number of angles added : 12 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3272 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 9 sheets defined 51.7% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'B' and resid 31 through 36 removed outlier: 3.820A pdb=" N ALA B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 56 through 67 removed outlier: 3.819A pdb=" N VAL B 60 " --> pdb=" O MET B 56 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN B 66 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 removed outlier: 3.645A pdb=" N ALA B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 119 through 130 removed outlier: 4.326A pdb=" N GLY B 124 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 172 through 180 removed outlier: 3.575A pdb=" N LEU B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 191 through 205 No H-bonds generated for 'chain 'B' and resid 191 through 205' Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.539A pdb=" N ALA B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.805A pdb=" N ALA B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 267 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 4.197A pdb=" N GLY B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.662A pdb=" N ASP B 289 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.730A pdb=" N GLN B 320 " --> pdb=" O ASP B 317 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 317 through 321' Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 362 through 376 removed outlier: 3.607A pdb=" N UNK B 370 " --> pdb=" O UNK B 366 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N UNK B 371 " --> pdb=" O UNK B 367 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N UNK B 374 " --> pdb=" O UNK B 370 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N UNK B 375 " --> pdb=" O UNK B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.023A pdb=" N ASP B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B 413 " --> pdb=" O TRP B 409 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 417 " --> pdb=" O HIS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 440 Processing helix chain 'B' and resid 441 through 450 removed outlier: 3.766A pdb=" N GLU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA B 447 " --> pdb=" O PRO B 443 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 481 removed outlier: 3.965A pdb=" N MET B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 493 removed outlier: 3.723A pdb=" N VAL B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 493 " --> pdb=" O MET B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 514 removed outlier: 3.554A pdb=" N ALA B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 506 " --> pdb=" O ARG B 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 528 removed outlier: 3.851A pdb=" N VAL B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 528' Processing helix chain 'B' and resid 558 through 572 removed outlier: 3.550A pdb=" N GLU B 567 " --> pdb=" O ALA B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 577 removed outlier: 4.525A pdb=" N GLY B 576 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 590 removed outlier: 3.888A pdb=" N ARG B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 589 " --> pdb=" O GLU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 598 removed outlier: 3.538A pdb=" N ALA B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B 597 " --> pdb=" O ASP B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 620 Processing helix chain 'B' and resid 636 through 642 removed outlier: 4.047A pdb=" N GLU B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 Processing helix chain 'B' and resid 735 through 742 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.984A pdb=" N ASP B 748 " --> pdb=" O GLN B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 759 removed outlier: 3.519A pdb=" N THR B 759 " --> pdb=" O TYR B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 794 removed outlier: 4.083A pdb=" N THR B 791 " --> pdb=" O CYS B 787 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 853 removed outlier: 3.648A pdb=" N GLY B 843 " --> pdb=" O HIS B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 876 removed outlier: 3.620A pdb=" N ASP B 869 " --> pdb=" O ALA B 865 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 873 " --> pdb=" O ASP B 869 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 876 " --> pdb=" O LEU B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 898 Processing helix chain 'B' and resid 903 through 911 removed outlier: 4.079A pdb=" N UNK B 911 " --> pdb=" O UNK B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 935 removed outlier: 4.212A pdb=" N THR B 925 " --> pdb=" O ALA B 921 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 927 " --> pdb=" O LEU B 923 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TRP B 930 " --> pdb=" O THR B 926 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 932 " --> pdb=" O HIS B 928 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 933 " --> pdb=" O GLU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 972 removed outlier: 3.667A pdb=" N SER B 972 " --> pdb=" O ALA B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1043 removed outlier: 4.128A pdb=" N GLN B1033 " --> pdb=" O HIS B1029 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL B1036 " --> pdb=" O VAL B1032 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B1037 " --> pdb=" O GLN B1033 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TRP B1041 " --> pdb=" O TYR B1037 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1080 Processing helix chain 'A' and resid 35 through 48 removed outlier: 3.808A pdb=" N VAL A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 45 " --> pdb=" O ASP A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.554A pdb=" N ALA A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 106 removed outlier: 3.838A pdb=" N ALA A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 124 removed outlier: 3.658A pdb=" N GLN A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.513A pdb=" N ASP A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.869A pdb=" N ALA A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.722A pdb=" N GLY A 172 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.582A pdb=" N GLN A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 removed outlier: 4.056A pdb=" N LEU A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 239 removed outlier: 4.772A pdb=" N GLY A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.562A pdb=" N ASN A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.674A pdb=" N HIS A 259 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 319 through 327 removed outlier: 3.780A pdb=" N THR A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 357 through 374 removed outlier: 3.749A pdb=" N GLY A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 415 through 418 removed outlier: 3.585A pdb=" N ARG A 418 " --> pdb=" O PRO A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 415 through 418' Processing helix chain 'A' and resid 419 through 435 removed outlier: 4.403A pdb=" N LEU A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 466 removed outlier: 3.867A pdb=" N ARG A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 486 removed outlier: 4.171A pdb=" N VAL A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 removed outlier: 3.981A pdb=" N LEU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.575A pdb=" N GLN A 526 " --> pdb=" O TYR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 549 through 559 removed outlier: 3.718A pdb=" N ASP A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 removed outlier: 3.815A pdb=" N ASP A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 4.091A pdb=" N ARG A 586 " --> pdb=" O ASP A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 669 through 677 removed outlier: 3.912A pdb=" N LEU A 673 " --> pdb=" O GLU A 669 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.980A pdb=" N SER A 708 " --> pdb=" O CYS A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 736 removed outlier: 3.546A pdb=" N VAL A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 removed outlier: 3.981A pdb=" N CYS A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 755 " --> pdb=" O ARG A 751 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 807 Processing helix chain 'A' and resid 807 through 816 removed outlier: 3.671A pdb=" N LEU A 812 " --> pdb=" O PRO A 808 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 815 " --> pdb=" O TRP A 811 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 837 removed outlier: 3.751A pdb=" N HIS A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.751A pdb=" N LYS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL A 853 " --> pdb=" O GLU A 849 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP A 854 " --> pdb=" O LEU A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 887 removed outlier: 3.569A pdb=" N SER A 865 " --> pdb=" O ALA A 861 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 867 " --> pdb=" O TRP A 863 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A 871 " --> pdb=" O ASN A 867 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 876 " --> pdb=" O HIS A 872 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 877 " --> pdb=" O ARG A 873 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 879 " --> pdb=" O MET A 875 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 884 " --> pdb=" O THR A 880 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A 885 " --> pdb=" O ARG A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 961 Processing helix chain 'A' and resid 1000 through 1011 removed outlier: 4.154A pdb=" N THR A1006 " --> pdb=" O GLU A1002 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1015 removed outlier: 3.714A pdb=" N ALA A1015 " --> pdb=" O ALA A1012 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1012 through 1015' Processing sheet with id=AA1, first strand: chain 'B' and resid 115 through 118 removed outlier: 6.061A pdb=" N VAL B 74 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N SER B 117 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLY B 76 " --> pdb=" O SER B 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 141 through 142 removed outlier: 5.904A 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 399 removed outlier: 6.008A pdb=" N ARG B 396 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N GLY B 769 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA B 398 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER B 768 " --> pdb=" O VAL B 677 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA B 432 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA B 431 " --> pdb=" O GLN B 660 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU B 662 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL B 433 " --> pdb=" O LEU B 662 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AA5, first strand: chain 'B' and resid 984 through 989 removed outlier: 3.731A pdb=" N PHE B 986 " --> pdb=" O GLY B 997 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY B 997 " --> pdb=" O PHE B 986 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 279 Processing sheet with id=AA7, first strand: chain 'A' and resid 91 through 92 removed outlier: 5.713A pdb=" N LEU A 58 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 354 removed outlier: 3.505A pdb=" N ALA A 688 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 604 " --> pdb=" O MET A 382 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 895 through 897 removed outlier: 7.095A pdb=" N THR A 895 " --> pdb=" O ARG A 921 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARG A 921 " --> pdb=" O THR A 895 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 923 " --> pdb=" O VAL A 931 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 932 " --> pdb=" O LYS A 975 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 3.28 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: 4856 1.43 - 1.64: 7272 1.64 - 1.85: 53 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 12193 Sorted by residual: bond pdb=" N3B ANP A1102 " pdb=" PG ANP A1102 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.03e+01 bond pdb=" O3A ANP A1102 " pdb=" PB ANP A1102 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" N VAL B 970 " pdb=" CA VAL B 970 " ideal model delta sigma weight residual 1.456 1.497 -0.041 9.50e-03 1.11e+04 1.83e+01 bond pdb=" N VAL B 677 " pdb=" CA VAL B 677 " ideal model delta sigma weight residual 1.460 1.491 -0.031 7.50e-03 1.78e+04 1.74e+01 bond pdb=" N TRP B 830 " pdb=" CA TRP B 830 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.20e-03 1.18e+04 1.22e+01 ... (remaining 12188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 15549 2.07 - 4.14: 981 4.14 - 6.21: 136 6.21 - 8.29: 34 8.29 - 10.36: 20 Bond angle restraints: 16720 Sorted by residual: angle pdb=" N ARG A 918 " pdb=" CA ARG A 918 " pdb=" C ARG A 918 " ideal model delta sigma weight residual 111.17 121.42 -10.25 1.41e+00 5.03e-01 5.28e+01 angle pdb=" N PRO B 678 " pdb=" CA PRO B 678 " pdb=" C PRO B 678 " ideal model delta sigma weight residual 113.47 123.53 -10.06 1.43e+00 4.89e-01 4.95e+01 angle pdb=" C GLY A 917 " pdb=" N ARG A 918 " pdb=" CA ARG A 918 " ideal model delta sigma weight residual 122.82 129.74 -6.92 1.42e+00 4.96e-01 2.37e+01 angle pdb=" CA ARG A 918 " pdb=" C ARG A 918 " pdb=" O ARG A 918 " ideal model delta sigma weight residual 122.27 116.71 5.56 1.16e+00 7.43e-01 2.30e+01 angle pdb=" N VAL A 960 " pdb=" CA VAL A 960 " pdb=" C VAL A 960 " ideal model delta sigma weight residual 110.42 105.92 4.50 9.60e-01 1.09e+00 2.20e+01 ... (remaining 16715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 7133 35.78 - 71.56: 59 71.56 - 107.34: 6 107.34 - 143.12: 0 143.12 - 178.90: 2 Dihedral angle restraints: 7200 sinusoidal: 2208 harmonic: 4992 Sorted by residual: dihedral pdb=" C LEU B 701 " pdb=" N LEU B 701 " pdb=" CA LEU B 701 " pdb=" CB LEU B 701 " ideal model delta harmonic sigma weight residual -122.60 -137.12 14.52 0 2.50e+00 1.60e-01 3.37e+01 dihedral pdb=" CA VAL B 982 " pdb=" C VAL B 982 " pdb=" N GLU B 983 " pdb=" CA GLU B 983 " ideal model delta harmonic sigma weight residual -180.00 -151.18 -28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA GLY A 274 " pdb=" C GLY A 274 " pdb=" N THR A 275 " pdb=" CA THR A 275 " ideal model delta harmonic sigma weight residual 180.00 151.43 28.57 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 7197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1899 0.098 - 0.196: 200 0.196 - 0.294: 16 0.294 - 0.392: 5 0.392 - 0.490: 1 Chirality restraints: 2121 Sorted by residual: chirality pdb=" CA LEU B 701 " pdb=" N LEU B 701 " pdb=" C LEU B 701 " pdb=" CB LEU B 701 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CA PRO B 678 " pdb=" N PRO B 678 " pdb=" C PRO B 678 " pdb=" CB PRO B 678 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ARG A 918 " pdb=" N ARG A 918 " pdb=" C ARG A 918 " pdb=" CB ARG A 918 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 2118 not shown) Planarity restraints: 2117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 917 " 0.019 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C GLY A 917 " -0.068 2.00e-02 2.50e+03 pdb=" O GLY A 917 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG A 918 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 113 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C SER B 113 " -0.054 2.00e-02 2.50e+03 pdb=" O SER B 113 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA B 114 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 576 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.65e+00 pdb=" C GLY B 576 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY B 576 " 0.020 2.00e-02 2.50e+03 pdb=" N HIS B 577 " 0.019 2.00e-02 2.50e+03 ... (remaining 2114 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1296 2.74 - 3.28: 10621 3.28 - 3.82: 17736 3.82 - 4.36: 20717 4.36 - 4.90: 35729 Nonbonded interactions: 86099 Sorted by model distance: nonbonded pdb=" NE1 TRP A 787 " pdb=" CA ALA A1015 " model vdw 2.202 3.550 nonbonded pdb=" OG SER A 312 " pdb=" O THR A 340 " model vdw 2.243 3.040 nonbonded pdb=" O THR A 33 " pdb=" O2A ANP A1102 " model vdw 2.272 3.040 nonbonded pdb=" O THR B 165 " pdb=" ND2 ASN A 867 " model vdw 2.294 3.120 nonbonded pdb=" O GLY B 863 " pdb=" NH2 ARG A 724 " model vdw 2.356 3.120 ... (remaining 86094 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: 1.320 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: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.730 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.017 0.789 12199 Z= 0.613 Angle : 1.319 38.232 16738 Z= 0.669 Chirality : 0.065 0.490 2121 Planarity : 0.008 0.072 2115 Dihedral : 11.634 178.898 3922 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.82 % Allowed : 6.16 % Favored : 92.03 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % 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: -5.81 (0.15), residues: 1580 helix: -4.55 (0.09), residues: 801 sheet: -1.48 (0.47), residues: 132 loop : -3.21 (0.19), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP A 616 HIS 0.014 0.002 HIS B 243 PHE 0.024 0.003 PHE A 477 TYR 0.030 0.003 TYR A 864 ARG 0.020 0.001 ARG B 597 Details of bonding type rmsd link_TRANS : bond 0.00425 ( 2) link_TRANS : angle 1.07448 ( 6) hydrogen bonds : bond 0.34104 ( 399) hydrogen bonds : angle 10.36186 ( 1152) metal coordination : bond 0.77570 ( 4) metal coordination : angle 24.00936 ( 12) covalent geometry : bond 0.00882 (12193) covalent geometry : angle 1.15161 (16720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 249 time to evaluate : 1.147 Fit side-chains REVERT: B 225 MET cc_start: 0.7703 (tmt) cc_final: 0.7409 (tmm) REVERT: B 612 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8908 (mt) REVERT: B 1013 LEU cc_start: 0.9034 (tm) cc_final: 0.8703 (tp) REVERT: A 284 PRO cc_start: 0.9030 (Cg_endo) cc_final: 0.8685 (Cg_exo) REVERT: A 313 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7745 (m-10) REVERT: A 568 TYR cc_start: 0.8268 (t80) cc_final: 0.7937 (t80) REVERT: A 964 LEU cc_start: 0.6105 (OUTLIER) cc_final: 0.5077 (tp) REVERT: A 1000 ARG cc_start: 0.7035 (tmm-80) cc_final: 0.6685 (tpp-160) outliers start: 18 outliers final: 7 residues processed: 262 average time/residue: 0.3565 time to fit residues: 119.9300 Evaluate side-chains 155 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 143 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS A 46 HIS A 259 HIS A 263 GLN A 311 GLN A 342 ASN A 816 HIS A 848 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114713 restraints weight = 18211.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.113699 restraints weight = 16561.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.114389 restraints weight = 15797.411| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12199 Z= 0.124 Angle : 0.767 29.151 16738 Z= 0.322 Chirality : 0.041 0.138 2121 Planarity : 0.005 0.053 2115 Dihedral : 9.246 172.896 1874 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.43 % Allowed : 11.50 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.59 (0.17), residues: 1580 helix: -3.51 (0.13), residues: 812 sheet: -0.77 (0.53), residues: 106 loop : -2.63 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 497 HIS 0.008 0.001 HIS A 259 PHE 0.010 0.001 PHE A 618 TYR 0.018 0.002 TYR B 755 ARG 0.006 0.001 ARG B 614 Details of bonding type rmsd link_TRANS : bond 0.00040 ( 2) link_TRANS : angle 0.31392 ( 6) hydrogen bonds : bond 0.04363 ( 399) hydrogen bonds : angle 4.97640 ( 1152) metal coordination : bond 0.02977 ( 4) metal coordination : angle 15.62443 ( 12) covalent geometry : bond 0.00272 (12193) covalent geometry : angle 0.64263 (16720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: B 225 MET cc_start: 0.7690 (tmt) cc_final: 0.7435 (tmm) REVERT: B 290 THR cc_start: 0.8650 (m) cc_final: 0.8314 (p) REVERT: B 412 ASP cc_start: 0.7649 (m-30) cc_final: 0.7402 (m-30) REVERT: B 679 HIS cc_start: 0.6787 (p90) cc_final: 0.6510 (p-80) REVERT: B 1013 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8875 (tp) REVERT: A 126 ILE cc_start: 0.8821 (mm) cc_final: 0.8550 (mm) REVERT: A 568 TYR cc_start: 0.8505 (t80) cc_final: 0.8160 (t80) REVERT: A 606 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8336 (pp) REVERT: A 685 MET cc_start: 0.8386 (ttm) cc_final: 0.8096 (ttt) REVERT: A 964 LEU cc_start: 0.6003 (OUTLIER) cc_final: 0.5160 (tt) REVERT: A 1000 ARG cc_start: 0.7245 (tmm-80) cc_final: 0.6925 (tpp-160) outliers start: 34 outliers final: 17 residues processed: 180 average time/residue: 0.3135 time to fit residues: 75.8547 Evaluate side-chains 145 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1027 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 89 optimal weight: 0.0970 chunk 137 optimal weight: 0.0970 chunk 91 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS A 419 GLN A 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.109333 restraints weight = 18567.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.108504 restraints weight = 21224.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.109692 restraints weight = 20602.192| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12199 Z= 0.139 Angle : 0.702 25.077 16738 Z= 0.295 Chirality : 0.042 0.136 2121 Planarity : 0.005 0.043 2115 Dihedral : 8.014 179.332 1864 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 5.25 % Allowed : 10.90 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.67 (0.18), residues: 1580 helix: -2.50 (0.16), residues: 811 sheet: -0.84 (0.47), residues: 129 loop : -2.50 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 497 HIS 0.006 0.001 HIS A 775 PHE 0.014 0.001 PHE A 618 TYR 0.017 0.002 TYR A 864 ARG 0.006 0.001 ARG A 127 Details of bonding type rmsd link_TRANS : bond 0.00015 ( 2) link_TRANS : angle 0.34013 ( 6) hydrogen bonds : bond 0.03597 ( 399) hydrogen bonds : angle 4.17565 ( 1152) metal coordination : bond 0.01610 ( 4) metal coordination : angle 13.87689 ( 12) covalent geometry : bond 0.00328 (12193) covalent geometry : angle 0.59588 (16720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 132 time to evaluate : 1.214 Fit side-chains REVERT: B 128 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7536 (ttm110) REVERT: B 225 MET cc_start: 0.7790 (tmt) cc_final: 0.7418 (tmm) REVERT: B 290 THR cc_start: 0.8576 (m) cc_final: 0.8309 (p) REVERT: B 872 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8329 (mm) REVERT: B 1013 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8850 (tp) REVERT: A 126 ILE cc_start: 0.8776 (mm) cc_final: 0.8513 (mm) REVERT: A 568 TYR cc_start: 0.8570 (t80) cc_final: 0.8180 (t80) REVERT: A 685 MET cc_start: 0.8348 (ttm) cc_final: 0.8062 (ttt) REVERT: A 964 LEU cc_start: 0.6003 (OUTLIER) cc_final: 0.4989 (tp) outliers start: 52 outliers final: 27 residues processed: 172 average time/residue: 0.2701 time to fit residues: 65.0450 Evaluate side-chains 149 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 155 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 135 optimal weight: 0.0470 chunk 139 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.109429 restraints weight = 18211.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.108510 restraints weight = 19912.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.109913 restraints weight = 19303.201| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12199 Z= 0.129 Angle : 0.668 23.839 16738 Z= 0.281 Chirality : 0.041 0.177 2121 Planarity : 0.004 0.038 2115 Dihedral : 7.566 175.583 1864 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.74 % Allowed : 12.71 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.04 (0.19), residues: 1580 helix: -1.89 (0.17), residues: 825 sheet: -0.70 (0.46), residues: 129 loop : -2.32 (0.22), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 497 HIS 0.005 0.001 HIS A 775 PHE 0.012 0.001 PHE A 618 TYR 0.015 0.001 TYR A 864 ARG 0.007 0.001 ARG B 614 Details of bonding type rmsd link_TRANS : bond 0.00011 ( 2) link_TRANS : angle 0.30619 ( 6) hydrogen bonds : bond 0.03027 ( 399) hydrogen bonds : angle 3.91882 ( 1152) metal coordination : bond 0.01180 ( 4) metal coordination : angle 13.10608 ( 12) covalent geometry : bond 0.00302 (12193) covalent geometry : angle 0.56815 (16720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 1.196 Fit side-chains REVERT: B 225 MET cc_start: 0.7786 (tmt) cc_final: 0.7420 (tmm) REVERT: B 290 THR cc_start: 0.8604 (m) cc_final: 0.8330 (p) REVERT: B 872 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8338 (mm) REVERT: B 1013 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8895 (tp) REVERT: A 86 VAL cc_start: 0.8829 (p) cc_final: 0.8564 (m) REVERT: A 126 ILE cc_start: 0.8755 (mm) cc_final: 0.8499 (mm) REVERT: A 568 TYR cc_start: 0.8574 (t80) cc_final: 0.8348 (t80) REVERT: A 685 MET cc_start: 0.8369 (ttm) cc_final: 0.8115 (ttm) REVERT: A 964 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.4906 (tp) outliers start: 47 outliers final: 35 residues processed: 163 average time/residue: 0.2707 time to fit residues: 61.4805 Evaluate side-chains 157 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 128 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 0.0570 chunk 52 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.122672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.106241 restraints weight = 18450.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.104353 restraints weight = 17690.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.104869 restraints weight = 17509.275| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12199 Z= 0.193 Angle : 0.727 24.610 16738 Z= 0.311 Chirality : 0.044 0.163 2121 Planarity : 0.005 0.044 2115 Dihedral : 7.685 176.827 1864 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 6.56 % Allowed : 12.71 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.72 (0.20), residues: 1580 helix: -1.52 (0.17), residues: 819 sheet: -0.78 (0.46), residues: 129 loop : -2.28 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 497 HIS 0.009 0.001 HIS A 775 PHE 0.012 0.002 PHE A 618 TYR 0.018 0.002 TYR A 864 ARG 0.010 0.001 ARG B 998 Details of bonding type rmsd link_TRANS : bond 0.00018 ( 2) link_TRANS : angle 0.37002 ( 6) hydrogen bonds : bond 0.03547 ( 399) hydrogen bonds : angle 4.09092 ( 1152) metal coordination : bond 0.01484 ( 4) metal coordination : angle 13.62539 ( 12) covalent geometry : bond 0.00470 (12193) covalent geometry : angle 0.62896 (16720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 116 time to evaluate : 1.268 Fit side-chains REVERT: B 225 MET cc_start: 0.7970 (tmt) cc_final: 0.7499 (tmm) REVERT: B 290 THR cc_start: 0.8626 (m) cc_final: 0.8374 (p) REVERT: B 872 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8368 (mm) REVERT: A 86 VAL cc_start: 0.8840 (p) cc_final: 0.8586 (m) REVERT: A 254 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8729 (t) REVERT: A 964 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.4821 (tp) outliers start: 65 outliers final: 42 residues processed: 171 average time/residue: 0.2697 time to fit residues: 64.6320 Evaluate side-chains 158 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 67 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 12 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.098253 restraints weight = 18843.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.098492 restraints weight = 17256.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099442 restraints weight = 16594.791| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12199 Z= 0.229 Angle : 0.769 24.612 16738 Z= 0.332 Chirality : 0.045 0.157 2121 Planarity : 0.005 0.046 2115 Dihedral : 7.833 178.317 1864 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 6.46 % Allowed : 13.12 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.56 (0.20), residues: 1580 helix: -1.36 (0.18), residues: 815 sheet: -0.90 (0.47), residues: 122 loop : -2.18 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 497 HIS 0.010 0.001 HIS A 775 PHE 0.028 0.002 PHE B 254 TYR 0.019 0.002 TYR A 864 ARG 0.009 0.001 ARG B 998 Details of bonding type rmsd link_TRANS : bond 0.00040 ( 2) link_TRANS : angle 0.44363 ( 6) hydrogen bonds : bond 0.03798 ( 399) hydrogen bonds : angle 4.21064 ( 1152) metal coordination : bond 0.01516 ( 4) metal coordination : angle 14.22597 ( 12) covalent geometry : bond 0.00561 (12193) covalent geometry : angle 0.66869 (16720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 118 time to evaluate : 1.189 Fit side-chains REVERT: B 225 MET cc_start: 0.8060 (tmt) cc_final: 0.7503 (tmm) REVERT: B 290 THR cc_start: 0.8610 (m) cc_final: 0.8344 (p) REVERT: B 579 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7856 (tp) REVERT: B 872 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8352 (mm) REVERT: A 86 VAL cc_start: 0.8791 (p) cc_final: 0.8563 (m) REVERT: A 390 PRO cc_start: 0.7662 (Cg_exo) cc_final: 0.7216 (Cg_endo) outliers start: 64 outliers final: 51 residues processed: 168 average time/residue: 0.2792 time to fit residues: 64.3987 Evaluate side-chains 168 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 115 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 33 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 131 optimal weight: 0.0870 chunk 105 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 86 optimal weight: 0.0470 chunk 75 optimal weight: 1.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.128738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.111232 restraints weight = 18295.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.110782 restraints weight = 20272.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.112002 restraints weight = 18928.188| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12199 Z= 0.094 Angle : 0.647 22.332 16738 Z= 0.269 Chirality : 0.039 0.171 2121 Planarity : 0.004 0.037 2115 Dihedral : 6.837 168.782 1862 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.53 % Allowed : 16.75 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.89 (0.21), residues: 1580 helix: -0.74 (0.18), residues: 810 sheet: -0.99 (0.42), residues: 138 loop : -1.89 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 497 HIS 0.005 0.001 HIS B 243 PHE 0.027 0.001 PHE B 254 TYR 0.020 0.001 TYR A 568 ARG 0.012 0.001 ARG B 998 Details of bonding type rmsd link_TRANS : bond 0.00041 ( 2) link_TRANS : angle 0.31218 ( 6) hydrogen bonds : bond 0.02311 ( 399) hydrogen bonds : angle 3.54039 ( 1152) metal coordination : bond 0.00899 ( 4) metal coordination : angle 12.39091 ( 12) covalent geometry : bond 0.00209 (12193) covalent geometry : angle 0.55518 (16720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: B 225 MET cc_start: 0.7796 (tmt) cc_final: 0.7432 (tmm) REVERT: B 290 THR cc_start: 0.8578 (m) cc_final: 0.8345 (p) REVERT: B 872 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8343 (mm) REVERT: A 86 VAL cc_start: 0.8804 (p) cc_final: 0.8477 (m) REVERT: A 390 PRO cc_start: 0.7581 (Cg_exo) cc_final: 0.7088 (Cg_endo) outliers start: 35 outliers final: 21 residues processed: 156 average time/residue: 0.3135 time to fit residues: 66.8149 Evaluate side-chains 140 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.8618 > 50: distance: 22 - 134: 9.685 distance: 38 - 137: 21.262 distance: 41 - 149: 28.656 distance: 80 - 84: 12.545 distance: 84 - 85: 36.005 distance: 85 - 86: 16.446 distance: 85 - 88: 50.318 distance: 86 - 87: 18.966 distance: 86 - 95: 27.971 distance: 88 - 89: 21.936 distance: 89 - 90: 24.659 distance: 90 - 91: 12.971 distance: 91 - 92: 26.048 distance: 92 - 93: 31.776 distance: 92 - 94: 5.328 distance: 95 - 96: 5.807 distance: 96 - 97: 20.861 distance: 96 - 99: 16.911 distance: 97 - 98: 27.340 distance: 97 - 100: 8.845 distance: 100 - 101: 34.684 distance: 101 - 102: 24.580 distance: 101 - 104: 17.020 distance: 102 - 103: 21.714 distance: 102 - 105: 15.299 distance: 105 - 106: 14.479 distance: 106 - 107: 40.212 distance: 106 - 109: 24.459 distance: 107 - 108: 30.333 distance: 107 - 112: 11.314 distance: 109 - 110: 15.346 distance: 109 - 111: 17.992 distance: 112 - 113: 29.224 distance: 113 - 114: 32.691 distance: 113 - 116: 34.745 distance: 114 - 115: 15.958 distance: 114 - 122: 45.675 distance: 116 - 117: 34.092 distance: 117 - 118: 38.265 distance: 117 - 119: 21.926 distance: 118 - 120: 25.871 distance: 119 - 121: 32.681 distance: 120 - 121: 34.018 distance: 122 - 123: 11.834 distance: 122 - 128: 37.912 distance: 123 - 124: 10.519 distance: 123 - 126: 23.028 distance: 124 - 125: 21.184 distance: 124 - 129: 40.803 distance: 126 - 127: 24.098 distance: 127 - 128: 27.470 distance: 129 - 130: 16.621 distance: 130 - 131: 42.862 distance: 130 - 133: 35.292 distance: 131 - 132: 32.774 distance: 131 - 134: 28.260 distance: 134 - 135: 10.186 distance: 135 - 136: 42.961 distance: 135 - 138: 17.400 distance: 136 - 137: 34.560 distance: 136 - 142: 39.625 distance: 138 - 139: 17.110 distance: 138 - 140: 5.512 distance: 139 - 141: 19.597 distance: 142 - 143: 18.953 distance: 143 - 144: 47.179 distance: 143 - 146: 7.960 distance: 144 - 145: 41.150 distance: 144 - 149: 52.077 distance: 146 - 147: 30.765 distance: 146 - 148: 41.007 distance: 149 - 150: 14.907 distance: 150 - 151: 16.446 distance: 150 - 153: 37.241 distance: 151 - 152: 26.154 distance: 151 - 157: 18.254 distance: 153 - 154: 24.134 distance: 154 - 155: 18.703 distance: 154 - 156: 29.030