Starting phenix.real_space_refine on Sat Aug 23 12:57:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ppj_20440/08_2025/6ppj_20440.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ppj_20440/08_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_20440/08_2025/6ppj_20440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ppj_20440/08_2025/6ppj_20440.map" model { file = "/net/cci-nas-00/data/ceres_data/6ppj_20440/08_2025/6ppj_20440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ppj_20440/08_2025/6ppj_20440.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.01s 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: 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: {'ASP:plan': 5, 'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} 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: {'UNK:plan-1': 11, 'ARG:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 5} 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: {'UNK:plan-1': 16, 'ARG:plan': 11, 'ASN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 16, 'GLU:plan': 16, 'GLN:plan1': 2, 'PHE:plan': 1} 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: {'UNK:plan-1': 33, 'HIS:plan': 3, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1} 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: {'GLU:plan': 34, 'ASN:plan1': 6, 'ASP:plan': 40, 'GLN:plan1': 11, 'ARG:plan': 27, 'HIS:plan': 1, 'TYR:plan': 1} 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: 2.81, per 1000 atoms: 0.23 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: 0.70 Conformation dependent library (CDL) restraints added in 516.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.46 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: 1.64 Time building geometry restraints manager: 1.11 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.560 Find NCS groups from input model: 0.090 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.910 ------------------------------------------------------------------------------- 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 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: -5.81 (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 ARG 0.020 0.001 ARG B 597 TYR 0.030 0.003 TYR A 864 PHE 0.024 0.003 PHE A 477 TRP 0.045 0.004 TRP A 616 HIS 0.014 0.002 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00882 (12193) covalent geometry : angle 1.15161 (16720) hydrogen bonds : bond 0.34104 ( 399) hydrogen bonds : angle 10.36186 ( 1152) metal coordination : bond 0.77570 ( 4) metal coordination : angle 24.00936 ( 12) link_TRANS : bond 0.00425 ( 2) link_TRANS : angle 1.07448 ( 6) *********************** 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 : 0.394 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: 0.1497 time to fit residues: 50.1916 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 : 0.296 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 0.0060 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.131137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.114680 restraints weight = 18322.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.113280 restraints weight = 18548.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113822 restraints weight = 17873.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.114148 restraints weight = 14489.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.114623 restraints weight = 12928.632| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12199 Z= 0.120 Angle : 0.756 27.814 16738 Z= 0.318 Chirality : 0.041 0.136 2121 Planarity : 0.005 0.051 2115 Dihedral : 9.106 172.357 1874 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.43 % Allowed : 11.10 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.57 (0.17), residues: 1580 helix: -3.48 (0.13), residues: 807 sheet: -0.79 (0.49), residues: 125 loop : -2.68 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 614 TYR 0.019 0.002 TYR B 755 PHE 0.010 0.001 PHE A 618 TRP 0.020 0.001 TRP B 497 HIS 0.007 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00265 (12193) covalent geometry : angle 0.63428 (16720) hydrogen bonds : bond 0.03887 ( 399) hydrogen bonds : angle 4.88328 ( 1152) metal coordination : bond 0.01891 ( 4) metal coordination : angle 15.38105 ( 12) link_TRANS : bond 0.00032 ( 2) link_TRANS : angle 0.31760 ( 6) *********************** 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 196 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: B 225 MET cc_start: 0.7693 (tmt) cc_final: 0.7425 (tmm) REVERT: B 290 THR cc_start: 0.8639 (m) cc_final: 0.8316 (p) REVERT: B 412 ASP cc_start: 0.7635 (m-30) cc_final: 0.7393 (m-30) REVERT: B 679 HIS cc_start: 0.6744 (p90) cc_final: 0.6520 (p-80) REVERT: B 1013 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8883 (tp) REVERT: A 126 ILE cc_start: 0.8805 (mm) cc_final: 0.8538 (mm) REVERT: A 568 TYR cc_start: 0.8507 (t80) cc_final: 0.8125 (t80) REVERT: A 606 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8331 (pp) REVERT: A 685 MET cc_start: 0.8346 (ttm) cc_final: 0.8064 (ttt) REVERT: A 964 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5155 (tt) outliers start: 34 outliers final: 15 residues processed: 183 average time/residue: 0.1248 time to fit residues: 31.0330 Evaluate side-chains 142 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 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 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 93 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 87 optimal weight: 0.0970 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.127143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.109497 restraints weight = 18549.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.108847 restraints weight = 21329.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.110075 restraints weight = 19920.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.110258 restraints weight = 15174.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110516 restraints weight = 13520.931| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12199 Z= 0.147 Angle : 0.710 25.260 16738 Z= 0.298 Chirality : 0.042 0.141 2121 Planarity : 0.004 0.042 2115 Dihedral : 8.044 179.273 1864 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.35 % Allowed : 11.20 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.68 (0.18), residues: 1580 helix: -2.53 (0.16), residues: 816 sheet: -0.80 (0.47), residues: 129 loop : -2.50 (0.21), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 127 TYR 0.018 0.002 TYR A 864 PHE 0.013 0.001 PHE A 618 TRP 0.020 0.001 TRP B 497 HIS 0.007 0.001 HIS A 775 Details of bonding type rmsd covalent geometry : bond 0.00348 (12193) covalent geometry : angle 0.60232 (16720) hydrogen bonds : bond 0.03768 ( 399) hydrogen bonds : angle 4.22179 ( 1152) metal coordination : bond 0.01800 ( 4) metal coordination : angle 14.03666 ( 12) link_TRANS : bond 0.00006 ( 2) link_TRANS : angle 0.34570 ( 6) *********************** 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 181 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 128 time to evaluate : 0.329 Fit side-chains REVERT: B 128 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7508 (ttm110) REVERT: B 225 MET cc_start: 0.7815 (tmt) cc_final: 0.7413 (tmm) REVERT: B 290 THR cc_start: 0.8587 (m) cc_final: 0.8283 (p) REVERT: B 412 ASP cc_start: 0.7570 (m-30) cc_final: 0.7369 (m-30) REVERT: B 872 LEU cc_start: 0.8654 (mm) cc_final: 0.8352 (mm) REVERT: B 1013 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8882 (tp) REVERT: A 126 ILE cc_start: 0.8774 (mm) cc_final: 0.8515 (mm) REVERT: A 568 TYR cc_start: 0.8547 (t80) cc_final: 0.8156 (t80) REVERT: A 685 MET cc_start: 0.8348 (ttm) cc_final: 0.8053 (ttt) REVERT: A 964 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5029 (tp) outliers start: 53 outliers final: 31 residues processed: 170 average time/residue: 0.1183 time to fit residues: 27.9165 Evaluate side-chains 148 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 168 THR 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 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 449 THR 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 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 28 LEU Chi-restraints excluded: chain A residue 181 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 645 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 886 THR 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 81 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 61 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.127379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.110055 restraints weight = 18363.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.108903 restraints weight = 20253.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110204 restraints weight = 20976.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110501 restraints weight = 14191.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110666 restraints weight = 12976.986| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12199 Z= 0.138 Angle : 0.683 24.307 16738 Z= 0.287 Chirality : 0.042 0.160 2121 Planarity : 0.004 0.039 2115 Dihedral : 7.680 176.898 1864 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.25 % Allowed : 12.11 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.19), residues: 1580 helix: -1.92 (0.17), residues: 819 sheet: -0.73 (0.46), residues: 129 loop : -2.34 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 127 TYR 0.015 0.002 TYR A 864 PHE 0.013 0.001 PHE B 336 TRP 0.017 0.001 TRP B 497 HIS 0.006 0.001 HIS A 775 Details of bonding type rmsd covalent geometry : bond 0.00331 (12193) covalent geometry : angle 0.58119 (16720) hydrogen bonds : bond 0.03127 ( 399) hydrogen bonds : angle 3.96350 ( 1152) metal coordination : bond 0.01204 ( 4) metal coordination : angle 13.39531 ( 12) link_TRANS : bond 0.00009 ( 2) link_TRANS : angle 0.33279 ( 6) *********************** 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 178 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 126 time to evaluate : 0.426 Fit side-chains REVERT: B 225 MET cc_start: 0.7787 (tmt) cc_final: 0.7401 (tmm) REVERT: B 290 THR cc_start: 0.8612 (m) cc_final: 0.8326 (p) REVERT: B 872 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8382 (mm) REVERT: B 1013 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8911 (tp) REVERT: A 86 VAL cc_start: 0.8823 (p) cc_final: 0.8561 (m) REVERT: A 126 ILE cc_start: 0.8764 (mm) cc_final: 0.8498 (mm) REVERT: A 568 TYR cc_start: 0.8596 (t80) cc_final: 0.8387 (t80) REVERT: A 685 MET cc_start: 0.8344 (ttm) cc_final: 0.8098 (ttm) REVERT: A 964 LEU cc_start: 0.5949 (OUTLIER) cc_final: 0.4904 (tp) outliers start: 52 outliers final: 36 residues processed: 165 average time/residue: 0.1240 time to fit residues: 28.5092 Evaluate side-chains 159 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 281 VAL 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 60 optimal weight: 0.0970 chunk 1 optimal weight: 0.0270 chunk 155 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 100 optimal weight: 0.2980 chunk 86 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.130749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113625 restraints weight = 18283.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.113120 restraints weight = 20597.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114689 restraints weight = 18672.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114307 restraints weight = 13398.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.114593 restraints weight = 12117.776| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12199 Z= 0.088 Angle : 0.616 22.501 16738 Z= 0.256 Chirality : 0.039 0.173 2121 Planarity : 0.004 0.033 2115 Dihedral : 7.037 170.807 1864 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.44 % Allowed : 13.93 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.20), residues: 1580 helix: -1.26 (0.18), residues: 805 sheet: -0.68 (0.44), residues: 138 loop : -2.08 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 998 TYR 0.014 0.001 TYR B 755 PHE 0.010 0.001 PHE B 941 TRP 0.013 0.001 TRP B 497 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00199 (12193) covalent geometry : angle 0.52246 (16720) hydrogen bonds : bond 0.02346 ( 399) hydrogen bonds : angle 3.57044 ( 1152) metal coordination : bond 0.00977 ( 4) metal coordination : angle 12.17807 ( 12) link_TRANS : bond 0.00036 ( 2) link_TRANS : angle 0.26847 ( 6) *********************** 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 178 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.465 Fit side-chains REVERT: B 225 MET cc_start: 0.7741 (tmt) cc_final: 0.7451 (tmm) REVERT: B 290 THR cc_start: 0.8538 (m) cc_final: 0.8286 (p) REVERT: B 872 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8385 (mm) REVERT: B 1013 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8842 (tp) REVERT: A 86 VAL cc_start: 0.8760 (p) cc_final: 0.8494 (m) REVERT: A 568 TYR cc_start: 0.8571 (t80) cc_final: 0.8358 (t80) REVERT: A 685 MET cc_start: 0.8353 (ttm) cc_final: 0.8117 (ttm) REVERT: A 964 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.4951 (tp) outliers start: 44 outliers final: 26 residues processed: 168 average time/residue: 0.1380 time to fit residues: 31.8346 Evaluate side-chains 149 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 319 ILE 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 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 B residue 1034 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 235 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 624 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 9 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.119794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.098811 restraints weight = 18800.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.099077 restraints weight = 17061.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.100673 restraints weight = 16625.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.101028 restraints weight = 11271.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.101254 restraints weight = 10411.624| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12199 Z= 0.229 Angle : 0.759 24.436 16738 Z= 0.328 Chirality : 0.046 0.166 2121 Planarity : 0.005 0.048 2115 Dihedral : 7.595 176.065 1864 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 5.75 % Allowed : 14.33 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.20), residues: 1580 helix: -1.18 (0.18), residues: 815 sheet: -0.74 (0.45), residues: 129 loop : -2.15 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 998 TYR 0.020 0.002 TYR A 864 PHE 0.026 0.002 PHE B 254 TRP 0.023 0.002 TRP B 497 HIS 0.010 0.001 HIS A 775 Details of bonding type rmsd covalent geometry : bond 0.00557 (12193) covalent geometry : angle 0.66556 (16720) hydrogen bonds : bond 0.03787 ( 399) hydrogen bonds : angle 4.14829 ( 1152) metal coordination : bond 0.01645 ( 4) metal coordination : angle 13.67840 ( 12) link_TRANS : bond 0.00037 ( 2) link_TRANS : angle 0.35933 ( 6) *********************** 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 178 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 121 time to evaluate : 0.364 Fit side-chains REVERT: B 225 MET cc_start: 0.8012 (tmt) cc_final: 0.7507 (tmm) REVERT: B 290 THR cc_start: 0.8616 (m) cc_final: 0.8334 (p) REVERT: B 872 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8414 (mm) REVERT: A 86 VAL cc_start: 0.8736 (p) cc_final: 0.8518 (m) REVERT: A 126 ILE cc_start: 0.8794 (mm) cc_final: 0.8590 (mm) REVERT: A 254 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8733 (t) REVERT: A 390 PRO cc_start: 0.7505 (Cg_exo) cc_final: 0.6997 (Cg_endo) outliers start: 57 outliers final: 42 residues processed: 167 average time/residue: 0.1176 time to fit residues: 27.1893 Evaluate side-chains 161 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 172 VAL 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 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 400 LEU Chi-restraints excluded: chain B residue 471 ASP 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 925 THR 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 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 886 THR Chi-restraints excluded: chain A residue 897 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 153 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.125979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.108398 restraints weight = 18231.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.107938 restraints weight = 22570.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.108960 restraints weight = 19932.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.109209 restraints weight = 13926.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.109615 restraints weight = 13726.530| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12199 Z= 0.131 Angle : 0.692 23.826 16738 Z= 0.288 Chirality : 0.041 0.161 2121 Planarity : 0.004 0.051 2115 Dihedral : 7.140 173.047 1862 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.34 % Allowed : 15.74 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.21), residues: 1580 helix: -0.79 (0.18), residues: 806 sheet: -0.73 (0.46), residues: 122 loop : -1.93 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 998 TYR 0.023 0.002 TYR A 568 PHE 0.026 0.001 PHE B 254 TRP 0.017 0.001 TRP B 497 HIS 0.005 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00314 (12193) covalent geometry : angle 0.59242 (16720) hydrogen bonds : bond 0.02888 ( 399) hydrogen bonds : angle 3.80830 ( 1152) metal coordination : bond 0.00946 ( 4) metal coordination : angle 13.34597 ( 12) link_TRANS : bond 0.00010 ( 2) link_TRANS : angle 0.33481 ( 6) *********************** 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 160 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.427 Fit side-chains REVERT: B 225 MET cc_start: 0.7754 (tmt) cc_final: 0.7509 (tmm) REVERT: B 872 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8396 (mm) REVERT: A 86 VAL cc_start: 0.8778 (p) cc_final: 0.8494 (m) REVERT: A 390 PRO cc_start: 0.7587 (Cg_exo) cc_final: 0.7073 (Cg_endo) outliers start: 43 outliers final: 34 residues processed: 149 average time/residue: 0.1351 time to fit residues: 27.6806 Evaluate side-chains 148 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR 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 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 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR 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 1034 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 203 ILE 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 36 optimal weight: 0.3980 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 64 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.128730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.111959 restraints weight = 18280.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111280 restraints weight = 22006.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.112197 restraints weight = 20628.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.112236 restraints weight = 14836.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112607 restraints weight = 13979.405| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12199 Z= 0.096 Angle : 0.635 21.979 16738 Z= 0.265 Chirality : 0.040 0.176 2121 Planarity : 0.004 0.045 2115 Dihedral : 6.527 165.795 1860 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.83 % Allowed : 16.55 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.21), residues: 1580 helix: -0.37 (0.19), residues: 810 sheet: -0.74 (0.41), residues: 147 loop : -1.86 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 998 TYR 0.018 0.001 TYR A 568 PHE 0.026 0.001 PHE B 254 TRP 0.015 0.001 TRP B 497 HIS 0.004 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00220 (12193) covalent geometry : angle 0.54674 (16720) hydrogen bonds : bond 0.02337 ( 399) hydrogen bonds : angle 3.48933 ( 1152) metal coordination : bond 0.00849 ( 4) metal coordination : angle 12.06893 ( 12) link_TRANS : bond 0.00024 ( 2) link_TRANS : angle 0.27481 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 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 155 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.461 Fit side-chains REVERT: B 194 ARG cc_start: 0.7727 (ttp80) cc_final: 0.7410 (ttp80) REVERT: B 872 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8397 (mm) REVERT: A 86 VAL cc_start: 0.8728 (p) cc_final: 0.8441 (m) REVERT: A 390 PRO cc_start: 0.7606 (Cg_exo) cc_final: 0.7123 (Cg_endo) outliers start: 38 outliers final: 32 residues processed: 145 average time/residue: 0.1355 time to fit residues: 27.2895 Evaluate side-chains 148 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR 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 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 319 ILE 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 693 THR 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 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 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 605 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 836 VAL 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: 65.1991 > 50: distance: 45 - 68: 16.042 distance: 52 - 76: 21.612 distance: 60 - 68: 13.373 distance: 69 - 70: 34.852 distance: 69 - 72: 23.085 distance: 70 - 71: 3.911 distance: 70 - 76: 38.965 distance: 72 - 73: 17.115 distance: 73 - 74: 26.985 distance: 73 - 75: 20.953 distance: 76 - 77: 12.295 distance: 77 - 78: 19.450 distance: 77 - 80: 24.653 distance: 78 - 79: 22.334 distance: 78 - 87: 15.160 distance: 80 - 81: 16.475 distance: 81 - 82: 17.104 distance: 82 - 83: 18.902 distance: 83 - 84: 5.219 distance: 84 - 85: 11.913 distance: 84 - 86: 15.608 distance: 87 - 88: 24.150 distance: 88 - 89: 11.230 distance: 88 - 91: 23.479 distance: 89 - 90: 4.094 distance: 89 - 92: 25.905 distance: 92 - 93: 26.021 distance: 93 - 96: 14.776 distance: 94 - 95: 8.795 distance: 94 - 99: 4.404 distance: 96 - 97: 39.135 distance: 96 - 98: 4.780 distance: 99 - 100: 17.204 distance: 100 - 101: 34.627 distance: 100 - 103: 6.831 distance: 101 - 102: 22.590 distance: 101 - 106: 23.351 distance: 103 - 104: 15.204 distance: 103 - 105: 35.908 distance: 106 - 107: 18.192 distance: 110 - 111: 8.843 distance: 113 - 114: 42.821 distance: 113 - 116: 39.117 distance: 114 - 115: 18.387 distance: 114 - 117: 21.628 distance: 117 - 118: 33.169 distance: 117 - 123: 37.139 distance: 118 - 119: 7.331 distance: 118 - 121: 40.439 distance: 119 - 120: 39.926 distance: 121 - 122: 37.144 distance: 122 - 123: 3.388 distance: 124 - 125: 17.846 distance: 125 - 126: 17.102 distance: 125 - 128: 11.008 distance: 126 - 127: 18.636 distance: 126 - 129: 19.138 distance: 129 - 130: 3.329 distance: 130 - 131: 4.048 distance: 130 - 133: 7.843 distance: 131 - 132: 11.008 distance: 131 - 134: 4.684