Starting phenix.real_space_refine on Wed Jan 14 21:29:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ywp_6855/01_2026/5ywp_6855.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ywp_6855/01_2026/5ywp_6855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5ywp_6855/01_2026/5ywp_6855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ywp_6855/01_2026/5ywp_6855.map" model { file = "/net/cci-nas-00/data/ceres_data/5ywp_6855/01_2026/5ywp_6855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ywp_6855/01_2026/5ywp_6855.cif" } resolution = 4.6 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= 0.006 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: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 12357 2.51 5 N 3346 2.21 5 O 3747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19561 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 482} Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 574 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 70} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 482} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 574 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 70} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 482} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 574 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 70} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1657 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 201} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1633 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 201} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "Q" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1657 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 201} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1633 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 201} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 4.70, per 1000 atoms: 0.24 Number of scatterers: 19561 At special positions: 0 Unit cell: (110.4, 147.66, 180.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 3747 8.00 N 3346 7.00 C 12357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.02 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 335 " distance=2.04 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.02 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 287 " distance=2.03 Simple disulfide: pdb=" SG CYS C 304 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 30 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 121 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 116 " distance=2.02 Simple disulfide: pdb=" SG CYS E 190 " - pdb=" SG CYS E 287 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 335 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 89 " distance=2.04 Simple disulfide: pdb=" SG CYS M 135 " - pdb=" SG CYS M 195 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 145 " - pdb=" SG CYS N 200 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 135 " - pdb=" SG CYS Q 195 " distance=2.02 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.02 Simple disulfide: pdb=" SG CYS R 145 " - pdb=" SG CYS R 200 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 859.3 milliseconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4692 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 44 sheets defined 22.3% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.989A pdb=" N GLN A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.502A pdb=" N HIS A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.971A pdb=" N LEU A 239 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.667A pdb=" N ALA A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 429 removed outlier: 3.689A pdb=" N PHE A 427 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.715A pdb=" N LYS A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.511A pdb=" N THR A 451 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.786A pdb=" N LEU A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 485 Processing helix chain 'A' and resid 491 through 498 Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 26 through 39 removed outlier: 4.123A pdb=" N LYS B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR B 32 " --> pdb=" O TYR B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 53 removed outlier: 3.904A pdb=" N LEU B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 48 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TRP B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 71 removed outlier: 3.876A pdb=" N VAL B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR B 64 " --> pdb=" O ARG B 60 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 87 Processing helix chain 'C' and resid 132 through 135 Processing helix chain 'C' and resid 154 through 161 Processing helix chain 'C' and resid 191 through 196 removed outlier: 4.607A pdb=" N LEU C 196 " --> pdb=" O PRO C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 220 removed outlier: 3.505A pdb=" N ASP C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 240 removed outlier: 3.991A pdb=" N LEU C 239 " --> pdb=" O ARG C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 401 through 418 removed outlier: 3.523A pdb=" N LYS C 405 " --> pdb=" O SER C 401 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS C 412 " --> pdb=" O LEU C 408 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 414 " --> pdb=" O THR C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 427 Processing helix chain 'C' and resid 433 through 447 removed outlier: 3.748A pdb=" N VAL C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 452 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.884A pdb=" N VAL C 473 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 485 removed outlier: 3.872A pdb=" N ALA C 483 " --> pdb=" O SER C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 498 Processing helix chain 'D' and resid 21 through 39 removed outlier: 3.660A pdb=" N ALA D 25 " --> pdb=" O ASP D 21 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS D 31 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 53 removed outlier: 3.513A pdb=" N ALA D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 59 removed outlier: 3.903A pdb=" N GLN D 59 " --> pdb=" O ASN D 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 59' Processing helix chain 'D' and resid 60 through 71 removed outlier: 4.174A pdb=" N THR D 64 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 66 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 69 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 Processing helix chain 'E' and resid 148 through 154 removed outlier: 3.521A pdb=" N GLY E 153 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'E' and resid 197 through 201 removed outlier: 3.544A pdb=" N PHE E 201 " --> pdb=" O THR E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 220 Processing helix chain 'E' and resid 258 through 266 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 401 through 418 removed outlier: 3.625A pdb=" N LYS E 405 " --> pdb=" O SER E 401 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 428 removed outlier: 3.792A pdb=" N PHE E 427 " --> pdb=" O ALA E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 447 removed outlier: 4.584A pdb=" N ILE E 437 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA E 440 " --> pdb=" O SER E 436 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL E 444 " --> pdb=" O ALA E 440 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE E 445 " --> pdb=" O VAL E 441 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY E 447 " --> pdb=" O GLN E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 452 Processing helix chain 'E' and resid 458 through 472 removed outlier: 3.607A pdb=" N MET E 464 " --> pdb=" O THR E 460 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY E 465 " --> pdb=" O GLN E 461 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA E 466 " --> pdb=" O GLY E 462 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TRP E 470 " --> pdb=" O ALA E 466 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N MET E 471 " --> pdb=" O LEU E 467 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY E 472 " --> pdb=" O LEU E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 485 Processing helix chain 'E' and resid 491 through 498 Processing helix chain 'F' and resid 21 through 39 removed outlier: 3.876A pdb=" N ALA F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR F 28 " --> pdb=" O LYS F 24 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET F 30 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS F 31 " --> pdb=" O ARG F 27 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR F 32 " --> pdb=" O TYR F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 47 removed outlier: 4.234A pdb=" N ALA F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 53 removed outlier: 4.572A pdb=" N TRP F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 59 through 71 removed outlier: 3.965A pdb=" N PHE F 63 " --> pdb=" O GLN F 59 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR F 64 " --> pdb=" O ARG F 60 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU F 66 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU F 69 " --> pdb=" O ILE F 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 127 Processing helix chain 'M' and resid 184 through 190 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.616A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'N' and resid 132 through 134 No H-bonds generated for 'chain 'N' and resid 132 through 134' Processing helix chain 'Q' and resid 122 through 127 Processing helix chain 'Q' and resid 184 through 190 Processing helix chain 'R' and resid 28 through 32 Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'R' and resid 132 through 134 No H-bonds generated for 'chain 'R' and resid 132 through 134' Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.223A pdb=" N SER A 29 " --> pdb=" O MET A 45 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N MET A 45 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 35 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 40 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 167 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 24 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 95 removed outlier: 3.702A pdb=" N SER A 210 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU A 273 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 49 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 95 removed outlier: 4.744A pdb=" N ASP A 67 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N SER A 120 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL A 65 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR A 122 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ALA A 63 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS A 124 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N TYR A 61 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE A 126 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR A 59 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG A 128 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ARG A 57 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ILE A 130 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N GLU A 55 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 181 removed outlier: 4.005A pdb=" N GLY A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 310 removed outlier: 3.583A pdb=" N ALA A 315 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 310 Processing sheet with id=AA8, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AA9, first strand: chain 'A' and resid 379 through 381 Processing sheet with id=AB1, first strand: chain 'C' and resid 9 through 13 removed outlier: 3.589A pdb=" N THR C 32 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ALA C 35 " --> pdb=" O PRO C 39 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU C 273 " --> pdb=" O LYS C 279 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER C 210 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 209 " --> pdb=" O VAL C 206 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 112 through 130 current: chain 'C' and resid 164 through 165 Processing sheet with id=AB2, first strand: chain 'C' and resid 90 through 95 removed outlier: 3.586A pdb=" N LYS C 209 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER C 210 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU C 273 " --> pdb=" O LYS C 279 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 50 current: chain 'C' and resid 225 through 226 Processing sheet with id=AB3, first strand: chain 'C' and resid 20 through 25 removed outlier: 3.523A pdb=" N LEU C 285 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP C 292 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU C 185 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 308 through 316 removed outlier: 6.416A pdb=" N GLU C 325 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN C 313 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C 323 " --> pdb=" O ASN C 313 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 322 " --> pdb=" O MET C 374 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET C 374 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 368 " --> pdb=" O TYR C 328 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 339 through 342 Processing sheet with id=AB6, first strand: chain 'E' and resid 8 through 13 removed outlier: 3.633A pdb=" N MET E 34 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N SER E 29 " --> pdb=" O MET E 45 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N MET E 45 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA E 35 " --> pdb=" O PRO E 39 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR E 40 " --> pdb=" O HIS E 144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 20 through 23 removed outlier: 4.614A pdb=" N GLY E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 48 through 50 removed outlier: 4.353A pdb=" N GLU E 273 " --> pdb=" O LYS E 279 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE E 270 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER E 210 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE E 113 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL E 71 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR E 115 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER E 69 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA E 117 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP E 67 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N PHE E 119 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL E 65 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS E 121 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA E 63 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER E 123 " --> pdb=" O TYR E 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 48 through 50 removed outlier: 4.353A pdb=" N GLU E 273 " --> pdb=" O LYS E 279 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE E 270 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER E 210 " --> pdb=" O VAL E 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 240 through 241 Processing sheet with id=AC2, first strand: chain 'E' and resid 308 through 316 removed outlier: 4.631A pdb=" N PHE E 310 " --> pdb=" O SER E 327 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N SER E 327 " --> pdb=" O PHE E 310 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU E 325 " --> pdb=" O LYS E 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL E 323 " --> pdb=" O PRO E 314 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 335 through 336 Processing sheet with id=AC4, first strand: chain 'E' and resid 383 through 385 Processing sheet with id=AC5, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.683A pdb=" N THR M 5 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE M 76 " --> pdb=" O ALA M 19 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 13 removed outlier: 5.932A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 115 through 119 removed outlier: 5.167A pdb=" N TYR M 174 " --> pdb=" O ASN M 139 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 154 through 155 Processing sheet with id=AC9, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.501A pdb=" N SER N 33 " --> pdb=" O GLY N 99 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N MET N 34 " --> pdb=" O TRP N 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TRP N 36 " --> pdb=" O MET N 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.604A pdb=" N ALA N 97 " --> pdb=" O TRP N 108 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP N 108 " --> pdb=" O ALA N 97 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY N 99 " --> pdb=" O ASP N 106 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ASP N 106 " --> pdb=" O GLY N 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 125 through 129 removed outlier: 3.641A pdb=" N GLY N 144 " --> pdb=" O LEU N 129 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 125 through 129 removed outlier: 3.641A pdb=" N GLY N 144 " --> pdb=" O LEU N 129 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 156 through 159 Processing sheet with id=AD6, first strand: chain 'N' and resid 174 through 176 Processing sheet with id=AD7, first strand: chain 'Q' and resid 10 through 13 Processing sheet with id=AD8, first strand: chain 'Q' and resid 19 through 24 removed outlier: 3.702A pdb=" N ILE Q 76 " --> pdb=" O ALA Q 19 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 49 through 50 Processing sheet with id=AE1, first strand: chain 'Q' and resid 115 through 119 removed outlier: 4.567A pdb=" N SER Q 132 " --> pdb=" O LEU Q 182 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU Q 182 " --> pdb=" O SER Q 132 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL Q 134 " --> pdb=" O LEU Q 180 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU Q 180 " --> pdb=" O VAL Q 134 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE Q 136 " --> pdb=" O SER Q 178 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER Q 178 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN Q 138 " --> pdb=" O MET Q 176 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N MET Q 176 " --> pdb=" O ASN Q 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 154 through 155 removed outlier: 6.972A pdb=" N TYR Q 193 " --> pdb=" O LYS Q 208 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS Q 208 " --> pdb=" O TYR Q 193 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N CYS Q 195 " --> pdb=" O ILE Q 206 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE Q 206 " --> pdb=" O CYS Q 195 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ALA Q 197 " --> pdb=" O SER Q 204 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER Q 204 " --> pdb=" O ALA Q 197 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS Q 199 " --> pdb=" O SER Q 202 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AE4, first strand: chain 'R' and resid 10 through 12 removed outlier: 5.390A pdb=" N LYS R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TRP R 47 " --> pdb=" O LYS R 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.535A pdb=" N ALA R 97 " --> pdb=" O TRP R 108 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP R 108 " --> pdb=" O ALA R 97 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY R 99 " --> pdb=" O ASP R 106 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ASP R 106 " --> pdb=" O GLY R 99 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 125 through 129 removed outlier: 5.268A pdb=" N TYR R 180 " --> pdb=" O GLY R 149 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 136 through 137 removed outlier: 5.268A pdb=" N TYR R 180 " --> pdb=" O GLY R 149 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 156 through 159 761 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6325 1.34 - 1.46: 4549 1.46 - 1.58: 8975 1.58 - 1.70: 0 1.70 - 1.82: 166 Bond restraints: 20015 Sorted by residual: bond pdb=" C LEU N 129 " pdb=" N ALA N 130 " ideal model delta sigma weight residual 1.331 1.258 0.074 1.63e-02 3.76e+03 2.05e+01 bond pdb=" CZ ARG A 193 " pdb=" NH2 ARG A 193 " ideal model delta sigma weight residual 1.330 1.299 0.031 1.30e-02 5.92e+03 5.76e+00 bond pdb=" CA HIS A 499 " pdb=" C HIS A 499 " ideal model delta sigma weight residual 1.525 1.548 -0.023 1.02e-02 9.61e+03 5.02e+00 bond pdb=" CA HIS C 499 " pdb=" C HIS C 499 " ideal model delta sigma weight residual 1.524 1.552 -0.028 1.24e-02 6.50e+03 4.98e+00 bond pdb=" CA HIS E 499 " pdb=" C HIS E 499 " ideal model delta sigma weight residual 1.525 1.551 -0.026 1.25e-02 6.40e+03 4.31e+00 ... (remaining 20010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 26072 2.16 - 4.32: 972 4.32 - 6.48: 114 6.48 - 8.64: 35 8.64 - 10.79: 14 Bond angle restraints: 27207 Sorted by residual: angle pdb=" CA HIS C 499 " pdb=" C HIS C 499 " pdb=" N ALA C 500 " ideal model delta sigma weight residual 117.02 124.51 -7.49 1.17e+00 7.31e-01 4.10e+01 angle pdb=" C HIS C 499 " pdb=" N ALA C 500 " pdb=" CA ALA C 500 " ideal model delta sigma weight residual 121.70 132.49 -10.79 1.80e+00 3.09e-01 3.60e+01 angle pdb=" C HIS E 499 " pdb=" N ALA E 500 " pdb=" CA ALA E 500 " ideal model delta sigma weight residual 121.70 132.40 -10.70 1.80e+00 3.09e-01 3.54e+01 angle pdb=" C SER Q 28 " pdb=" CA SER Q 28 " pdb=" CB SER Q 28 " ideal model delta sigma weight residual 116.34 108.23 8.11 1.40e+00 5.10e-01 3.36e+01 angle pdb=" C HIS A 499 " pdb=" N ALA A 500 " pdb=" CA ALA A 500 " ideal model delta sigma weight residual 121.70 132.09 -10.39 1.80e+00 3.09e-01 3.33e+01 ... (remaining 27202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 11294 16.26 - 32.52: 417 32.52 - 48.78: 73 48.78 - 65.04: 8 65.04 - 81.30: 5 Dihedral angle restraints: 11797 sinusoidal: 4452 harmonic: 7345 Sorted by residual: dihedral pdb=" CA PRO E 227 " pdb=" C PRO E 227 " pdb=" N PRO E 228 " pdb=" CA PRO E 228 " ideal model delta harmonic sigma weight residual -180.00 -135.53 -44.47 0 5.00e+00 4.00e-02 7.91e+01 dihedral pdb=" CA TRP E 225 " pdb=" C TRP E 225 " pdb=" N THR E 226 " pdb=" CA THR E 226 " ideal model delta harmonic sigma weight residual -180.00 -141.59 -38.41 0 5.00e+00 4.00e-02 5.90e+01 dihedral pdb=" CA LEU A 196 " pdb=" C LEU A 196 " pdb=" N ASN A 197 " pdb=" CA ASN A 197 " ideal model delta harmonic sigma weight residual 180.00 143.14 36.86 0 5.00e+00 4.00e-02 5.43e+01 ... (remaining 11794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2011 0.043 - 0.086: 782 0.086 - 0.129: 216 0.129 - 0.172: 63 0.172 - 0.215: 12 Chirality restraints: 3084 Sorted by residual: chirality pdb=" CB ILE M 2 " pdb=" CA ILE M 2 " pdb=" CG1 ILE M 2 " pdb=" CG2 ILE M 2 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE Q 76 " pdb=" N ILE Q 76 " pdb=" C ILE Q 76 " pdb=" CB ILE Q 76 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB THR F 16 " pdb=" CA THR F 16 " pdb=" OG1 THR F 16 " pdb=" CG2 THR F 16 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3081 not shown) Planarity restraints: 3467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 74 " -0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO A 75 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 74 " 0.043 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO C 75 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 75 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 75 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 74 " -0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO E 75 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " -0.033 5.00e-02 4.00e+02 ... (remaining 3464 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 539 2.60 - 3.17: 19524 3.17 - 3.75: 35394 3.75 - 4.32: 50001 4.32 - 4.90: 74708 Nonbonded interactions: 180166 Sorted by model distance: nonbonded pdb=" OG1 THR C 40 " pdb=" O VAL C 355 " model vdw 2.023 3.040 nonbonded pdb=" OG1 THR E 40 " pdb=" O VAL E 355 " model vdw 2.050 3.040 nonbonded pdb=" OE1 GLN C 131 " pdb=" ND2 ASN N 52 " model vdw 2.059 3.120 nonbonded pdb=" OG SER A 457 " pdb=" NZ LYS B 24 " model vdw 2.081 3.120 nonbonded pdb=" OG1 THR A 40 " pdb=" O VAL A 355 " model vdw 2.090 3.040 ... (remaining 180161 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'R' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'M' selection = chain 'Q' } pdb_interpretation.ncs_group { reference = chain 'N' selection = chain 'R' } Set refine NCS operators NCS operators will be refined. 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: 34.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.760 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0272 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 : 0.005 0.090 20038 Z= 0.259 Angle : 0.978 10.794 27253 Z= 0.564 Chirality : 0.051 0.215 3084 Planarity : 0.006 0.084 3467 Dihedral : 9.478 81.297 7036 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 48.44 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.32 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.82 % Cis-general : 0.32 % Twisted Proline : 0.91 % Twisted General : 0.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.13), residues: 2568 helix: -3.74 (0.16), residues: 405 sheet: -2.15 (0.15), residues: 831 loop : -2.07 (0.14), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 97 TYR 0.033 0.003 TYR N 103 PHE 0.041 0.003 PHE A 308 TRP 0.034 0.003 TRP C 458 HIS 0.013 0.003 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00515 (20015) covalent geometry : angle 0.97627 (27207) SS BOND : bond 0.00621 ( 23) SS BOND : angle 1.79900 ( 46) hydrogen bonds : bond 0.38096 ( 693) hydrogen bonds : angle 11.31754 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 204 MET cc_start: 0.0703 (ttt) cc_final: 0.0436 (ptm) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0646 time to fit residues: 2.7401 Evaluate side-chains 20 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.127 Evaluate side-chains 6 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.025 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0250 time to fit residues: 0.2028 Evaluate side-chains 4 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.022 Evaluate side-chains 8 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.048 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0921 time to fit residues: 0.8705 Evaluate side-chains 3 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.060 Evaluate side-chains 16 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0550 time to fit residues: 1.0836 Evaluate side-chains 10 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 0.0670 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.2980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.0270 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 30.0000 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 HIS C 415 GLN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 27 GLN Q 162 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5089 r_free = 0.5089 target = 0.233979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.214451 restraints weight = 32697.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.214451 restraints weight = 33018.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.214451 restraints weight = 33018.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.214451 restraints weight = 33018.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.214451 restraints weight = 33018.977| |-----------------------------------------------------------------------------| r_work (final): 0.4823 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.168241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.137375 restraints weight = 4487.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.137324 restraints weight = 5033.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.137324 restraints weight = 5102.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.137324 restraints weight = 5102.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.137324 restraints weight = 5102.870| |-----------------------------------------------------------------------------| r_work (final): 0.4272 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.168048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.155047 restraints weight = 12399.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.155047 restraints weight = 14950.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.155047 restraints weight = 14950.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.155047 restraints weight = 14950.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.155047 restraints weight = 14950.850| |-----------------------------------------------------------------------------| r_work (final): 0.4791 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.128600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.119989 restraints weight = 15382.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.120888 restraints weight = 13125.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.121556 restraints weight = 11234.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.122046 restraints weight = 9934.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.122519 restraints weight = 9047.766| |-----------------------------------------------------------------------------| r_work (final): 0.4608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0736 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20038 Z= 0.223 Angle : 0.924 13.073 27253 Z= 0.500 Chirality : 0.052 0.211 3084 Planarity : 0.006 0.065 3467 Dihedral : 7.545 32.496 2742 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 25.14 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.52 % Favored : 95.05 % Rotamer: Outliers : 0.19 % Allowed : 2.69 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.82 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.15), residues: 2568 helix: -1.52 (0.21), residues: 451 sheet: -1.79 (0.15), residues: 897 loop : -1.41 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 98 TYR 0.025 0.003 TYR Q 193 PHE 0.026 0.003 PHE R 29 TRP 0.027 0.002 TRP E 225 HIS 0.012 0.002 HIS Q 35 Details of bonding type rmsd covalent geometry : bond 0.00444 (20015) covalent geometry : angle 0.92284 (27207) SS BOND : bond 0.00437 ( 23) SS BOND : angle 1.41236 ( 46) hydrogen bonds : bond 0.07582 ( 693) hydrogen bonds : angle 9.00403 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: C 218 PHE cc_start: 0.7855 (t80) cc_final: 0.6438 (t80) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0657 time to fit residues: 3.3725 Evaluate side-chains 22 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.160 Evaluate side-chains 4 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.027 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0262 time to fit residues: 0.1483 Evaluate side-chains 4 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.030 Evaluate side-chains 19 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.070 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 18 average time/residue: 0.1071 time to fit residues: 2.1649 Evaluate side-chains 8 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.069 Evaluate side-chains 13 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: N 171 PHE cc_start: 0.6617 (m-80) cc_final: 0.6371 (m-10) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0780 time to fit residues: 1.2162 Evaluate side-chains 11 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 89 optimal weight: 0.2980 chunk 58 optimal weight: 40.0000 chunk 236 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 202 optimal weight: 2.9990 chunk 190 optimal weight: 0.0470 chunk 124 optimal weight: 7.9990 chunk 184 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 overall best weight: 1.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 158 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 HIS Q 139 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5093 r_free = 0.5093 target = 0.232755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.216389 restraints weight = 30044.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.216375 restraints weight = 29980.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.216342 restraints weight = 29881.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.216343 restraints weight = 29823.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.216343 restraints weight = 29811.421| |-----------------------------------------------------------------------------| r_work (final): 0.4854 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.166257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.4480 r_free = 0.4480 target = 0.143161 restraints weight = 4975.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.143087 restraints weight = 9576.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.143087 restraints weight = 11250.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.143087 restraints weight = 11082.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.143087 restraints weight = 11080.423| |-----------------------------------------------------------------------------| r_work (final): 0.4350 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.166053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.151166 restraints weight = 19822.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.151480 restraints weight = 18261.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.151796 restraints weight = 17454.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.152148 restraints weight = 16817.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.152148 restraints weight = 15439.673| |-----------------------------------------------------------------------------| r_work (final): 0.4764 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.129633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.118367 restraints weight = 18746.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.118367 restraints weight = 18232.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.118367 restraints weight = 18232.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.118367 restraints weight = 18232.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.118367 restraints weight = 18232.873| |-----------------------------------------------------------------------------| r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0802 moved from start: 0.6818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.176 20038 Z= 0.305 Angle : 1.171 17.961 27253 Z= 0.621 Chirality : 0.056 0.330 3084 Planarity : 0.018 0.503 3467 Dihedral : 8.361 101.579 2742 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 29.02 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.96 % Favored : 93.54 % Rotamer: Outliers : 0.57 % Allowed : 3.49 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.82 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.15), residues: 2568 helix: -1.66 (0.21), residues: 448 sheet: -1.81 (0.15), residues: 888 loop : -1.56 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.004 ARG E 9 TYR 0.091 0.006 TYR C 59 PHE 0.080 0.005 PHE R 29 TRP 0.041 0.004 TRP E 101 HIS 0.022 0.004 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00687 (20015) covalent geometry : angle 1.17023 (27207) SS BOND : bond 0.00535 ( 23) SS BOND : angle 1.65109 ( 46) hydrogen bonds : bond 0.08149 ( 693) hydrogen bonds : angle 8.92655 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: C 45 MET cc_start: -0.0938 (mtt) cc_final: -0.2170 (mtt) REVERT: C 188 LEU cc_start: 0.5441 (tp) cc_final: 0.5100 (tp) outliers start: 4 outliers final: 0 residues processed: 34 average time/residue: 0.0742 time to fit residues: 3.2824 Evaluate side-chains 20 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.134 Evaluate side-chains 4 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.022 Fit side-chains REVERT: B 30 MET cc_start: -0.1471 (ppp) cc_final: -0.2888 (mtm) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0269 time to fit residues: 0.1539 Evaluate side-chains 4 residues out of total 63 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.022 Evaluate side-chains 11 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0732 time to fit residues: 0.9834 Evaluate side-chains 8 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.063 Evaluate side-chains 11 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.061 Fit side-chains revert: symmetry clash REVERT: N 171 PHE cc_start: 0.6396 (m-80) cc_final: 0.6147 (m-10) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0870 time to fit residues: 1.1055 Evaluate side-chains 9 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/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-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/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-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/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-2.0-5927/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-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/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-2.0-5927/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-2.0-5927/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: 66.2861 > 50: distance: 0 - 1: 11.965 distance: 1 - 2: 21.822 distance: 1 - 4: 7.811 distance: 2 - 3: 7.777 distance: 2 - 7: 30.876 distance: 4 - 5: 14.117 distance: 4 - 6: 9.909 distance: 7 - 8: 16.114 distance: 7 - 27: 41.750 distance: 8 - 9: 6.005 distance: 8 - 11: 28.832 distance: 9 - 10: 29.519 distance: 9 - 14: 30.036 distance: 10 - 24: 50.025 distance: 11 - 12: 29.216 distance: 11 - 13: 26.578 distance: 14 - 15: 46.901 distance: 15 - 16: 21.755 distance: 16 - 17: 35.154 distance: 16 - 18: 24.798 distance: 18 - 19: 18.796 distance: 19 - 20: 39.269 distance: 19 - 22: 66.286 distance: 20 - 21: 39.546 distance: 20 - 24: 40.596 distance: 22 - 23: 36.470 distance: 24 - 25: 35.518 distance: 25 - 26: 29.088 distance: 25 - 28: 7.867 distance: 26 - 27: 8.564 distance: 26 - 33: 15.865 distance: 28 - 29: 21.824 distance: 29 - 30: 32.440 distance: 30 - 31: 23.536 distance: 31 - 32: 19.885 distance: 33 - 34: 20.949 distance: 34 - 35: 22.878 distance: 34 - 37: 26.548 distance: 35 - 36: 44.696 distance: 35 - 39: 40.554 distance: 37 - 38: 51.319 distance: 39 - 40: 17.999 distance: 40 - 41: 31.333 distance: 40 - 43: 10.254 distance: 41 - 42: 39.284 distance: 41 - 50: 20.331 distance: 43 - 44: 18.776 distance: 44 - 45: 26.830 distance: 44 - 46: 17.003 distance: 45 - 47: 27.933 distance: 46 - 48: 10.682 distance: 47 - 49: 17.472 distance: 48 - 49: 15.725 distance: 50 - 51: 32.403 distance: 51 - 52: 22.369 distance: 51 - 54: 43.185 distance: 52 - 53: 36.771 distance: 52 - 58: 5.011 distance: 54 - 55: 22.542 distance: 55 - 56: 16.480 distance: 55 - 57: 24.439 distance: 58 - 59: 20.616 distance: 59 - 60: 32.197 distance: 59 - 62: 43.903 distance: 60 - 61: 41.602 distance: 60 - 65: 14.093 distance: 62 - 63: 25.808 distance: 62 - 64: 30.612 distance: 65 - 66: 39.605 distance: 66 - 67: 24.421 distance: 66 - 69: 26.102 distance: 67 - 68: 15.861 distance: 70 - 71: 10.486