Starting phenix.real_space_refine on Thu Aug 8 02:07:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q84_18246/08_2024/8q84_18246.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q84_18246/08_2024/8q84_18246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q84_18246/08_2024/8q84_18246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q84_18246/08_2024/8q84_18246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q84_18246/08_2024/8q84_18246.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q84_18246/08_2024/8q84_18246.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.040 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 80 5.16 5 C 13453 2.51 5 N 3918 2.21 5 O 4351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I ASP 72": "OD1" <-> "OD2" Residue "I GLU 96": "OE1" <-> "OE2" Residue "I GLU 113": "OE1" <-> "OE2" Residue "I ASP 136": "OD1" <-> "OD2" Residue "J ASP 108": "OD1" <-> "OD2" Residue "J ASP 146": "OD1" <-> "OD2" Residue "K GLU 75": "OE1" <-> "OE2" Residue "K GLU 122": "OE1" <-> "OE2" Residue "L GLU 22": "OE1" <-> "OE2" Residue "M GLU 2": "OE1" <-> "OE2" Residue "M GLU 45": "OE1" <-> "OE2" Residue "M GLU 63": "OE1" <-> "OE2" Residue "N ASP 22": "OD1" <-> "OD2" Residue "N ASP 27": "OD1" <-> "OD2" Residue "N GLU 32": "OE1" <-> "OE2" Residue "O TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "O TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 119": "OD1" <-> "OD2" Residue "O GLU 189": "OE1" <-> "OE2" Residue "O PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "P GLU 51": "OE1" <-> "OE2" Residue "P ASP 55": "OD1" <-> "OD2" Residue "R PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 69": "OE1" <-> "OE2" Residue "U GLU 89": "OE1" <-> "OE2" Residue "U ASP 93": "OD1" <-> "OD2" Residue "U GLU 96": "OE1" <-> "OE2" Residue "U ASP 120": "OD1" <-> "OD2" Residue "U GLU 135": "OE1" <-> "OE2" Residue "V TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 135": "OD1" <-> "OD2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W ASP 47": "OD1" <-> "OD2" Residue "W ASP 57": "OD1" <-> "OD2" Residue "X GLU 58": "OE1" <-> "OE2" Residue "X ASP 64": "OD1" <-> "OD2" Residue "X GLU 74": "OE1" <-> "OE2" Residue "Y GLU 25": "OE1" <-> "OE2" Residue "Z GLU 2": "OE1" <-> "OE2" Residue "Z ASP 22": "OD1" <-> "OD2" Residue "Z ASP 27": "OD1" <-> "OD2" Residue "Z TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 51": "OD1" <-> "OD2" Residue "Z GLU 61": "OE1" <-> "OE2" Residue "a ASP 17": "OD1" <-> "OD2" Residue "a PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 182": "OE1" <-> "OE2" Residue "a PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 8": "OE1" <-> "OE2" Residue "b GLU 11": "OE1" <-> "OE2" Residue "b GLU 16": "OE1" <-> "OE2" Residue "b ASP 25": "OD1" <-> "OD2" Residue "b GLU 48": "OE1" <-> "OE2" Residue "c GLU 18": "OE1" <-> "OE2" Residue "c GLU 39": "OE1" <-> "OE2" Residue "d GLU 13": "OE1" <-> "OE2" Residue "d GLU 24": "OE1" <-> "OE2" Residue "d GLU 31": "OE1" <-> "OE2" Residue "d PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 52": "OE1" <-> "OE2" Residue "d TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 64": "OE1" <-> "OE2" Residue "d GLU 65": "OE1" <-> "OE2" Residue "d GLU 67": "OE1" <-> "OE2" Residue "d ASP 75": "OD1" <-> "OD2" Residue "d GLU 87": "OE1" <-> "OE2" Residue "d ASP 89": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 21802 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 1463 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 282} Link IDs: {'PTRANS': 2, 'TRANS': 291} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 966 Unresolved non-hydrogen angles: 1196 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 15, 'TYR:plan': 3, 'ASN:plan1': 20, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 39, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 490 Chain: "B" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1180 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 230} Link IDs: {'PTRANS': 1, 'TRANS': 235} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 785 Unresolved non-hydrogen angles: 987 Unresolved non-hydrogen dihedrals: 617 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 17, 'ASP:plan': 18, 'PHE:plan': 5, 'GLU:plan': 30, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 398 Chain: "F" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 1463 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 282} Link IDs: {'PTRANS': 2, 'TRANS': 291} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 966 Unresolved non-hydrogen angles: 1196 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 15, 'TYR:plan': 3, 'ASN:plan1': 20, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 39, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 490 Chain: "G" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1175 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 229} Link IDs: {'PTRANS': 1, 'TRANS': 234} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 782 Unresolved non-hydrogen angles: 983 Unresolved non-hydrogen dihedrals: 615 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 17, 'ASP:plan': 18, 'PHE:plan': 5, 'GLU:plan': 30, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 398 Chain: "I" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "J" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 935 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain: "K" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 837 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "L" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 485 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "M" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "N" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 744 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "O" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1929 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "P" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 527 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "Q" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 527 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "R" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 859 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "U" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "V" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 935 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain: "W" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 837 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "X" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 535 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "Y" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "Z" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "a" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1925 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Chain breaks: 1 Chain: "b" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 561 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "c" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 527 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "d" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 859 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "e" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 82 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Time building chain proxies: 13.04, per 1000 atoms: 0.60 Number of scatterers: 21802 At special positions: 0 Unit cell: (296.8, 157.94, 263.94, 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 80 16.00 O 4351 8.00 N 3918 7.00 C 13453 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 - 3.50 Amino acid : False - 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: 9.98 Conformation dependent library (CDL) restraints added in 4.2 seconds 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6022 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 8 sheets defined 86.9% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 372 through 393 removed outlier: 4.420A pdb=" N GLY A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 409 removed outlier: 3.757A pdb=" N ASN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 479 removed outlier: 3.794A pdb=" N GLN A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.619A pdb=" N LEU A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.846A pdb=" N LEU A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 663 Processing helix chain 'B' and resid 212 through 244 removed outlier: 3.543A pdb=" N GLU B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER B 239 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 244 " --> pdb=" O ASN B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 Processing helix chain 'B' and resid 252 through 307 removed outlier: 3.708A pdb=" N SER B 256 " --> pdb=" O MET B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 337 Processing helix chain 'B' and resid 339 through 386 Processing helix chain 'B' and resid 386 through 401 Processing helix chain 'B' and resid 405 through 446 removed outlier: 3.547A pdb=" N ASN B 444 " --> pdb=" O ASN B 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 393 removed outlier: 4.527A pdb=" N GLY F 376 " --> pdb=" O GLN F 372 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS F 393 " --> pdb=" O GLU F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.841A pdb=" N ASN F 398 " --> pdb=" O ALA F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 479 removed outlier: 3.874A pdb=" N GLN F 421 " --> pdb=" O GLU F 417 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU F 422 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU F 479 " --> pdb=" O SER F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 489 removed outlier: 3.776A pdb=" N LEU F 488 " --> pdb=" O ASN F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 499 Processing helix chain 'F' and resid 506 through 511 removed outlier: 3.743A pdb=" N LEU F 510 " --> pdb=" O SER F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 663 Processing helix chain 'G' and resid 213 through 244 removed outlier: 4.057A pdb=" N LEU G 237 " --> pdb=" O GLN G 233 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU G 238 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER G 239 " --> pdb=" O VAL G 235 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN G 240 " --> pdb=" O GLU G 236 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU G 244 " --> pdb=" O ASN G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 248 Processing helix chain 'G' and resid 252 through 307 removed outlier: 3.735A pdb=" N SER G 256 " --> pdb=" O MET G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 337 Processing helix chain 'G' and resid 339 through 386 Processing helix chain 'G' and resid 386 through 401 Processing helix chain 'G' and resid 405 through 446 removed outlier: 3.559A pdb=" N ASN G 444 " --> pdb=" O ASN G 440 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET G 446 " --> pdb=" O TYR G 442 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 110 Proline residue: I 65 - end of helix Processing helix chain 'I' and resid 120 through 151 Processing helix chain 'J' and resid 61 through 126 removed outlier: 4.433A pdb=" N LEU J 89 " --> pdb=" O LEU J 85 " (cutoff:3.500A) Proline residue: J 90 - end of helix removed outlier: 3.655A pdb=" N ASP J 126 " --> pdb=" O LYS J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 143 removed outlier: 3.817A pdb=" N LEU J 130 " --> pdb=" O ASP J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 176 Processing helix chain 'K' and resid 3 through 54 Processing helix chain 'K' and resid 54 through 67 removed outlier: 3.800A pdb=" N SER K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 73 removed outlier: 3.545A pdb=" N GLN K 72 " --> pdb=" O LEU K 68 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR K 73 " --> pdb=" O GLY K 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 68 through 73' Processing helix chain 'K' and resid 74 through 79 removed outlier: 3.602A pdb=" N TYR K 78 " --> pdb=" O GLU K 75 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU K 79 " --> pdb=" O GLY K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 Processing helix chain 'L' and resid 16 through 57 Processing helix chain 'L' and resid 58 through 67 removed outlier: 3.958A pdb=" N VAL L 62 " --> pdb=" O GLU L 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 65 removed outlier: 3.695A pdb=" N GLN M 7 " --> pdb=" O ASN M 3 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ASN M 43 " --> pdb=" O ASN M 39 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU M 44 " --> pdb=" O ARG M 40 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU M 45 " --> pdb=" O ASN M 41 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR M 65 " --> pdb=" O ASN M 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 35 Processing helix chain 'N' and resid 53 through 65 removed outlier: 3.827A pdb=" N ASP N 59 " --> pdb=" O GLN N 55 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS N 63 " --> pdb=" O ASP N 59 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY N 65 " --> pdb=" O GLU N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 94 removed outlier: 3.753A pdb=" N LYS N 72 " --> pdb=" O GLY N 68 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS N 94 " --> pdb=" O GLY N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 22 Processing helix chain 'O' and resid 28 through 38 removed outlier: 3.568A pdb=" N ASN O 32 " --> pdb=" O GLY O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 51 removed outlier: 3.811A pdb=" N ARG O 45 " --> pdb=" O LYS O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 63 Processing helix chain 'O' and resid 81 through 99 Processing helix chain 'O' and resid 111 through 125 removed outlier: 3.521A pdb=" N TYR O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS O 118 " --> pdb=" O VAL O 114 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU O 121 " --> pdb=" O ASN O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 168 Processing helix chain 'O' and resid 171 through 184 Processing helix chain 'O' and resid 206 through 221 Processing helix chain 'O' and resid 223 through 265 removed outlier: 3.647A pdb=" N LEU O 253 " --> pdb=" O LYS O 249 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 57 removed outlier: 3.698A pdb=" N GLU P 11 " --> pdb=" O GLU P 7 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE P 40 " --> pdb=" O THR P 36 " (cutoff:3.500A) Proline residue: P 41 - end of helix Processing helix chain 'P' and resid 57 through 69 removed outlier: 4.271A pdb=" N THR P 67 " --> pdb=" O MET P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 40 removed outlier: 3.591A pdb=" N HIS Q 14 " --> pdb=" O ASN Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 63 Processing helix chain 'R' and resid 2 through 40 Proline residue: R 32 - end of helix removed outlier: 4.112A pdb=" N MET R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 65 Processing helix chain 'R' and resid 65 through 108 Processing helix chain 'U' and resid 58 through 111 Proline residue: U 65 - end of helix removed outlier: 3.556A pdb=" N CYS U 111 " --> pdb=" O SER U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 120 through 151 Processing helix chain 'V' and resid 61 through 126 removed outlier: 4.450A pdb=" N LEU V 89 " --> pdb=" O LEU V 85 " (cutoff:3.500A) Proline residue: V 90 - end of helix removed outlier: 3.809A pdb=" N ASP V 126 " --> pdb=" O LYS V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 143 Processing helix chain 'V' and resid 146 through 150 Processing helix chain 'V' and resid 151 through 176 Processing helix chain 'W' and resid 3 through 67 removed outlier: 4.562A pdb=" N ASN W 55 " --> pdb=" O GLN W 51 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TRP W 56 " --> pdb=" O LEU W 52 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP W 57 " --> pdb=" O MET W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 73 Processing helix chain 'W' and resid 75 through 79 removed outlier: 3.812A pdb=" N GLU W 79 " --> pdb=" O GLY W 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 84 Processing helix chain 'X' and resid 14 through 57 Processing helix chain 'X' and resid 58 through 67 removed outlier: 4.080A pdb=" N VAL X 62 " --> pdb=" O GLU X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 80 Processing helix chain 'Y' and resid 4 through 42 removed outlier: 4.041A pdb=" N VAL Y 8 " --> pdb=" O PRO Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 65 Processing helix chain 'Z' and resid 6 through 35 Processing helix chain 'Z' and resid 53 through 65 removed outlier: 3.922A pdb=" N ASP Z 59 " --> pdb=" O GLN Z 55 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS Z 63 " --> pdb=" O ASP Z 59 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY Z 65 " --> pdb=" O GLU Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 94 removed outlier: 3.827A pdb=" N LYS Z 72 " --> pdb=" O GLY Z 68 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL Z 75 " --> pdb=" O LEU Z 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 22 Processing helix chain 'a' and resid 29 through 37 Processing helix chain 'a' and resid 40 through 51 Processing helix chain 'a' and resid 56 through 63 Processing helix chain 'a' and resid 81 through 99 Processing helix chain 'a' and resid 111 through 125 removed outlier: 4.221A pdb=" N LYS a 118 " --> pdb=" O VAL a 114 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU a 121 " --> pdb=" O ASN a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 158 through 168 Processing helix chain 'a' and resid 171 through 183 Processing helix chain 'a' and resid 206 through 221 Processing helix chain 'a' and resid 223 through 265 removed outlier: 4.272A pdb=" N SER a 242 " --> pdb=" O GLU a 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 38 Processing helix chain 'b' and resid 38 through 57 Processing helix chain 'b' and resid 57 through 69 Processing helix chain 'c' and resid 2 through 39 Processing helix chain 'c' and resid 44 through 63 Processing helix chain 'd' and resid 2 through 40 Proline residue: d 32 - end of helix removed outlier: 3.741A pdb=" N THR d 39 " --> pdb=" O ASN d 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 65 Processing helix chain 'd' and resid 65 through 108 Processing sheet with id=AA1, first strand: chain 'I' and resid 112 through 114 Processing sheet with id=AA2, first strand: chain 'O' and resid 52 through 54 Processing sheet with id=AA3, first strand: chain 'O' and resid 64 through 67 Processing sheet with id=AA4, first strand: chain 'O' and resid 185 through 189 Processing sheet with id=AA5, first strand: chain 'U' and resid 112 through 113 Processing sheet with id=AA6, first strand: chain 'a' and resid 52 through 54 removed outlier: 3.660A pdb=" N ILE W 127 " --> pdb=" O ARG d 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 64 through 67 Processing sheet with id=AA8, first strand: chain 'a' and resid 185 through 189 2257 hydrogen bonds defined for protein. 6720 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: 7.44 Time building geometry restraints manager: 10.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5190 1.33 - 1.45: 3923 1.45 - 1.58: 12737 1.58 - 1.70: 0 1.70 - 1.82: 142 Bond restraints: 21992 Sorted by residual: bond pdb=" N LYS N 72 " pdb=" CA LYS N 72 " ideal model delta sigma weight residual 1.459 1.405 0.054 1.17e-02 7.31e+03 2.13e+01 bond pdb=" C LEU N 71 " pdb=" N LYS N 72 " ideal model delta sigma weight residual 1.334 1.298 0.036 1.23e-02 6.61e+03 8.47e+00 bond pdb=" CA LYS N 72 " pdb=" CB LYS N 72 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.57e-02 4.06e+03 7.95e+00 bond pdb=" C LYS N 72 " pdb=" O LYS N 72 " ideal model delta sigma weight residual 1.236 1.211 0.025 1.15e-02 7.56e+03 4.89e+00 bond pdb=" CA LYS N 72 " pdb=" C LYS N 72 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.24e-02 6.50e+03 2.98e+00 ... (remaining 21987 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.88: 225 105.88 - 112.91: 12272 112.91 - 119.94: 7018 119.94 - 126.96: 10239 126.96 - 133.99: 123 Bond angle restraints: 29877 Sorted by residual: angle pdb=" CA MET I 143 " pdb=" CB MET I 143 " pdb=" CG MET I 143 " ideal model delta sigma weight residual 114.10 123.86 -9.76 2.00e+00 2.50e-01 2.38e+01 angle pdb=" CA MET U 143 " pdb=" CB MET U 143 " pdb=" CG MET U 143 " ideal model delta sigma weight residual 114.10 123.43 -9.33 2.00e+00 2.50e-01 2.17e+01 angle pdb=" CA ARG d 57 " pdb=" CB ARG d 57 " pdb=" CG ARG d 57 " ideal model delta sigma weight residual 114.10 122.47 -8.37 2.00e+00 2.50e-01 1.75e+01 angle pdb=" CA TYR Z 16 " pdb=" CB TYR Z 16 " pdb=" CG TYR Z 16 " ideal model delta sigma weight residual 113.90 121.42 -7.52 1.80e+00 3.09e-01 1.75e+01 angle pdb=" CA GLN d 85 " pdb=" CB GLN d 85 " pdb=" CG GLN d 85 " ideal model delta sigma weight residual 114.10 122.27 -8.17 2.00e+00 2.50e-01 1.67e+01 ... (remaining 29872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 12030 17.22 - 34.43: 1131 34.43 - 51.65: 316 51.65 - 68.86: 57 68.86 - 86.08: 27 Dihedral angle restraints: 13561 sinusoidal: 4396 harmonic: 9165 Sorted by residual: dihedral pdb=" CA ILE Z 53 " pdb=" C ILE Z 53 " pdb=" N LEU Z 54 " pdb=" CA LEU Z 54 " ideal model delta harmonic sigma weight residual -180.00 -154.92 -25.08 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA LEU I 63 " pdb=" C LEU I 63 " pdb=" N LEU I 64 " pdb=" CA LEU I 64 " ideal model delta harmonic sigma weight residual -180.00 -161.68 -18.32 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ASP O 119 " pdb=" CB ASP O 119 " pdb=" CG ASP O 119 " pdb=" OD1 ASP O 119 " ideal model delta sinusoidal sigma weight residual -30.00 -89.96 59.96 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 13558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3265 0.066 - 0.132: 337 0.132 - 0.197: 22 0.197 - 0.263: 3 0.263 - 0.329: 2 Chirality restraints: 3629 Sorted by residual: chirality pdb=" CG LEU R 97 " pdb=" CB LEU R 97 " pdb=" CD1 LEU R 97 " pdb=" CD2 LEU R 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB VAL O 251 " pdb=" CA VAL O 251 " pdb=" CG1 VAL O 251 " pdb=" CG2 VAL O 251 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CG LEU Z 78 " pdb=" CB LEU Z 78 " pdb=" CD1 LEU Z 78 " pdb=" CD2 LEU Z 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 3626 not shown) Planarity restraints: 3977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU I 64 " 0.056 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO I 65 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO I 65 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 65 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP U 120 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" C ASP U 120 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP U 120 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE U 121 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU X 58 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C GLU X 58 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU X 58 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE X 59 " -0.016 2.00e-02 2.50e+03 ... (remaining 3974 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 267 2.62 - 3.19: 21632 3.19 - 3.76: 38930 3.76 - 4.33: 44268 4.33 - 4.90: 72870 Nonbonded interactions: 177967 Sorted by model distance: nonbonded pdb=" O ILE O 247 " pdb=" OH TYR R 95 " model vdw 2.054 3.040 nonbonded pdb=" OG SER W 3 " pdb=" OD1 ASP W 5 " model vdw 2.125 3.040 nonbonded pdb=" OE1 GLU a 182 " pdb=" ND2 ASN a 183 " model vdw 2.143 3.120 nonbonded pdb=" NZ LYS V 79 " pdb=" OD2 ASP Z 22 " model vdw 2.182 3.120 nonbonded pdb=" OE2 GLU U 96 " pdb=" N ILE a 29 " model vdw 2.185 3.120 ... (remaining 177962 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = (chain 'B' and resid 212 through 447) selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'W' } ncs_group { reference = chain 'L' selection = (chain 'X' and resid 15 through 75) } ncs_group { reference = chain 'M' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = (chain 'Z' and resid 3 through 94) } ncs_group { reference = (chain 'O' and resid 3 through 265) selection = chain 'a' } ncs_group { reference = chain 'P' selection = (chain 'b' and resid 5 through 69) } ncs_group { reference = chain 'Q' selection = chain 'c' } ncs_group { reference = chain 'R' selection = chain 'd' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.760 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: 1.040 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 61.500 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 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 : 0.003 0.054 21992 Z= 0.224 Angle : 0.740 12.988 29877 Z= 0.400 Chirality : 0.040 0.329 3629 Planarity : 0.004 0.085 3977 Dihedral : 15.742 86.080 7539 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 0.58 % Allowed : 22.99 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.15), residues: 3057 helix: 2.80 (0.10), residues: 2543 sheet: 0.06 (0.97), residues: 32 loop : -0.32 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 59 HIS 0.006 0.001 HIS a 31 PHE 0.022 0.002 PHE M 60 TYR 0.045 0.002 TYR Z 16 ARG 0.017 0.001 ARG O 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 377 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 GLN cc_start: 0.8449 (tt0) cc_final: 0.7800 (tp40) REVERT: Q 6 GLN cc_start: 0.9398 (mt0) cc_final: 0.9067 (mm-40) REVERT: U 66 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8769 (mmmm) REVERT: W 41 GLU cc_start: 0.8434 (tp30) cc_final: 0.8067 (tp30) REVERT: W 47 ASP cc_start: 0.8972 (t0) cc_final: 0.8651 (p0) REVERT: Z 11 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8235 (tm-30) REVERT: a 168 PHE cc_start: 0.8271 (m-80) cc_final: 0.7960 (m-80) REVERT: a 201 PHE cc_start: 0.8544 (t80) cc_final: 0.8290 (t80) outliers start: 11 outliers final: 6 residues processed: 380 average time/residue: 0.3386 time to fit residues: 198.7744 Evaluate side-chains 318 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 312 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain V residue 144 THR Chi-restraints excluded: chain W residue 72 GLN Chi-restraints excluded: chain Y residue 66 ASN Chi-restraints excluded: chain d residue 98 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 77 optimal weight: 50.0000 chunk 153 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 235 optimal weight: 1.9990 chunk 90 optimal weight: 30.0000 chunk 142 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 272 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN O 36 GLN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN V 134 ASN W 72 GLN Y 19 ASN b 22 GLN ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN c 44 GLN d 105 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21992 Z= 0.216 Angle : 0.612 11.066 29877 Z= 0.321 Chirality : 0.038 0.242 3629 Planarity : 0.004 0.071 3977 Dihedral : 4.316 44.722 3251 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.13 % Favored : 97.81 % Rotamer: Outliers : 3.58 % Allowed : 18.36 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.15), residues: 3057 helix: 3.08 (0.10), residues: 2533 sheet: -0.23 (0.89), residues: 32 loop : -0.30 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 59 HIS 0.006 0.001 HIS a 31 PHE 0.034 0.002 PHE a 246 TYR 0.040 0.002 TYR Z 16 ARG 0.007 0.001 ARG X 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 349 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 72 ASP cc_start: 0.9021 (m-30) cc_final: 0.8694 (m-30) REVERT: K 77 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8250 (t0) REVERT: K 85 ASP cc_start: 0.8406 (t0) cc_final: 0.8194 (t0) REVERT: N 83 LYS cc_start: 0.9339 (tppp) cc_final: 0.9137 (tppp) REVERT: P 65 GLN cc_start: 0.8341 (tt0) cc_final: 0.7671 (tp-100) REVERT: Q 33 MET cc_start: 0.8929 (tmm) cc_final: 0.8685 (tmm) REVERT: U 66 LYS cc_start: 0.9209 (mmtt) cc_final: 0.8862 (mmmm) REVERT: U 123 ASP cc_start: 0.9019 (t0) cc_final: 0.8655 (t0) REVERT: V 140 GLU cc_start: 0.7487 (mp0) cc_final: 0.6942 (pm20) REVERT: X 58 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8152 (tm-30) REVERT: Z 13 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8609 (mt) REVERT: Z 29 THR cc_start: 0.8523 (m) cc_final: 0.8302 (m) REVERT: Z 35 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: Z 59 ASP cc_start: 0.7973 (t0) cc_final: 0.7757 (t0) REVERT: a 168 PHE cc_start: 0.8433 (m-80) cc_final: 0.8197 (m-80) REVERT: b 1 MET cc_start: 0.5160 (tmm) cc_final: 0.4131 (ppp) REVERT: d 98 ASN cc_start: 0.8488 (m110) cc_final: 0.7585 (t0) outliers start: 68 outliers final: 31 residues processed: 397 average time/residue: 0.3252 time to fit residues: 201.1367 Evaluate side-chains 336 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 302 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 83 PHE Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain V residue 124 MET Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 77 SER Chi-restraints excluded: chain Z residue 13 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain b residue 2 ASP Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 10.0000 chunk 84 optimal weight: 30.0000 chunk 226 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 272 optimal weight: 0.6980 chunk 294 optimal weight: 3.9990 chunk 243 optimal weight: 0.9990 chunk 270 optimal weight: 5.9990 chunk 93 optimal weight: 30.0000 chunk 218 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 GLN K 31 GLN L 29 GLN M 61 ASN Q 2 ASN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 GLN a 57 HIS a 195 GLN ** c 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN c 44 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21992 Z= 0.334 Angle : 0.651 11.702 29877 Z= 0.341 Chirality : 0.039 0.336 3629 Planarity : 0.004 0.058 3977 Dihedral : 4.143 44.940 3243 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.26 % Favored : 97.68 % Rotamer: Outliers : 4.00 % Allowed : 19.31 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.15), residues: 3057 helix: 2.98 (0.10), residues: 2557 sheet: -0.57 (1.03), residues: 22 loop : -0.48 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 59 HIS 0.008 0.001 HIS a 31 PHE 0.020 0.002 PHE a 201 TYR 0.023 0.002 TYR a 85 ARG 0.008 0.001 ARG X 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 338 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 72 ASP cc_start: 0.8967 (m-30) cc_final: 0.8699 (m-30) REVERT: K 8 ILE cc_start: 0.7555 (mm) cc_final: 0.6004 (mm) REVERT: K 12 ARG cc_start: 0.8327 (mpp80) cc_final: 0.7882 (mtm-85) REVERT: K 20 LYS cc_start: 0.8497 (mttm) cc_final: 0.8203 (mmtm) REVERT: K 85 ASP cc_start: 0.8436 (t0) cc_final: 0.8090 (t0) REVERT: M 16 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8926 (tt) REVERT: N 24 LYS cc_start: 0.9330 (mtmm) cc_final: 0.8999 (pttm) REVERT: N 28 GLU cc_start: 0.8907 (tp30) cc_final: 0.8553 (tp30) REVERT: N 83 LYS cc_start: 0.9424 (tppp) cc_final: 0.9096 (tppp) REVERT: U 61 GLN cc_start: 0.8936 (mm110) cc_final: 0.8705 (mm110) REVERT: U 66 LYS cc_start: 0.9205 (mmtt) cc_final: 0.8941 (mmmm) REVERT: U 123 ASP cc_start: 0.9062 (t0) cc_final: 0.8708 (t0) REVERT: V 148 ASP cc_start: 0.8745 (t0) cc_final: 0.8429 (p0) REVERT: W 79 GLU cc_start: 0.7906 (mp0) cc_final: 0.7595 (pm20) REVERT: X 58 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8117 (tm-30) REVERT: Z 13 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8593 (mt) REVERT: Z 19 LEU cc_start: 0.9427 (tt) cc_final: 0.9227 (mm) REVERT: Z 29 THR cc_start: 0.8543 (m) cc_final: 0.8251 (m) REVERT: Z 35 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8243 (t80) REVERT: Z 59 ASP cc_start: 0.8055 (t0) cc_final: 0.7776 (t0) REVERT: a 168 PHE cc_start: 0.8450 (m-80) cc_final: 0.8214 (m-80) REVERT: b 8 GLU cc_start: 0.7790 (tp30) cc_final: 0.7340 (tp30) REVERT: b 58 GLU cc_start: 0.8503 (tp30) cc_final: 0.8113 (tm-30) REVERT: d 98 ASN cc_start: 0.8560 (m110) cc_final: 0.7764 (t0) REVERT: d 108 MET cc_start: 0.2373 (tmm) cc_final: 0.1869 (pmm) REVERT: e 17 TYR cc_start: 0.8613 (t80) cc_final: 0.8394 (t80) outliers start: 76 outliers final: 46 residues processed: 389 average time/residue: 0.3197 time to fit residues: 195.4262 Evaluate side-chains 351 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 302 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 129 LYS Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 124 MET Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 77 SER Chi-restraints excluded: chain Z residue 13 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 57 HIS Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 160 THR Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 243 LYS Chi-restraints excluded: chain b residue 2 ASP Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 141 optimal weight: 0.5980 chunk 30 optimal weight: 30.0000 chunk 130 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 chunk 273 optimal weight: 3.9990 chunk 289 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 259 optimal weight: 10.0000 chunk 78 optimal weight: 40.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 31 GLN L 29 GLN N 34 ASN O 36 GLN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 57 HIS c 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21992 Z= 0.192 Angle : 0.596 9.551 29877 Z= 0.313 Chirality : 0.037 0.257 3629 Planarity : 0.004 0.057 3977 Dihedral : 4.050 45.216 3243 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 3.37 % Allowed : 20.78 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.15), residues: 3057 helix: 3.11 (0.10), residues: 2554 sheet: -0.30 (0.87), residues: 32 loop : -0.41 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 66 HIS 0.008 0.001 HIS a 31 PHE 0.026 0.002 PHE O 168 TYR 0.025 0.002 TYR Z 16 ARG 0.012 0.001 ARG R 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 351 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8259 (pp) REVERT: J 72 ASP cc_start: 0.8953 (m-30) cc_final: 0.8670 (m-30) REVERT: K 8 ILE cc_start: 0.7552 (mm) cc_final: 0.5868 (mm) REVERT: K 12 ARG cc_start: 0.8264 (mpp80) cc_final: 0.7853 (mtm-85) REVERT: K 20 LYS cc_start: 0.8400 (mttm) cc_final: 0.8111 (mmtm) REVERT: K 85 ASP cc_start: 0.8411 (t0) cc_final: 0.7996 (t0) REVERT: M 16 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8878 (tt) REVERT: N 24 LYS cc_start: 0.9280 (mtmm) cc_final: 0.8921 (pttm) REVERT: N 59 ASP cc_start: 0.8211 (t0) cc_final: 0.8003 (t0) REVERT: N 83 LYS cc_start: 0.9379 (tppp) cc_final: 0.9039 (tppt) REVERT: O 57 HIS cc_start: 0.8365 (p-80) cc_final: 0.8117 (p-80) REVERT: O 237 TYR cc_start: 0.7770 (t80) cc_final: 0.7545 (t80) REVERT: Q 33 MET cc_start: 0.8901 (tmm) cc_final: 0.8471 (tmm) REVERT: U 61 GLN cc_start: 0.8904 (mm110) cc_final: 0.8623 (mm-40) REVERT: U 66 LYS cc_start: 0.9196 (mmtt) cc_final: 0.8877 (mmmm) REVERT: U 123 ASP cc_start: 0.9025 (t0) cc_final: 0.8678 (t0) REVERT: V 98 GLU cc_start: 0.8661 (tp30) cc_final: 0.8377 (tp30) REVERT: V 148 ASP cc_start: 0.8707 (t0) cc_final: 0.8341 (p0) REVERT: W 124 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7711 (ptm) REVERT: X 58 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8210 (tm-30) REVERT: X 60 GLN cc_start: 0.8670 (tp40) cc_final: 0.8379 (pm20) REVERT: X 74 GLU cc_start: 0.8093 (mp0) cc_final: 0.7837 (mp0) REVERT: Y 6 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7920 (mm-30) REVERT: Z 29 THR cc_start: 0.8505 (m) cc_final: 0.8272 (m) REVERT: Z 35 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.8188 (t80) REVERT: Z 59 ASP cc_start: 0.8042 (t0) cc_final: 0.7802 (t0) REVERT: a 168 PHE cc_start: 0.8522 (m-80) cc_final: 0.8282 (m-80) REVERT: b 8 GLU cc_start: 0.7763 (tp30) cc_final: 0.7282 (tp30) REVERT: d 98 ASN cc_start: 0.8536 (m110) cc_final: 0.7755 (t0) REVERT: d 108 MET cc_start: 0.2629 (tmm) cc_final: 0.2079 (pmm) outliers start: 64 outliers final: 39 residues processed: 396 average time/residue: 0.3331 time to fit residues: 206.6758 Evaluate side-chains 351 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 308 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 183 ASN Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 57 HIS Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 243 LYS Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 0.6980 chunk 164 optimal weight: 0.5980 chunk 4 optimal weight: 50.0000 chunk 215 optimal weight: 0.7980 chunk 119 optimal weight: 0.0670 chunk 247 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 0 optimal weight: 80.0000 chunk 148 optimal weight: 0.6980 chunk 260 optimal weight: 3.9990 chunk 73 optimal weight: 40.0000 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 2 ASN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 45 ASN a 56 ASN a 57 HIS ** c 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21992 Z= 0.187 Angle : 0.599 13.234 29877 Z= 0.314 Chirality : 0.037 0.247 3629 Planarity : 0.003 0.055 3977 Dihedral : 3.997 45.474 3243 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.29 % Favored : 97.64 % Rotamer: Outliers : 3.63 % Allowed : 21.04 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.02 (0.15), residues: 3057 helix: 3.18 (0.10), residues: 2554 sheet: -0.21 (0.86), residues: 32 loop : -0.40 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 59 HIS 0.007 0.001 HIS a 31 PHE 0.022 0.002 PHE M 60 TYR 0.029 0.001 TYR Z 16 ARG 0.009 0.001 ARG R 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 344 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8172 (pp) REVERT: I 69 GLU cc_start: 0.9043 (pm20) cc_final: 0.8606 (pm20) REVERT: I 112 VAL cc_start: 0.8945 (t) cc_final: 0.8678 (p) REVERT: J 72 ASP cc_start: 0.8971 (m-30) cc_final: 0.8699 (m-30) REVERT: K 8 ILE cc_start: 0.7596 (mm) cc_final: 0.5918 (mm) REVERT: K 12 ARG cc_start: 0.8217 (mpp80) cc_final: 0.7852 (mtm-85) REVERT: K 20 LYS cc_start: 0.8335 (mttm) cc_final: 0.7965 (mmtm) REVERT: K 85 ASP cc_start: 0.8384 (t0) cc_final: 0.7962 (t0) REVERT: M 16 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8846 (tt) REVERT: N 24 LYS cc_start: 0.9272 (mtmm) cc_final: 0.8883 (pttm) REVERT: N 59 ASP cc_start: 0.8284 (t0) cc_final: 0.7964 (t0) REVERT: N 83 LYS cc_start: 0.9410 (tppp) cc_final: 0.8941 (tppt) REVERT: O 57 HIS cc_start: 0.8351 (p-80) cc_final: 0.8128 (p-80) REVERT: O 230 TYR cc_start: 0.8949 (t80) cc_final: 0.8719 (t80) REVERT: O 237 TYR cc_start: 0.7788 (t80) cc_final: 0.7376 (t80) REVERT: P 8 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7705 (tm-30) REVERT: Q 6 GLN cc_start: 0.9363 (mt0) cc_final: 0.9154 (mp10) REVERT: Q 33 MET cc_start: 0.9007 (tmm) cc_final: 0.8612 (tmm) REVERT: R 20 LYS cc_start: 0.9193 (mmmt) cc_final: 0.8936 (tptp) REVERT: U 66 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8950 (mmmm) REVERT: U 123 ASP cc_start: 0.9054 (t0) cc_final: 0.8752 (t0) REVERT: V 98 GLU cc_start: 0.8709 (tp30) cc_final: 0.8384 (tp30) REVERT: V 147 GLU cc_start: 0.3643 (tm-30) cc_final: 0.3442 (tm-30) REVERT: V 148 ASP cc_start: 0.8744 (t0) cc_final: 0.8386 (p0) REVERT: W 40 LYS cc_start: 0.8902 (tppt) cc_final: 0.8700 (tptp) REVERT: X 58 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8188 (tm-30) REVERT: X 60 GLN cc_start: 0.8710 (tp40) cc_final: 0.8374 (pm20) REVERT: Y 6 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7976 (mm-30) REVERT: Z 29 THR cc_start: 0.8451 (m) cc_final: 0.8188 (m) REVERT: Z 35 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.8121 (t80) REVERT: Z 59 ASP cc_start: 0.8122 (t0) cc_final: 0.7897 (t0) REVERT: a 168 PHE cc_start: 0.8532 (m-80) cc_final: 0.8283 (m-80) REVERT: b 1 MET cc_start: 0.4959 (OUTLIER) cc_final: 0.4723 (ppp) REVERT: b 8 GLU cc_start: 0.7700 (tp30) cc_final: 0.7182 (tp30) REVERT: d 20 LYS cc_start: 0.9135 (tppt) cc_final: 0.8718 (tppt) REVERT: d 98 ASN cc_start: 0.8583 (m110) cc_final: 0.7855 (t0) outliers start: 69 outliers final: 42 residues processed: 394 average time/residue: 0.3260 time to fit residues: 198.9137 Evaluate side-chains 358 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 312 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 183 ASN Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 69 GLU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 57 HIS Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 243 LYS Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 30.0000 chunk 261 optimal weight: 0.6980 chunk 57 optimal weight: 40.0000 chunk 170 optimal weight: 5.9990 chunk 71 optimal weight: 40.0000 chunk 290 optimal weight: 0.7980 chunk 240 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 24 optimal weight: 50.0000 chunk 96 optimal weight: 8.9990 chunk 152 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 18 GLN Q 2 ASN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 GLN X 46 ASN ** a 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21992 Z= 0.226 Angle : 0.620 10.456 29877 Z= 0.325 Chirality : 0.038 0.243 3629 Planarity : 0.004 0.053 3977 Dihedral : 3.983 45.708 3243 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 3.79 % Allowed : 21.78 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.15), residues: 3057 helix: 3.18 (0.10), residues: 2566 sheet: -0.15 (0.86), residues: 32 loop : -0.39 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 59 HIS 0.014 0.001 HIS a 57 PHE 0.024 0.002 PHE O 83 TYR 0.027 0.002 TYR Z 16 ARG 0.011 0.001 ARG R 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 346 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8171 (pp) REVERT: I 69 GLU cc_start: 0.8876 (pm20) cc_final: 0.8544 (pm20) REVERT: I 112 VAL cc_start: 0.9045 (t) cc_final: 0.8776 (p) REVERT: J 72 ASP cc_start: 0.8931 (m-30) cc_final: 0.8640 (m-30) REVERT: K 12 ARG cc_start: 0.8272 (mpp80) cc_final: 0.8054 (mtt90) REVERT: K 16 GLN cc_start: 0.8384 (pp30) cc_final: 0.8122 (pp30) REVERT: K 20 LYS cc_start: 0.8430 (mttm) cc_final: 0.8004 (mmtm) REVERT: K 85 ASP cc_start: 0.8393 (t0) cc_final: 0.7971 (t0) REVERT: M 16 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8882 (tt) REVERT: N 32 GLU cc_start: 0.8820 (tp30) cc_final: 0.8458 (tp30) REVERT: N 59 ASP cc_start: 0.8345 (t0) cc_final: 0.7959 (t0) REVERT: O 205 PHE cc_start: 0.4989 (OUTLIER) cc_final: 0.2234 (t80) REVERT: O 230 TYR cc_start: 0.8990 (t80) cc_final: 0.8733 (t80) REVERT: O 237 TYR cc_start: 0.7800 (t80) cc_final: 0.7417 (t80) REVERT: P 66 GLU cc_start: 0.7698 (tt0) cc_final: 0.7410 (tp30) REVERT: Q 6 GLN cc_start: 0.9342 (mt0) cc_final: 0.8979 (mm-40) REVERT: R 1 MET cc_start: 0.7680 (mmm) cc_final: 0.7377 (mmt) REVERT: R 20 LYS cc_start: 0.9206 (mmmt) cc_final: 0.8943 (tptp) REVERT: U 66 LYS cc_start: 0.9190 (mmtt) cc_final: 0.8961 (mmmm) REVERT: U 123 ASP cc_start: 0.9060 (t0) cc_final: 0.8785 (t0) REVERT: V 148 ASP cc_start: 0.8721 (t0) cc_final: 0.8379 (p0) REVERT: W 126 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7070 (tmm-80) REVERT: X 43 ASN cc_start: 0.4824 (t0) cc_final: 0.4601 (t0) REVERT: X 58 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8088 (tm-30) REVERT: X 74 GLU cc_start: 0.7956 (mp0) cc_final: 0.7706 (mp0) REVERT: Y 6 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8081 (mm-30) REVERT: Z 29 THR cc_start: 0.8432 (m) cc_final: 0.8172 (m) REVERT: Z 35 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8070 (t80) REVERT: Z 58 ARG cc_start: 0.6432 (mmt180) cc_final: 0.6228 (mmt180) REVERT: a 168 PHE cc_start: 0.8556 (m-80) cc_final: 0.8314 (m-80) REVERT: b 8 GLU cc_start: 0.7743 (tp30) cc_final: 0.7208 (tp30) REVERT: c 24 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8110 (tm-30) REVERT: d 20 LYS cc_start: 0.9146 (tppt) cc_final: 0.8710 (tppt) REVERT: d 98 ASN cc_start: 0.8492 (m110) cc_final: 0.7741 (t0) REVERT: d 108 MET cc_start: 0.2960 (ppp) cc_final: 0.2434 (pmm) outliers start: 72 outliers final: 48 residues processed: 400 average time/residue: 0.3215 time to fit residues: 199.3668 Evaluate side-chains 366 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 313 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain L residue 19 TYR Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 183 ASN Chi-restraints excluded: chain O residue 205 PHE Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 235 HIS Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain W residue 126 ARG Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 243 LYS Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 0.3980 chunk 32 optimal weight: 30.0000 chunk 165 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 chunk 289 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 133 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 36 GLN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN V 116 GLN ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 98 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21992 Z= 0.189 Angle : 0.627 10.063 29877 Z= 0.327 Chirality : 0.037 0.242 3629 Planarity : 0.004 0.050 3977 Dihedral : 3.958 45.808 3243 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 3.68 % Allowed : 23.04 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.15 (0.15), residues: 3057 helix: 3.26 (0.10), residues: 2562 sheet: -0.09 (0.86), residues: 32 loop : -0.36 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 59 HIS 0.007 0.001 HIS a 31 PHE 0.023 0.002 PHE M 60 TYR 0.027 0.001 TYR Z 16 ARG 0.006 0.000 ARG R 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 351 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 69 GLU cc_start: 0.8872 (pm20) cc_final: 0.8573 (pm20) REVERT: I 112 VAL cc_start: 0.9017 (t) cc_final: 0.8744 (p) REVERT: J 72 ASP cc_start: 0.8940 (m-30) cc_final: 0.8648 (m-30) REVERT: J 77 MET cc_start: 0.9055 (ppp) cc_final: 0.8727 (ppp) REVERT: K 16 GLN cc_start: 0.8348 (pp30) cc_final: 0.8129 (pp30) REVERT: K 20 LYS cc_start: 0.8379 (mttm) cc_final: 0.7972 (mmtm) REVERT: K 85 ASP cc_start: 0.8448 (t0) cc_final: 0.8019 (t0) REVERT: L 58 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8213 (tm-30) REVERT: M 16 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8821 (tt) REVERT: N 32 GLU cc_start: 0.8723 (tp30) cc_final: 0.8392 (tp30) REVERT: O 205 PHE cc_start: 0.3927 (OUTLIER) cc_final: 0.3615 (t80) REVERT: O 230 TYR cc_start: 0.9017 (t80) cc_final: 0.8689 (t80) REVERT: O 237 TYR cc_start: 0.7874 (t80) cc_final: 0.7488 (t80) REVERT: O 261 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.6085 (ppp) REVERT: P 66 GLU cc_start: 0.7661 (tt0) cc_final: 0.7435 (tp30) REVERT: Q 6 GLN cc_start: 0.9353 (mt0) cc_final: 0.9130 (mp10) REVERT: Q 33 MET cc_start: 0.8957 (tmm) cc_final: 0.8595 (tmm) REVERT: R 1 MET cc_start: 0.7606 (mmm) cc_final: 0.7286 (mmm) REVERT: R 20 LYS cc_start: 0.9196 (mmmt) cc_final: 0.8946 (tptp) REVERT: U 66 LYS cc_start: 0.9168 (mmtt) cc_final: 0.8950 (mmmm) REVERT: U 93 ASP cc_start: 0.8116 (t0) cc_final: 0.7514 (t0) REVERT: U 123 ASP cc_start: 0.9062 (t0) cc_final: 0.8776 (t0) REVERT: W 126 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6821 (tmm-80) REVERT: X 58 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8260 (tm-30) REVERT: X 60 GLN cc_start: 0.8615 (tp40) cc_final: 0.8340 (pm20) REVERT: Y 6 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8095 (mm-30) REVERT: Y 40 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.8292 (ttp80) REVERT: Z 29 THR cc_start: 0.8327 (m) cc_final: 0.8066 (m) REVERT: Z 35 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.8025 (t80) REVERT: a 168 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: b 8 GLU cc_start: 0.7769 (tp30) cc_final: 0.7236 (tp30) REVERT: c 24 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8142 (tm-30) REVERT: d 20 LYS cc_start: 0.9161 (tppt) cc_final: 0.8803 (tppt) REVERT: d 98 ASN cc_start: 0.8504 (m-40) cc_final: 0.7756 (t0) REVERT: d 108 MET cc_start: 0.3118 (ppp) cc_final: 0.2535 (pmm) outliers start: 70 outliers final: 48 residues processed: 399 average time/residue: 0.3241 time to fit residues: 200.0895 Evaluate side-chains 377 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 323 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 183 ASN Chi-restraints excluded: chain O residue 205 PHE Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 235 HIS Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain W residue 126 ARG Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 243 LYS Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain c residue 23 LEU Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 172 optimal weight: 30.0000 chunk 87 optimal weight: 9.9990 chunk 56 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 196 optimal weight: 0.4980 chunk 142 optimal weight: 0.9990 chunk 26 optimal weight: 40.0000 chunk 227 optimal weight: 0.8980 chunk 263 optimal weight: 0.0770 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 41 GLN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 95 ASN U 108 ASN V 127 GLN W 132 ASN a 57 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21992 Z= 0.189 Angle : 0.639 12.491 29877 Z= 0.332 Chirality : 0.038 0.244 3629 Planarity : 0.004 0.050 3977 Dihedral : 3.967 45.687 3243 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.96 % Favored : 97.97 % Rotamer: Outliers : 3.26 % Allowed : 24.20 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.17 (0.15), residues: 3057 helix: 3.27 (0.10), residues: 2564 sheet: 0.04 (0.87), residues: 32 loop : -0.34 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 59 HIS 0.015 0.001 HIS N 38 PHE 0.023 0.002 PHE O 205 TYR 0.027 0.001 TYR Z 16 ARG 0.008 0.001 ARG R 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 353 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 69 GLU cc_start: 0.8863 (pm20) cc_final: 0.8490 (pm20) REVERT: I 112 VAL cc_start: 0.9003 (t) cc_final: 0.8742 (p) REVERT: J 72 ASP cc_start: 0.8943 (m-30) cc_final: 0.8650 (m-30) REVERT: J 77 MET cc_start: 0.9060 (ppp) cc_final: 0.8707 (ppp) REVERT: K 20 LYS cc_start: 0.8355 (mttm) cc_final: 0.8145 (mttp) REVERT: K 85 ASP cc_start: 0.8454 (t0) cc_final: 0.8011 (t0) REVERT: M 16 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8789 (tt) REVERT: N 32 GLU cc_start: 0.8691 (tp30) cc_final: 0.8389 (tp30) REVERT: O 226 PHE cc_start: 0.8382 (m-80) cc_final: 0.7599 (m-80) REVERT: O 230 TYR cc_start: 0.9007 (t80) cc_final: 0.8664 (t80) REVERT: O 237 TYR cc_start: 0.7938 (t80) cc_final: 0.7582 (t80) REVERT: O 261 MET cc_start: 0.6350 (OUTLIER) cc_final: 0.5979 (ppp) REVERT: Q 6 GLN cc_start: 0.9339 (mt0) cc_final: 0.9122 (mp10) REVERT: Q 33 MET cc_start: 0.8984 (tmm) cc_final: 0.8669 (tmm) REVERT: R 1 MET cc_start: 0.7556 (mmm) cc_final: 0.7356 (mmm) REVERT: R 20 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8935 (tptp) REVERT: V 148 ASP cc_start: 0.8663 (t0) cc_final: 0.8312 (p0) REVERT: W 126 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6772 (tmm-80) REVERT: X 60 GLN cc_start: 0.8590 (tp40) cc_final: 0.8306 (pm20) REVERT: X 67 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8486 (tppt) REVERT: Y 6 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8107 (mm-30) REVERT: Y 40 ARG cc_start: 0.8612 (mmm-85) cc_final: 0.8303 (ttp80) REVERT: Z 29 THR cc_start: 0.8310 (m) cc_final: 0.8044 (m) REVERT: Z 35 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7988 (t80) REVERT: a 168 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8258 (m-80) REVERT: b 8 GLU cc_start: 0.7766 (tp30) cc_final: 0.7230 (tp30) REVERT: c 24 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8158 (tm-30) REVERT: d 20 LYS cc_start: 0.9164 (tppt) cc_final: 0.8749 (tppt) REVERT: d 48 ARG cc_start: 0.8914 (tpt170) cc_final: 0.8685 (ttm-80) REVERT: d 81 MET cc_start: 0.4473 (mmt) cc_final: 0.4208 (tpt) REVERT: d 98 ASN cc_start: 0.8392 (m-40) cc_final: 0.7595 (t0) outliers start: 62 outliers final: 44 residues processed: 395 average time/residue: 0.3358 time to fit residues: 205.2151 Evaluate side-chains 379 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 329 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 235 HIS Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 153 HIS Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain W residue 126 ARG Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 243 LYS Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain c residue 23 LEU Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.7301 > 50: distance: 28 - 46: 18.157 distance: 32 - 57: 20.069 distance: 36 - 65: 16.715 distance: 39 - 46: 15.475 distance: 40 - 73: 17.932 distance: 46 - 47: 17.734 distance: 47 - 48: 11.347 distance: 47 - 50: 20.137 distance: 48 - 49: 20.311 distance: 48 - 57: 15.500 distance: 49 - 82: 43.410 distance: 50 - 51: 11.941 distance: 51 - 52: 9.771 distance: 51 - 53: 11.965 distance: 52 - 54: 18.775 distance: 53 - 55: 23.103 distance: 54 - 56: 15.932 distance: 55 - 56: 16.820 distance: 57 - 58: 6.755 distance: 58 - 59: 9.236 distance: 58 - 61: 13.307 distance: 59 - 60: 23.639 distance: 59 - 65: 23.116 distance: 60 - 87: 22.223 distance: 61 - 62: 17.805 distance: 62 - 63: 18.797 distance: 62 - 64: 15.119 distance: 65 - 66: 22.886 distance: 66 - 67: 8.758 distance: 66 - 69: 16.449 distance: 67 - 68: 10.692 distance: 67 - 73: 23.725 distance: 69 - 70: 12.207 distance: 70 - 71: 15.938 distance: 70 - 72: 16.023 distance: 73 - 74: 18.293 distance: 74 - 75: 17.731 distance: 74 - 77: 7.742 distance: 75 - 76: 17.949 distance: 75 - 82: 9.611 distance: 77 - 78: 27.017 distance: 78 - 79: 15.862 distance: 79 - 80: 24.131 distance: 79 - 81: 22.687 distance: 82 - 83: 5.571 distance: 83 - 84: 9.418 distance: 83 - 86: 20.181 distance: 84 - 85: 30.023 distance: 84 - 87: 14.001 distance: 87 - 88: 22.314 distance: 88 - 89: 18.339 distance: 88 - 91: 16.671 distance: 89 - 90: 22.173 distance: 89 - 94: 6.330 distance: 91 - 92: 29.939 distance: 91 - 93: 32.031 distance: 94 - 95: 3.137 distance: 95 - 96: 6.957 distance: 95 - 98: 6.279 distance: 96 - 97: 29.825 distance: 96 - 102: 31.508 distance: 98 - 99: 12.927 distance: 99 - 100: 3.345 distance: 99 - 101: 16.101 distance: 102 - 103: 13.550 distance: 103 - 104: 46.389 distance: 103 - 106: 4.428 distance: 104 - 105: 53.281 distance: 104 - 110: 41.773 distance: 106 - 107: 21.098 distance: 107 - 108: 16.330 distance: 107 - 109: 21.261 distance: 110 - 111: 13.805 distance: 111 - 112: 20.603 distance: 111 - 114: 32.734 distance: 112 - 113: 10.782 distance: 112 - 119: 25.239 distance: 114 - 115: 34.303 distance: 115 - 116: 35.934 distance: 116 - 117: 32.829 distance: 117 - 118: 19.706 distance: 119 - 120: 25.669 distance: 120 - 121: 33.612 distance: 120 - 123: 23.642 distance: 121 - 122: 39.451 distance: 121 - 128: 32.670 distance: 123 - 124: 41.853 distance: 124 - 125: 7.249 distance: 125 - 126: 39.755 distance: 126 - 127: 53.904