Starting phenix.real_space_refine on Mon Mar 25 19:37:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykg_6833/03_2024/5ykg_6833_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykg_6833/03_2024/5ykg_6833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykg_6833/03_2024/5ykg_6833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykg_6833/03_2024/5ykg_6833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykg_6833/03_2024/5ykg_6833_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykg_6833/03_2024/5ykg_6833_updated.pdb" } resolution = 4.57 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 284 5.16 5 Cl 4 4.86 5 C 33044 2.51 5 N 8608 2.21 5 O 8904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 32": "NH1" <-> "NH2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B ARG 486": "NH1" <-> "NH2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B ARG 521": "NH1" <-> "NH2" Residue "B ARG 527": "NH1" <-> "NH2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B ARG 702": "NH1" <-> "NH2" Residue "B ARG 705": "NH1" <-> "NH2" Residue "B ARG 826": "NH1" <-> "NH2" Residue "B ARG 835": "NH1" <-> "NH2" Residue "B ARG 878": "NH1" <-> "NH2" Residue "B ARG 882": "NH1" <-> "NH2" Residue "B ARG 919": "NH1" <-> "NH2" Residue "B ARG 999": "NH1" <-> "NH2" Residue "B ARG 1099": "NH1" <-> "NH2" Residue "B ARG 1104": "NH1" <-> "NH2" Residue "B ARG 1111": "NH1" <-> "NH2" Residue "B ARG 1145": "NH1" <-> "NH2" Residue "B TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1183": "NH1" <-> "NH2" Residue "B ARG 1218": "NH1" <-> "NH2" Residue "B ARG 1274": "NH1" <-> "NH2" Residue "B ARG 1300": "NH1" <-> "NH2" Residue "B ARG 1353": "NH1" <-> "NH2" Residue "B ARG 1394": "NH1" <-> "NH2" Residue "B ARG 1402": "NH1" <-> "NH2" Residue "B ARG 1421": "NH1" <-> "NH2" Residue "B ARG 1487": "NH1" <-> "NH2" Residue "B ARG 1498": "NH1" <-> "NH2" Residue "B ARG 1531": "NH1" <-> "NH2" Residue "B ARG 1539": "NH1" <-> "NH2" Residue "B ARG 1554": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "D ARG 486": "NH1" <-> "NH2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D ARG 521": "NH1" <-> "NH2" Residue "D ARG 527": "NH1" <-> "NH2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "D ARG 598": "NH1" <-> "NH2" Residue "D ARG 702": "NH1" <-> "NH2" Residue "D ARG 705": "NH1" <-> "NH2" Residue "D ARG 826": "NH1" <-> "NH2" Residue "D ARG 835": "NH1" <-> "NH2" Residue "D ARG 878": "NH1" <-> "NH2" Residue "D ARG 882": "NH1" <-> "NH2" Residue "D ARG 919": "NH1" <-> "NH2" Residue "D ARG 999": "NH1" <-> "NH2" Residue "D ARG 1099": "NH1" <-> "NH2" Residue "D ARG 1104": "NH1" <-> "NH2" Residue "D ARG 1111": "NH1" <-> "NH2" Residue "D ARG 1145": "NH1" <-> "NH2" Residue "D TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1183": "NH1" <-> "NH2" Residue "D ARG 1218": "NH1" <-> "NH2" Residue "D ARG 1274": "NH1" <-> "NH2" Residue "D ARG 1300": "NH1" <-> "NH2" Residue "D ARG 1353": "NH1" <-> "NH2" Residue "D ARG 1394": "NH1" <-> "NH2" Residue "D ARG 1402": "NH1" <-> "NH2" Residue "D ARG 1421": "NH1" <-> "NH2" Residue "D ARG 1487": "NH1" <-> "NH2" Residue "D ARG 1498": "NH1" <-> "NH2" Residue "D ARG 1531": "NH1" <-> "NH2" Residue "D ARG 1539": "NH1" <-> "NH2" Residue "D ARG 1554": "NH1" <-> "NH2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "F ARG 248": "NH1" <-> "NH2" Residue "F ARG 258": "NH1" <-> "NH2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "F PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ARG 370": "NH1" <-> "NH2" Residue "F ARG 486": "NH1" <-> "NH2" Residue "F ARG 504": "NH1" <-> "NH2" Residue "F ARG 521": "NH1" <-> "NH2" Residue "F ARG 527": "NH1" <-> "NH2" Residue "F ARG 534": "NH1" <-> "NH2" Residue "F ARG 598": "NH1" <-> "NH2" Residue "F ARG 702": "NH1" <-> "NH2" Residue "F ARG 705": "NH1" <-> "NH2" Residue "F ARG 826": "NH1" <-> "NH2" Residue "F ARG 835": "NH1" <-> "NH2" Residue "F ARG 878": "NH1" <-> "NH2" Residue "F ARG 882": "NH1" <-> "NH2" Residue "F ARG 919": "NH1" <-> "NH2" Residue "F ARG 999": "NH1" <-> "NH2" Residue "F ARG 1099": "NH1" <-> "NH2" Residue "F ARG 1104": "NH1" <-> "NH2" Residue "F ARG 1111": "NH1" <-> "NH2" Residue "F ARG 1145": "NH1" <-> "NH2" Residue "F TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1183": "NH1" <-> "NH2" Residue "F ARG 1218": "NH1" <-> "NH2" Residue "F ARG 1274": "NH1" <-> "NH2" Residue "F ARG 1300": "NH1" <-> "NH2" Residue "F ARG 1353": "NH1" <-> "NH2" Residue "F ARG 1394": "NH1" <-> "NH2" Residue "F ARG 1402": "NH1" <-> "NH2" Residue "F ARG 1421": "NH1" <-> "NH2" Residue "F ARG 1487": "NH1" <-> "NH2" Residue "F ARG 1498": "NH1" <-> "NH2" Residue "F ARG 1531": "NH1" <-> "NH2" Residue "F ARG 1539": "NH1" <-> "NH2" Residue "F ARG 1554": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "H ARG 248": "NH1" <-> "NH2" Residue "H ARG 258": "NH1" <-> "NH2" Residue "H ARG 265": "NH1" <-> "NH2" Residue "H PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 275": "NH1" <-> "NH2" Residue "H ARG 370": "NH1" <-> "NH2" Residue "H ARG 486": "NH1" <-> "NH2" Residue "H ARG 504": "NH1" <-> "NH2" Residue "H ARG 521": "NH1" <-> "NH2" Residue "H ARG 527": "NH1" <-> "NH2" Residue "H ARG 534": "NH1" <-> "NH2" Residue "H ARG 598": "NH1" <-> "NH2" Residue "H ARG 702": "NH1" <-> "NH2" Residue "H ARG 705": "NH1" <-> "NH2" Residue "H ARG 826": "NH1" <-> "NH2" Residue "H ARG 835": "NH1" <-> "NH2" Residue "H ARG 878": "NH1" <-> "NH2" Residue "H ARG 882": "NH1" <-> "NH2" Residue "H ARG 919": "NH1" <-> "NH2" Residue "H ARG 999": "NH1" <-> "NH2" Residue "H ARG 1099": "NH1" <-> "NH2" Residue "H ARG 1104": "NH1" <-> "NH2" Residue "H ARG 1111": "NH1" <-> "NH2" Residue "H ARG 1145": "NH1" <-> "NH2" Residue "H TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 1183": "NH1" <-> "NH2" Residue "H ARG 1218": "NH1" <-> "NH2" Residue "H ARG 1274": "NH1" <-> "NH2" Residue "H ARG 1300": "NH1" <-> "NH2" Residue "H ARG 1353": "NH1" <-> "NH2" Residue "H ARG 1394": "NH1" <-> "NH2" Residue "H ARG 1402": "NH1" <-> "NH2" Residue "H ARG 1421": "NH1" <-> "NH2" Residue "H ARG 1487": "NH1" <-> "NH2" Residue "H ARG 1498": "NH1" <-> "NH2" Residue "H ARG 1531": "NH1" <-> "NH2" Residue "H ARG 1539": "NH1" <-> "NH2" Residue "H ARG 1554": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 50868 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2433 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 29} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 10189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1309, 10189 Classifications: {'peptide': 1309} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 45, 'TRANS': 1263} Chain breaks: 11 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 131 Chain: "C" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2433 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 29} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "D" Number of atoms: 10189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1309, 10189 Classifications: {'peptide': 1309} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 45, 'TRANS': 1263} Chain breaks: 11 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 131 Chain: "E" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2433 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 29} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "F" Number of atoms: 10189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1309, 10189 Classifications: {'peptide': 1309} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 45, 'TRANS': 1263} Chain breaks: 11 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 131 Chain: "G" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2433 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 29} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "H" Number of atoms: 10189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1309, 10189 Classifications: {'peptide': 1309} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 45, 'TRANS': 1263} Chain breaks: 11 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 131 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'AGS': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'AGS': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'AGS': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'AGS': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.63, per 1000 atoms: 0.50 Number of scatterers: 50868 At special positions: 0 Unit cell: (209.945, 209.945, 142.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 284 16.00 P 24 15.00 O 8904 8.00 N 8608 7.00 C 33044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 142 " distance=2.03 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: 19.10 Conformation dependent library (CDL) restraints added in 8.3 seconds 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 36 sheets defined 57.2% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.76 Creating SS restraints... Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 68 through 96 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 171 removed outlier: 3.931A pdb=" N ILE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 removed outlier: 4.231A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 269' Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'B' and resid 25 through 51 Proline residue: B 35 - end of helix removed outlier: 3.908A pdb=" N PHE B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Proline residue: B 45 - end of helix Processing helix chain 'B' and resid 71 through 95 Processing helix chain 'B' and resid 108 through 129 removed outlier: 3.681A pdb=" N MET B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 158 removed outlier: 3.723A pdb=" N TYR B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 192 Processing helix chain 'B' and resid 226 through 229 No H-bonds generated for 'chain 'B' and resid 226 through 229' Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.942A pdb=" N ALA B 235 " --> pdb=" O TRP B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 284 through 328 removed outlier: 6.309A pdb=" N ARG B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 356 through 401 removed outlier: 3.630A pdb=" N MET B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 422 Processing helix chain 'B' and resid 424 through 500 Proline residue: B 436 - end of helix removed outlier: 3.535A pdb=" N TRP B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Proline residue: B 442 - end of helix removed outlier: 8.211A pdb=" N VAL B 458 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N SER B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix Processing helix chain 'B' and resid 506 through 512 removed outlier: 4.018A pdb=" N TYR B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 559 removed outlier: 3.655A pdb=" N ARG B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 528 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 548 " --> pdb=" O ILE B 544 " (cutoff:3.500A) Proline residue: B 551 - end of helix removed outlier: 3.554A pdb=" N VAL B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 614 Proline residue: B 589 - end of helix removed outlier: 4.446A pdb=" N LEU B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 593 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 784 through 789 Processing helix chain 'B' and resid 797 through 806 Processing helix chain 'B' and resid 809 through 814 Processing helix chain 'B' and resid 832 through 845 Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'B' and resid 894 through 896 No H-bonds generated for 'chain 'B' and resid 894 through 896' Processing helix chain 'B' and resid 914 through 918 Processing helix chain 'B' and resid 998 through 1008 removed outlier: 3.802A pdb=" N ALA B1008 " --> pdb=" O TYR B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1038 removed outlier: 4.194A pdb=" N SER B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B1019 " --> pdb=" O LEU B1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B1036 " --> pdb=" O TYR B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1106 Processing helix chain 'B' and resid 1110 through 1115 Processing helix chain 'B' and resid 1118 through 1126 removed outlier: 4.265A pdb=" N PHE B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1128 through 1160 Proline residue: B1137 - end of helix Processing helix chain 'B' and resid 1162 through 1216 removed outlier: 3.820A pdb=" N VAL B1166 " --> pdb=" O PRO B1162 " (cutoff:3.500A) Proline residue: B1170 - end of helix removed outlier: 3.539A pdb=" N PHE B1177 " --> pdb=" O VAL B1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B1181 " --> pdb=" O PHE B1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B1182 " --> pdb=" O ILE B1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B1185 " --> pdb=" O TYR B1181 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP B1188 " --> pdb=" O VAL B1184 " (cutoff:3.500A) Proline residue: B1199 - end of helix removed outlier: 3.524A pdb=" N GLY B1210 " --> pdb=" O GLU B1206 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR B1212 " --> pdb=" O VAL B1208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR B1213 " --> pdb=" O GLU B1209 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1270 removed outlier: 3.725A pdb=" N ALA B1237 " --> pdb=" O SER B1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1242 " --> pdb=" O SER B1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B1260 " --> pdb=" O GLY B1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B1269 " --> pdb=" O ALA B1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 1278 through 1288 removed outlier: 4.013A pdb=" N GLY B1282 " --> pdb=" O ALA B1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B1283 " --> pdb=" O GLY B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1291 through 1319 removed outlier: 4.142A pdb=" N ARG B1314 " --> pdb=" O GLY B1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE B1315 " --> pdb=" O ALA B1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B1316 " --> pdb=" O VAL B1312 " (cutoff:3.500A) Processing helix chain 'B' and resid 1385 through 1392 Processing helix chain 'B' and resid 1415 through 1419 Processing helix chain 'B' and resid 1436 through 1440 Processing helix chain 'B' and resid 1448 through 1457 Processing helix chain 'B' and resid 1461 through 1465 Processing helix chain 'B' and resid 1484 through 1498 Processing helix chain 'B' and resid 1514 through 1527 removed outlier: 4.096A pdb=" N ILE B1519 " --> pdb=" O ALA B1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1545 Processing helix chain 'B' and resid 1563 through 1569 removed outlier: 4.306A pdb=" N SER B1568 " --> pdb=" O GLU B1564 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 68 through 96 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 171 removed outlier: 3.931A pdb=" N ILE C 154 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE C 167 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 269 removed outlier: 4.231A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 269' Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'D' and resid 25 through 51 Proline residue: D 35 - end of helix removed outlier: 3.908A pdb=" N PHE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Proline residue: D 45 - end of helix Processing helix chain 'D' and resid 71 through 95 Processing helix chain 'D' and resid 108 through 129 removed outlier: 3.681A pdb=" N MET D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 158 removed outlier: 3.723A pdb=" N TYR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 192 Processing helix chain 'D' and resid 226 through 229 No H-bonds generated for 'chain 'D' and resid 226 through 229' Processing helix chain 'D' and resid 231 through 242 removed outlier: 3.942A pdb=" N ALA D 235 " --> pdb=" O TRP D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 284 through 328 removed outlier: 6.309A pdb=" N ARG D 297 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Proline residue: D 317 - end of helix Processing helix chain 'D' and resid 356 through 401 removed outlier: 3.630A pdb=" N MET D 400 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 422 Processing helix chain 'D' and resid 424 through 500 Proline residue: D 436 - end of helix removed outlier: 3.535A pdb=" N TRP D 439 " --> pdb=" O CYS D 435 " (cutoff:3.500A) Proline residue: D 442 - end of helix removed outlier: 8.211A pdb=" N VAL D 458 " --> pdb=" O TYR D 454 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N SER D 459 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 461 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Proline residue: D 472 - end of helix Processing helix chain 'D' and resid 506 through 512 removed outlier: 4.018A pdb=" N TYR D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 559 removed outlier: 3.655A pdb=" N ARG D 521 " --> pdb=" O ILE D 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS D 528 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA D 535 " --> pdb=" O THR D 531 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR D 548 " --> pdb=" O ILE D 544 " (cutoff:3.500A) Proline residue: D 551 - end of helix removed outlier: 3.554A pdb=" N VAL D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 614 Proline residue: D 589 - end of helix removed outlier: 4.446A pdb=" N LEU D 592 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 593 " --> pdb=" O PRO D 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER D 595 " --> pdb=" O PHE D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 726 Processing helix chain 'D' and resid 784 through 789 Processing helix chain 'D' and resid 797 through 806 Processing helix chain 'D' and resid 809 through 814 Processing helix chain 'D' and resid 832 through 845 Processing helix chain 'D' and resid 862 through 871 Processing helix chain 'D' and resid 894 through 896 No H-bonds generated for 'chain 'D' and resid 894 through 896' Processing helix chain 'D' and resid 914 through 918 Processing helix chain 'D' and resid 998 through 1008 removed outlier: 3.802A pdb=" N ALA D1008 " --> pdb=" O TYR D1004 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1038 removed outlier: 4.194A pdb=" N SER D1014 " --> pdb=" O ILE D1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D1015 " --> pdb=" O LEU D1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER D1019 " --> pdb=" O LEU D1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP D1031 " --> pdb=" O LEU D1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D1036 " --> pdb=" O TYR D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1106 Processing helix chain 'D' and resid 1110 through 1115 Processing helix chain 'D' and resid 1118 through 1126 removed outlier: 4.265A pdb=" N PHE D1125 " --> pdb=" O ILE D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1128 through 1160 Proline residue: D1137 - end of helix Processing helix chain 'D' and resid 1162 through 1216 removed outlier: 3.820A pdb=" N VAL D1166 " --> pdb=" O PRO D1162 " (cutoff:3.500A) Proline residue: D1170 - end of helix removed outlier: 3.539A pdb=" N PHE D1177 " --> pdb=" O VAL D1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D1181 " --> pdb=" O PHE D1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D1182 " --> pdb=" O ILE D1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D1185 " --> pdb=" O TYR D1181 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP D1188 " --> pdb=" O VAL D1184 " (cutoff:3.500A) Proline residue: D1199 - end of helix removed outlier: 3.524A pdb=" N GLY D1210 " --> pdb=" O GLU D1206 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR D1212 " --> pdb=" O VAL D1208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR D1213 " --> pdb=" O GLU D1209 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1270 removed outlier: 3.725A pdb=" N ALA D1237 " --> pdb=" O SER D1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR D1242 " --> pdb=" O SER D1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D1260 " --> pdb=" O GLY D1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER D1269 " --> pdb=" O ALA D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1278 through 1288 removed outlier: 4.013A pdb=" N GLY D1282 " --> pdb=" O ALA D1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU D1283 " --> pdb=" O GLY D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1291 through 1319 removed outlier: 4.142A pdb=" N ARG D1314 " --> pdb=" O GLY D1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE D1315 " --> pdb=" O ALA D1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS D1316 " --> pdb=" O VAL D1312 " (cutoff:3.500A) Processing helix chain 'D' and resid 1385 through 1392 Processing helix chain 'D' and resid 1415 through 1419 Processing helix chain 'D' and resid 1436 through 1440 Processing helix chain 'D' and resid 1448 through 1457 Processing helix chain 'D' and resid 1461 through 1465 Processing helix chain 'D' and resid 1484 through 1498 Processing helix chain 'D' and resid 1514 through 1527 removed outlier: 4.096A pdb=" N ILE D1519 " --> pdb=" O ALA D1515 " (cutoff:3.500A) Processing helix chain 'D' and resid 1540 through 1545 Processing helix chain 'D' and resid 1563 through 1569 removed outlier: 4.306A pdb=" N SER D1568 " --> pdb=" O GLU D1564 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 64 Processing helix chain 'E' and resid 68 through 96 Processing helix chain 'E' and resid 117 through 128 Processing helix chain 'E' and resid 143 through 171 removed outlier: 3.931A pdb=" N ILE E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE E 167 " --> pdb=" O MET E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 269 removed outlier: 4.231A pdb=" N ASP E 269 " --> pdb=" O PRO E 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 266 through 269' Processing helix chain 'E' and resid 346 through 355 Processing helix chain 'F' and resid 25 through 51 Proline residue: F 35 - end of helix removed outlier: 3.908A pdb=" N PHE F 44 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Proline residue: F 45 - end of helix Processing helix chain 'F' and resid 71 through 95 Processing helix chain 'F' and resid 108 through 129 removed outlier: 3.681A pdb=" N MET F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 158 removed outlier: 3.723A pdb=" N TYR F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 192 Processing helix chain 'F' and resid 226 through 229 No H-bonds generated for 'chain 'F' and resid 226 through 229' Processing helix chain 'F' and resid 231 through 242 removed outlier: 3.942A pdb=" N ALA F 235 " --> pdb=" O TRP F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 274 Processing helix chain 'F' and resid 284 through 328 removed outlier: 6.309A pdb=" N ARG F 297 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU F 299 " --> pdb=" O PHE F 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE F 300 " --> pdb=" O GLY F 296 " (cutoff:3.500A) Proline residue: F 317 - end of helix Processing helix chain 'F' and resid 356 through 401 removed outlier: 3.630A pdb=" N MET F 400 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 422 Processing helix chain 'F' and resid 424 through 500 Proline residue: F 436 - end of helix removed outlier: 3.535A pdb=" N TRP F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) Proline residue: F 442 - end of helix removed outlier: 8.211A pdb=" N VAL F 458 " --> pdb=" O TYR F 454 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N SER F 459 " --> pdb=" O ILE F 455 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU F 461 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE F 462 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE F 468 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 471 " --> pdb=" O ILE F 467 " (cutoff:3.500A) Proline residue: F 472 - end of helix Processing helix chain 'F' and resid 506 through 512 removed outlier: 4.018A pdb=" N TYR F 512 " --> pdb=" O LEU F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 559 removed outlier: 3.655A pdb=" N ARG F 521 " --> pdb=" O ILE F 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS F 528 " --> pdb=" O VAL F 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA F 535 " --> pdb=" O THR F 531 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR F 548 " --> pdb=" O ILE F 544 " (cutoff:3.500A) Proline residue: F 551 - end of helix removed outlier: 3.554A pdb=" N VAL F 555 " --> pdb=" O PRO F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 614 Proline residue: F 589 - end of helix removed outlier: 4.446A pdb=" N LEU F 592 " --> pdb=" O THR F 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU F 593 " --> pdb=" O PRO F 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER F 594 " --> pdb=" O LEU F 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER F 595 " --> pdb=" O PHE F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 719 through 726 Processing helix chain 'F' and resid 784 through 789 Processing helix chain 'F' and resid 797 through 806 Processing helix chain 'F' and resid 809 through 814 Processing helix chain 'F' and resid 832 through 845 Processing helix chain 'F' and resid 862 through 871 Processing helix chain 'F' and resid 894 through 896 No H-bonds generated for 'chain 'F' and resid 894 through 896' Processing helix chain 'F' and resid 914 through 918 Processing helix chain 'F' and resid 998 through 1008 removed outlier: 3.802A pdb=" N ALA F1008 " --> pdb=" O TYR F1004 " (cutoff:3.500A) Processing helix chain 'F' and resid 1010 through 1038 removed outlier: 4.194A pdb=" N SER F1014 " --> pdb=" O ILE F1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU F1015 " --> pdb=" O LEU F1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER F1019 " --> pdb=" O LEU F1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP F1031 " --> pdb=" O LEU F1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F1036 " --> pdb=" O TYR F1032 " (cutoff:3.500A) Processing helix chain 'F' and resid 1061 through 1106 Processing helix chain 'F' and resid 1110 through 1115 Processing helix chain 'F' and resid 1118 through 1126 removed outlier: 4.265A pdb=" N PHE F1125 " --> pdb=" O ILE F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1128 through 1160 Proline residue: F1137 - end of helix Processing helix chain 'F' and resid 1162 through 1216 removed outlier: 3.820A pdb=" N VAL F1166 " --> pdb=" O PRO F1162 " (cutoff:3.500A) Proline residue: F1170 - end of helix removed outlier: 3.539A pdb=" N PHE F1177 " --> pdb=" O VAL F1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR F1181 " --> pdb=" O PHE F1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE F1182 " --> pdb=" O ILE F1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA F1185 " --> pdb=" O TYR F1181 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP F1188 " --> pdb=" O VAL F1184 " (cutoff:3.500A) Proline residue: F1199 - end of helix removed outlier: 3.524A pdb=" N GLY F1210 " --> pdb=" O GLU F1206 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR F1212 " --> pdb=" O VAL F1208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR F1213 " --> pdb=" O GLU F1209 " (cutoff:3.500A) Processing helix chain 'F' and resid 1220 through 1270 removed outlier: 3.725A pdb=" N ALA F1237 " --> pdb=" O SER F1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR F1242 " --> pdb=" O SER F1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL F1260 " --> pdb=" O GLY F1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER F1269 " --> pdb=" O ALA F1265 " (cutoff:3.500A) Processing helix chain 'F' and resid 1278 through 1288 removed outlier: 4.013A pdb=" N GLY F1282 " --> pdb=" O ALA F1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU F1283 " --> pdb=" O GLY F1279 " (cutoff:3.500A) Processing helix chain 'F' and resid 1291 through 1319 removed outlier: 4.142A pdb=" N ARG F1314 " --> pdb=" O GLY F1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE F1315 " --> pdb=" O ALA F1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS F1316 " --> pdb=" O VAL F1312 " (cutoff:3.500A) Processing helix chain 'F' and resid 1385 through 1392 Processing helix chain 'F' and resid 1415 through 1419 Processing helix chain 'F' and resid 1436 through 1440 Processing helix chain 'F' and resid 1448 through 1457 Processing helix chain 'F' and resid 1461 through 1465 Processing helix chain 'F' and resid 1484 through 1498 Processing helix chain 'F' and resid 1514 through 1527 removed outlier: 4.096A pdb=" N ILE F1519 " --> pdb=" O ALA F1515 " (cutoff:3.500A) Processing helix chain 'F' and resid 1540 through 1545 Processing helix chain 'F' and resid 1563 through 1569 removed outlier: 4.306A pdb=" N SER F1568 " --> pdb=" O GLU F1564 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 64 Processing helix chain 'G' and resid 68 through 96 Processing helix chain 'G' and resid 117 through 128 Processing helix chain 'G' and resid 143 through 171 removed outlier: 3.931A pdb=" N ILE G 154 " --> pdb=" O ILE G 150 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE G 167 " --> pdb=" O MET G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 269 removed outlier: 4.231A pdb=" N ASP G 269 " --> pdb=" O PRO G 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 266 through 269' Processing helix chain 'G' and resid 346 through 355 Processing helix chain 'H' and resid 25 through 51 Proline residue: H 35 - end of helix removed outlier: 3.908A pdb=" N PHE H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Proline residue: H 45 - end of helix Processing helix chain 'H' and resid 71 through 95 Processing helix chain 'H' and resid 108 through 129 removed outlier: 3.681A pdb=" N MET H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 158 removed outlier: 3.723A pdb=" N TYR H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 192 Processing helix chain 'H' and resid 226 through 229 No H-bonds generated for 'chain 'H' and resid 226 through 229' Processing helix chain 'H' and resid 231 through 242 removed outlier: 3.942A pdb=" N ALA H 235 " --> pdb=" O TRP H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 274 Processing helix chain 'H' and resid 284 through 328 removed outlier: 6.309A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU H 299 " --> pdb=" O PHE H 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE H 300 " --> pdb=" O GLY H 296 " (cutoff:3.500A) Proline residue: H 317 - end of helix Processing helix chain 'H' and resid 356 through 401 removed outlier: 3.630A pdb=" N MET H 400 " --> pdb=" O TYR H 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS H 401 " --> pdb=" O ASN H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 422 Processing helix chain 'H' and resid 424 through 500 Proline residue: H 436 - end of helix removed outlier: 3.535A pdb=" N TRP H 439 " --> pdb=" O CYS H 435 " (cutoff:3.500A) Proline residue: H 442 - end of helix removed outlier: 8.211A pdb=" N VAL H 458 " --> pdb=" O TYR H 454 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N SER H 459 " --> pdb=" O ILE H 455 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA H 460 " --> pdb=" O LEU H 456 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU H 461 " --> pdb=" O GLY H 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE H 462 " --> pdb=" O VAL H 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE H 468 " --> pdb=" O ALA H 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA H 471 " --> pdb=" O ILE H 467 " (cutoff:3.500A) Proline residue: H 472 - end of helix Processing helix chain 'H' and resid 506 through 512 removed outlier: 4.018A pdb=" N TYR H 512 " --> pdb=" O LEU H 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 559 removed outlier: 3.655A pdb=" N ARG H 521 " --> pdb=" O ILE H 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS H 528 " --> pdb=" O VAL H 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA H 535 " --> pdb=" O THR H 531 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR H 548 " --> pdb=" O ILE H 544 " (cutoff:3.500A) Proline residue: H 551 - end of helix removed outlier: 3.554A pdb=" N VAL H 555 " --> pdb=" O PRO H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 614 Proline residue: H 589 - end of helix removed outlier: 4.446A pdb=" N LEU H 592 " --> pdb=" O THR H 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H 593 " --> pdb=" O PRO H 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER H 594 " --> pdb=" O LEU H 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER H 595 " --> pdb=" O PHE H 591 " (cutoff:3.500A) Processing helix chain 'H' and resid 719 through 726 Processing helix chain 'H' and resid 784 through 789 Processing helix chain 'H' and resid 797 through 806 Processing helix chain 'H' and resid 809 through 814 Processing helix chain 'H' and resid 832 through 845 Processing helix chain 'H' and resid 862 through 871 Processing helix chain 'H' and resid 894 through 896 No H-bonds generated for 'chain 'H' and resid 894 through 896' Processing helix chain 'H' and resid 914 through 918 Processing helix chain 'H' and resid 998 through 1008 removed outlier: 3.802A pdb=" N ALA H1008 " --> pdb=" O TYR H1004 " (cutoff:3.500A) Processing helix chain 'H' and resid 1010 through 1038 removed outlier: 4.194A pdb=" N SER H1014 " --> pdb=" O ILE H1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU H1015 " --> pdb=" O LEU H1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER H1019 " --> pdb=" O LEU H1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP H1031 " --> pdb=" O LEU H1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS H1036 " --> pdb=" O TYR H1032 " (cutoff:3.500A) Processing helix chain 'H' and resid 1061 through 1106 Processing helix chain 'H' and resid 1110 through 1115 Processing helix chain 'H' and resid 1118 through 1126 removed outlier: 4.265A pdb=" N PHE H1125 " --> pdb=" O ILE H1121 " (cutoff:3.500A) Processing helix chain 'H' and resid 1128 through 1160 Proline residue: H1137 - end of helix Processing helix chain 'H' and resid 1162 through 1216 removed outlier: 3.820A pdb=" N VAL H1166 " --> pdb=" O PRO H1162 " (cutoff:3.500A) Proline residue: H1170 - end of helix removed outlier: 3.539A pdb=" N PHE H1177 " --> pdb=" O VAL H1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR H1181 " --> pdb=" O PHE H1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE H1182 " --> pdb=" O ILE H1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA H1185 " --> pdb=" O TYR H1181 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP H1188 " --> pdb=" O VAL H1184 " (cutoff:3.500A) Proline residue: H1199 - end of helix removed outlier: 3.524A pdb=" N GLY H1210 " --> pdb=" O GLU H1206 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR H1212 " --> pdb=" O VAL H1208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR H1213 " --> pdb=" O GLU H1209 " (cutoff:3.500A) Processing helix chain 'H' and resid 1220 through 1270 removed outlier: 3.725A pdb=" N ALA H1237 " --> pdb=" O SER H1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR H1242 " --> pdb=" O SER H1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL H1260 " --> pdb=" O GLY H1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER H1269 " --> pdb=" O ALA H1265 " (cutoff:3.500A) Processing helix chain 'H' and resid 1278 through 1288 removed outlier: 4.013A pdb=" N GLY H1282 " --> pdb=" O ALA H1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU H1283 " --> pdb=" O GLY H1279 " (cutoff:3.500A) Processing helix chain 'H' and resid 1291 through 1319 removed outlier: 4.142A pdb=" N ARG H1314 " --> pdb=" O GLY H1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE H1315 " --> pdb=" O ALA H1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS H1316 " --> pdb=" O VAL H1312 " (cutoff:3.500A) Processing helix chain 'H' and resid 1385 through 1392 Processing helix chain 'H' and resid 1415 through 1419 Processing helix chain 'H' and resid 1436 through 1440 Processing helix chain 'H' and resid 1448 through 1457 Processing helix chain 'H' and resid 1461 through 1465 Processing helix chain 'H' and resid 1484 through 1498 Processing helix chain 'H' and resid 1514 through 1527 removed outlier: 4.096A pdb=" N ILE H1519 " --> pdb=" O ALA H1515 " (cutoff:3.500A) Processing helix chain 'H' and resid 1540 through 1545 Processing helix chain 'H' and resid 1563 through 1569 removed outlier: 4.306A pdb=" N SER H1568 " --> pdb=" O GLU H1564 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 188 through 192 removed outlier: 3.539A pdb=" N HIS A 259 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 200 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 214 through 220 removed outlier: 3.606A pdb=" N GLU A 282 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= D, first strand: chain 'A' and resid 319 through 321 Processing sheet with id= E, first strand: chain 'B' and resid 701 through 703 Processing sheet with id= F, first strand: chain 'B' and resid 911 through 913 removed outlier: 3.669A pdb=" N GLY B 912 " --> pdb=" O ILE B 900 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 771 " --> pdb=" O PHE B 852 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP B 854 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA B 773 " --> pdb=" O ASP B 854 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 1367 through 1369 removed outlier: 3.602A pdb=" N GLN B1346 " --> pdb=" O ILE B1404 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN B1348 " --> pdb=" O ARG B1402 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG B1402 " --> pdb=" O GLN B1348 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 1351 through 1353 removed outlier: 3.547A pdb=" N MET B1398 " --> pdb=" O ARG B1353 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 1557 through 1560 removed outlier: 3.774A pdb=" N MET B1550 " --> pdb=" O GLY B1376 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B1503 " --> pdb=" O VAL B1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE B1536 " --> pdb=" O PHE B1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET B1505 " --> pdb=" O ILE B1536 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER B1423 " --> pdb=" O ILE B1504 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP B1506 " --> pdb=" O SER B1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE B1425 " --> pdb=" O ASP B1506 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 188 through 192 removed outlier: 3.539A pdb=" N HIS C 259 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 200 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 214 through 220 removed outlier: 3.606A pdb=" N GLU C 282 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= M, first strand: chain 'C' and resid 319 through 321 Processing sheet with id= N, first strand: chain 'D' and resid 701 through 703 Processing sheet with id= O, first strand: chain 'D' and resid 911 through 913 removed outlier: 3.669A pdb=" N GLY D 912 " --> pdb=" O ILE D 900 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA D 771 " --> pdb=" O PHE D 852 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP D 854 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA D 773 " --> pdb=" O ASP D 854 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 1367 through 1369 removed outlier: 3.602A pdb=" N GLN D1346 " --> pdb=" O ILE D1404 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN D1348 " --> pdb=" O ARG D1402 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG D1402 " --> pdb=" O GLN D1348 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 1351 through 1353 removed outlier: 3.547A pdb=" N MET D1398 " --> pdb=" O ARG D1353 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 1557 through 1560 removed outlier: 3.774A pdb=" N MET D1550 " --> pdb=" O GLY D1376 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE D1503 " --> pdb=" O VAL D1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE D1536 " --> pdb=" O PHE D1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET D1505 " --> pdb=" O ILE D1536 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER D1423 " --> pdb=" O ILE D1504 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP D1506 " --> pdb=" O SER D1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE D1425 " --> pdb=" O ASP D1506 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 188 through 192 removed outlier: 3.539A pdb=" N HIS E 259 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU E 200 " --> pdb=" O ILE E 257 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 214 through 220 removed outlier: 3.606A pdb=" N GLU E 282 " --> pdb=" O VAL E 220 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 313 through 315 Processing sheet with id= V, first strand: chain 'E' and resid 319 through 321 Processing sheet with id= W, first strand: chain 'F' and resid 701 through 703 Processing sheet with id= X, first strand: chain 'F' and resid 911 through 913 removed outlier: 3.669A pdb=" N GLY F 912 " --> pdb=" O ILE F 900 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA F 771 " --> pdb=" O PHE F 852 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP F 854 " --> pdb=" O ALA F 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA F 773 " --> pdb=" O ASP F 854 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 1367 through 1369 removed outlier: 3.602A pdb=" N GLN F1346 " --> pdb=" O ILE F1404 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN F1348 " --> pdb=" O ARG F1402 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG F1402 " --> pdb=" O GLN F1348 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 1351 through 1353 removed outlier: 3.547A pdb=" N MET F1398 " --> pdb=" O ARG F1353 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 1557 through 1560 removed outlier: 3.774A pdb=" N MET F1550 " --> pdb=" O GLY F1376 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE F1503 " --> pdb=" O VAL F1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE F1536 " --> pdb=" O PHE F1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET F1505 " --> pdb=" O ILE F1536 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER F1423 " --> pdb=" O ILE F1504 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP F1506 " --> pdb=" O SER F1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE F1425 " --> pdb=" O ASP F1506 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 188 through 192 removed outlier: 3.539A pdb=" N HIS G 259 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 200 " --> pdb=" O ILE G 257 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 214 through 220 removed outlier: 3.606A pdb=" N GLU G 282 " --> pdb=" O VAL G 220 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 313 through 315 Processing sheet with id= AE, first strand: chain 'G' and resid 319 through 321 Processing sheet with id= AF, first strand: chain 'H' and resid 701 through 703 Processing sheet with id= AG, first strand: chain 'H' and resid 911 through 913 removed outlier: 3.669A pdb=" N GLY H 912 " --> pdb=" O ILE H 900 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA H 771 " --> pdb=" O PHE H 852 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP H 854 " --> pdb=" O ALA H 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA H 773 " --> pdb=" O ASP H 854 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 1367 through 1369 removed outlier: 3.602A pdb=" N GLN H1346 " --> pdb=" O ILE H1404 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN H1348 " --> pdb=" O ARG H1402 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG H1402 " --> pdb=" O GLN H1348 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 1351 through 1353 removed outlier: 3.547A pdb=" N MET H1398 " --> pdb=" O ARG H1353 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 1557 through 1560 removed outlier: 3.774A pdb=" N MET H1550 " --> pdb=" O GLY H1376 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE H1503 " --> pdb=" O VAL H1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE H1536 " --> pdb=" O PHE H1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET H1505 " --> pdb=" O ILE H1536 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER H1423 " --> pdb=" O ILE H1504 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP H1506 " --> pdb=" O SER H1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE H1425 " --> pdb=" O ASP H1506 " (cutoff:3.500A) 2872 hydrogen bonds defined for protein. 8388 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: 19.96 Time building geometry restraints manager: 20.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 19040 1.38 - 1.56: 32384 1.56 - 1.73: 56 1.73 - 1.90: 436 1.90 - 2.08: 8 Bond restraints: 51924 Sorted by residual: bond pdb=" C4 AGS A 401 " pdb=" C5 AGS A 401 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.24e+01 bond pdb=" C4 AGS G 401 " pdb=" C5 AGS G 401 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.24e+01 bond pdb=" C4 AGS C 401 " pdb=" C5 AGS C 401 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.24e+01 bond pdb=" C4 AGS E 401 " pdb=" C5 AGS E 401 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.24e+01 bond pdb=" C4 AGS H2002 " pdb=" C5 AGS H2002 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 7.10e+01 ... (remaining 51919 not shown) Histogram of bond angle deviations from ideal: 99.80 - 107.02: 1408 107.02 - 114.25: 31676 114.25 - 121.47: 26220 121.47 - 128.70: 10872 128.70 - 135.93: 448 Bond angle restraints: 70624 Sorted by residual: angle pdb=" C5 AGS F2002 " pdb=" C4 AGS F2002 " pdb=" N3 AGS F2002 " ideal model delta sigma weight residual 126.80 118.57 8.23 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS D2002 " pdb=" C4 AGS D2002 " pdb=" N3 AGS D2002 " ideal model delta sigma weight residual 126.80 118.57 8.23 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS H2002 " pdb=" C4 AGS H2002 " pdb=" N3 AGS H2002 " ideal model delta sigma weight residual 126.80 118.57 8.23 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS B2002 " pdb=" C4 AGS B2002 " pdb=" N3 AGS B2002 " ideal model delta sigma weight residual 126.80 118.57 8.23 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS G 401 " pdb=" C4 AGS G 401 " pdb=" N3 AGS G 401 " ideal model delta sigma weight residual 126.80 118.58 8.22 7.41e-01 1.82e+00 1.23e+02 ... (remaining 70619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.39: 29860 30.39 - 60.77: 948 60.77 - 91.16: 32 91.16 - 121.55: 4 121.55 - 151.94: 8 Dihedral angle restraints: 30852 sinusoidal: 11872 harmonic: 18980 Sorted by residual: dihedral pdb=" CA PHE D 295 " pdb=" C PHE D 295 " pdb=" N GLY D 296 " pdb=" CA GLY D 296 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PHE F 295 " pdb=" C PHE F 295 " pdb=" N GLY F 296 " pdb=" CA GLY F 296 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PHE B 295 " pdb=" C PHE B 295 " pdb=" N GLY B 296 " pdb=" CA GLY B 296 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 30849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 7816 0.075 - 0.149: 660 0.149 - 0.224: 40 0.224 - 0.298: 16 0.298 - 0.373: 8 Chirality restraints: 8540 Sorted by residual: chirality pdb=" CA LYS F1444 " pdb=" N LYS F1444 " pdb=" C LYS F1444 " pdb=" CB LYS F1444 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA LYS H1444 " pdb=" N LYS H1444 " pdb=" C LYS H1444 " pdb=" CB LYS H1444 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA LYS D1444 " pdb=" N LYS D1444 " pdb=" C LYS D1444 " pdb=" CB LYS D1444 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 8537 not shown) Planarity restraints: 8640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C25 GBM B2001 " -0.322 2.00e-02 2.50e+03 2.73e-01 9.30e+02 pdb=" C26 GBM B2001 " 0.077 2.00e-02 2.50e+03 pdb=" C27 GBM B2001 " -0.172 2.00e-02 2.50e+03 pdb=" N10 GBM B2001 " 0.479 2.00e-02 2.50e+03 pdb=" O6 GBM B2001 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 GBM H2001 " -0.322 2.00e-02 2.50e+03 2.73e-01 9.30e+02 pdb=" C26 GBM H2001 " 0.077 2.00e-02 2.50e+03 pdb=" C27 GBM H2001 " -0.172 2.00e-02 2.50e+03 pdb=" N10 GBM H2001 " 0.479 2.00e-02 2.50e+03 pdb=" O6 GBM H2001 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 GBM F2001 " 0.322 2.00e-02 2.50e+03 2.73e-01 9.30e+02 pdb=" C26 GBM F2001 " -0.077 2.00e-02 2.50e+03 pdb=" C27 GBM F2001 " 0.172 2.00e-02 2.50e+03 pdb=" N10 GBM F2001 " -0.479 2.00e-02 2.50e+03 pdb=" O6 GBM F2001 " 0.062 2.00e-02 2.50e+03 ... (remaining 8637 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 10056 2.78 - 3.31: 51336 3.31 - 3.84: 84380 3.84 - 4.37: 92110 4.37 - 4.90: 158088 Nonbonded interactions: 395970 Sorted by model distance: nonbonded pdb=" OD2 ASP D1031 " pdb=" OH TYR D1287 " model vdw 2.245 2.440 nonbonded pdb=" OD2 ASP F1031 " pdb=" OH TYR F1287 " model vdw 2.245 2.440 nonbonded pdb=" OD2 ASP H1031 " pdb=" OH TYR H1287 " model vdw 2.245 2.440 nonbonded pdb=" OD2 ASP B1031 " pdb=" OH TYR B1287 " model vdw 2.245 2.440 nonbonded pdb=" CB TYR D 512 " pdb=" NH2 ARG D1498 " model vdw 2.269 3.520 ... (remaining 395965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.560 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: 0.050 Extract box with map and model: 9.610 Check model and map are aligned: 0.820 Set scattering table: 0.490 Process input model: 125.690 Find NCS groups from input model: 3.320 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 51924 Z= 0.295 Angle : 0.707 11.965 70624 Z= 0.454 Chirality : 0.045 0.373 8540 Planarity : 0.008 0.273 8640 Dihedral : 13.815 151.936 18496 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.23 % Favored : 95.65 % Rotamer: Outliers : 7.90 % Allowed : 9.08 % Favored : 83.03 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.09), residues: 6432 helix: -0.86 (0.07), residues: 3892 sheet: -2.00 (0.19), residues: 540 loop : -2.80 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F1339 HIS 0.004 0.001 HIS G 259 PHE 0.016 0.001 PHE B 305 TYR 0.015 0.001 TYR H 378 ARG 0.002 0.000 ARG D1494 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 80 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8840 (tmm) REVERT: A 170 LYS cc_start: 0.8587 (ttmt) cc_final: 0.8114 (ptmt) REVERT: A 218 GLN cc_start: 0.9079 (mt0) cc_final: 0.8808 (mp10) REVERT: A 331 SER cc_start: 0.8650 (m) cc_final: 0.8269 (t) REVERT: A 348 GLN cc_start: 0.9363 (mm-40) cc_final: 0.9065 (mm-40) outliers start: 34 outliers final: 4 residues processed: 106 average time/residue: 0.1330 time to fit residues: 16.5213 Evaluate side-chains 50 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.222 Evaluate side-chains 272 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 199 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 TRP cc_start: 0.9179 (m100) cc_final: 0.8875 (m100) REVERT: B 78 THR cc_start: 0.9197 (m) cc_final: 0.8887 (p) REVERT: B 82 LEU cc_start: 0.8809 (tp) cc_final: 0.8518 (tp) REVERT: B 104 LEU cc_start: 0.8260 (mt) cc_final: 0.8022 (tp) REVERT: B 108 MET cc_start: 0.8914 (mmm) cc_final: 0.8669 (mmp) REVERT: B 126 ASN cc_start: 0.8778 (m-40) cc_final: 0.8459 (t0) REVERT: B 137 ILE cc_start: 0.8716 (mt) cc_final: 0.8462 (mt) REVERT: B 140 LEU cc_start: 0.9506 (tp) cc_final: 0.8700 (tt) REVERT: B 156 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7966 (tptt) REVERT: B 223 ASN cc_start: 0.6191 (OUTLIER) cc_final: 0.5872 (m-40) REVERT: B 262 ASN cc_start: 0.7724 (m-40) cc_final: 0.7388 (m110) REVERT: B 374 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8776 (mm-40) REVERT: B 456 LEU cc_start: 0.9130 (mp) cc_final: 0.8430 (tt) REVERT: B 470 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8530 (pp) REVERT: B 530 MET cc_start: 0.8524 (mmt) cc_final: 0.8211 (mmt) REVERT: B 598 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.9104 (tpt90) REVERT: B 869 MET cc_start: 0.7677 (tmm) cc_final: 0.7245 (tpt) REVERT: B 903 MET cc_start: 0.6639 (mmm) cc_final: 0.5632 (mmm) REVERT: B 1031 ASP cc_start: 0.8942 (m-30) cc_final: 0.8535 (p0) REVERT: B 1068 PHE cc_start: 0.7986 (t80) cc_final: 0.7485 (t80) REVERT: B 1114 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8149 (pp20) REVERT: B 1171 LEU cc_start: 0.9048 (mt) cc_final: 0.8668 (pp) REVERT: B 1252 MET cc_start: 0.9178 (ttm) cc_final: 0.8688 (tpt) REVERT: B 1254 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8603 (t80) REVERT: B 1287 TYR cc_start: 0.9044 (m-80) cc_final: 0.8736 (m-10) REVERT: B 1305 MET cc_start: 0.7504 (tpt) cc_final: 0.7142 (mmm) REVERT: B 1514 MET cc_start: 0.7183 (mtm) cc_final: 0.6870 (tpt) outliers start: 73 outliers final: 18 residues processed: 258 average time/residue: 0.2153 time to fit residues: 79.4035 Evaluate side-chains 127 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 547 optimal weight: 0.8980 chunk 491 optimal weight: 0.8980 chunk 272 optimal weight: 6.9990 chunk 167 optimal weight: 0.8980 chunk 331 optimal weight: 20.0000 chunk 262 optimal weight: 0.0010 chunk 507 optimal weight: 0.8980 chunk 196 optimal weight: 0.0970 chunk 308 optimal weight: 0.0010 chunk 378 optimal weight: 5.9990 chunk 588 optimal weight: 0.2980 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 186 HIS C 259 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 397 ASN F 485 GLN F1225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 51924 Z= 0.226 Angle : 0.705 13.849 70624 Z= 0.351 Chirality : 0.044 0.213 8540 Planarity : 0.005 0.058 8640 Dihedral : 8.930 152.600 7168 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.22 % Allowed : 3.69 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.10), residues: 6432 helix: 0.23 (0.08), residues: 3912 sheet: -1.56 (0.19), residues: 548 loop : -2.26 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 439 HIS 0.004 0.001 HIS H1024 PHE 0.035 0.002 PHE H1223 TYR 0.020 0.001 TYR F 512 ARG 0.008 0.000 ARG D1498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: C 88 MET cc_start: 0.9411 (tpt) cc_final: 0.8925 (tmm) REVERT: C 111 VAL cc_start: 0.9611 (m) cc_final: 0.9215 (m) REVERT: C 158 MET cc_start: 0.8291 (mmt) cc_final: 0.7978 (mmm) REVERT: C 163 MET cc_start: 0.8439 (ttp) cc_final: 0.8173 (ppp) REVERT: C 216 HIS cc_start: 0.8556 (m170) cc_final: 0.8124 (m-70) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1641 time to fit residues: 12.1188 Evaluate side-chains 36 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.291 Evaluate side-chains 125 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 THR cc_start: 0.9205 (m) cc_final: 0.8993 (p) REVERT: F 104 LEU cc_start: 0.8191 (mt) cc_final: 0.7920 (tp) REVERT: F 108 MET cc_start: 0.9018 (mmm) cc_final: 0.8608 (mmp) REVERT: F 115 MET cc_start: 0.8723 (mmm) cc_final: 0.8468 (mmp) REVERT: F 126 ASN cc_start: 0.8747 (m-40) cc_final: 0.8503 (t0) REVERT: F 257 MET cc_start: 0.8336 (pmm) cc_final: 0.8084 (mpp) REVERT: F 400 MET cc_start: 0.8227 (mtt) cc_final: 0.7934 (mtt) REVERT: F 456 LEU cc_start: 0.8909 (mp) cc_final: 0.8528 (tp) REVERT: F 530 MET cc_start: 0.8156 (mmt) cc_final: 0.7910 (mmt) REVERT: F 869 MET cc_start: 0.7338 (tmm) cc_final: 0.7052 (tpp) REVERT: F 1031 ASP cc_start: 0.9049 (m-30) cc_final: 0.8713 (p0) REVERT: F 1252 MET cc_start: 0.9034 (ttm) cc_final: 0.8763 (tpt) REVERT: F 1268 ILE cc_start: 0.8439 (tt) cc_final: 0.8230 (tt) REVERT: F 1287 TYR cc_start: 0.9179 (m-80) cc_final: 0.8744 (m-10) REVERT: F 1514 MET cc_start: 0.7209 (mtm) cc_final: 0.6884 (tpt) outliers start: 3 outliers final: 0 residues processed: 125 average time/residue: 0.1940 time to fit residues: 36.3968 Evaluate side-chains 85 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 0.9990 chunk 489 optimal weight: 7.9990 chunk 400 optimal weight: 40.0000 chunk 162 optimal weight: 20.0000 chunk 589 optimal weight: 5.9990 chunk 636 optimal weight: 7.9990 chunk 525 optimal weight: 10.0000 chunk 584 optimal weight: 0.0050 chunk 200 optimal weight: 9.9990 chunk 472 optimal weight: 6.9990 overall best weight: 4.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 219 GLN D 262 ASN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN D1245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 51924 Z= 0.340 Angle : 0.891 16.660 70624 Z= 0.458 Chirality : 0.054 0.488 8540 Planarity : 0.008 0.134 8640 Dihedral : 9.030 149.445 7168 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.54 % Favored : 95.40 % Rotamer: Outliers : 0.74 % Allowed : 4.72 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.10), residues: 6432 helix: -0.09 (0.08), residues: 3908 sheet: -1.54 (0.19), residues: 540 loop : -2.23 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.005 TRP H 430 HIS 0.032 0.003 HIS F 241 PHE 0.149 0.005 PHE B 363 TYR 0.042 0.004 TYR D 396 ARG 0.023 0.001 ARG H1096 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 MET cc_start: 0.9416 (tpt) cc_final: 0.9035 (tmm) REVERT: C 91 TRP cc_start: 0.8997 (t60) cc_final: 0.8705 (t-100) REVERT: C 163 MET cc_start: 0.8316 (ttt) cc_final: 0.7671 (ppp) REVERT: C 170 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8289 (mtpt) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 0.1351 time to fit residues: 7.9928 Evaluate side-chains 28 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.259 Evaluate side-chains 113 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 THR cc_start: 0.9195 (m) cc_final: 0.8904 (p) REVERT: D 104 LEU cc_start: 0.8476 (mt) cc_final: 0.8207 (tp) REVERT: D 108 MET cc_start: 0.8868 (mmm) cc_final: 0.8634 (mmm) REVERT: D 126 ASN cc_start: 0.8870 (m-40) cc_final: 0.8526 (t0) REVERT: D 400 MET cc_start: 0.8295 (mtt) cc_final: 0.7947 (mtt) REVERT: D 456 LEU cc_start: 0.8969 (mp) cc_final: 0.8487 (tp) REVERT: D 530 MET cc_start: 0.8110 (mmt) cc_final: 0.7899 (mmt) REVERT: D 869 MET cc_start: 0.7494 (tmm) cc_final: 0.7197 (tpp) REVERT: D 1031 ASP cc_start: 0.8970 (m-30) cc_final: 0.8650 (p0) REVERT: D 1068 PHE cc_start: 0.8010 (t80) cc_final: 0.7532 (t80) REVERT: D 1252 MET cc_start: 0.9207 (ttm) cc_final: 0.8921 (tpt) REVERT: D 1268 ILE cc_start: 0.8416 (tt) cc_final: 0.8213 (tt) REVERT: D 1287 TYR cc_start: 0.9216 (m-80) cc_final: 0.8778 (m-10) REVERT: D 1514 MET cc_start: 0.7243 (mtm) cc_final: 0.6903 (tpt) REVERT: D 1550 MET cc_start: 0.5865 (ptp) cc_final: 0.5596 (ppp) outliers start: 8 outliers final: 1 residues processed: 109 average time/residue: 0.1852 time to fit residues: 30.7706 Evaluate side-chains 79 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 582 optimal weight: 0.9980 chunk 443 optimal weight: 0.0270 chunk 305 optimal weight: 30.0000 chunk 65 optimal weight: 0.9980 chunk 281 optimal weight: 0.0270 chunk 395 optimal weight: 0.9990 chunk 591 optimal weight: 3.9990 chunk 626 optimal weight: 0.0980 chunk 309 optimal weight: 0.9980 chunk 560 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN B 397 ASN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 51924 Z= 0.351 Angle : 0.893 16.659 70624 Z= 0.458 Chirality : 0.054 0.488 8540 Planarity : 0.009 0.134 8640 Dihedral : 9.030 149.445 7168 Min Nonbonded Distance : 0.982 Molprobity Statistics. All-atom Clashscore : 27.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.54 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.10), residues: 6432 helix: -0.09 (0.08), residues: 3908 sheet: -1.54 (0.19), residues: 540 loop : -2.23 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.005 TRP D 430 HIS 0.032 0.003 HIS F 241 PHE 0.149 0.005 PHE D 363 TYR 0.042 0.004 TYR B 396 ARG 0.023 0.001 ARG D1096 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6430 Ramachandran restraints generated. 3215 Oldfield, 0 Emsley, 3215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6430 Ramachandran restraints generated. 3215 Oldfield, 0 Emsley, 3215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 88 MET cc_start: 0.9428 (tpt) cc_final: 0.9031 (tmm) REVERT: E 91 TRP cc_start: 0.9011 (t60) cc_final: 0.8699 (t-100) REVERT: E 163 MET cc_start: 0.8320 (ttt) cc_final: 0.7720 (ppp) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1358 time to fit residues: 7.4553 Evaluate side-chains 28 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.281 Evaluate side-chains 95 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 THR cc_start: 0.9247 (m) cc_final: 0.8902 (p) REVERT: B 104 LEU cc_start: 0.8474 (mt) cc_final: 0.8202 (tp) REVERT: B 108 MET cc_start: 0.8893 (mmm) cc_final: 0.8645 (mmm) REVERT: B 126 ASN cc_start: 0.8877 (m-40) cc_final: 0.8507 (t0) REVERT: B 262 ASN cc_start: 0.7896 (m-40) cc_final: 0.7598 (m110) REVERT: B 400 MET cc_start: 0.8292 (mtt) cc_final: 0.7943 (mtt) REVERT: B 429 MET cc_start: 0.8705 (ppp) cc_final: 0.8336 (ppp) REVERT: B 456 LEU cc_start: 0.8907 (mp) cc_final: 0.8673 (tp) REVERT: B 801 MET cc_start: 0.8967 (ptt) cc_final: 0.8519 (tmm) REVERT: B 1031 ASP cc_start: 0.8984 (m-30) cc_final: 0.8663 (p0) REVERT: B 1068 PHE cc_start: 0.7983 (t80) cc_final: 0.7525 (t80) REVERT: B 1252 MET cc_start: 0.9206 (ttm) cc_final: 0.8923 (tpt) REVERT: B 1287 TYR cc_start: 0.9195 (m-80) cc_final: 0.8734 (m-10) REVERT: B 1514 MET cc_start: 0.7245 (mtm) cc_final: 0.6901 (tpt) REVERT: B 1550 MET cc_start: 0.5858 (ptp) cc_final: 0.5604 (ppp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2046 time to fit residues: 30.2518 Evaluate side-chains 76 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 521 optimal weight: 10.0000 chunk 355 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 466 optimal weight: 0.7980 chunk 258 optimal weight: 0.1980 chunk 534 optimal weight: 20.0000 chunk 432 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 319 optimal weight: 30.0000 chunk 562 optimal weight: 20.0000 chunk 158 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 51924 Z= 0.305 Angle : 0.851 14.550 70624 Z= 0.437 Chirality : 0.051 0.518 8540 Planarity : 0.007 0.068 8640 Dihedral : 9.070 148.248 7168 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.07 % Allowed : 3.76 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.09), residues: 6432 helix: -0.65 (0.07), residues: 3928 sheet: -1.71 (0.19), residues: 548 loop : -2.30 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP H1247 HIS 0.032 0.003 HIS F 241 PHE 0.082 0.004 PHE E 168 TYR 0.044 0.005 TYR H 396 ARG 0.024 0.001 ARG B1096 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6430 Ramachandran restraints generated. 3215 Oldfield, 0 Emsley, 3215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6430 Ramachandran restraints generated. 3215 Oldfield, 0 Emsley, 3215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 77 MET cc_start: 0.8482 (tpp) cc_final: 0.7529 (tmm) REVERT: C 88 MET cc_start: 0.9399 (tpt) cc_final: 0.8928 (tmm) REVERT: C 91 TRP cc_start: 0.8941 (t60) cc_final: 0.8636 (t-100) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.1218 time to fit residues: 7.2678 Evaluate side-chains 32 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.319 Evaluate side-chains 97 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 THR cc_start: 0.9196 (m) cc_final: 0.8866 (p) REVERT: B 108 MET cc_start: 0.8921 (mmm) cc_final: 0.8698 (mmp) REVERT: B 126 ASN cc_start: 0.8800 (m-40) cc_final: 0.8546 (t0) REVERT: B 262 ASN cc_start: 0.7884 (m-40) cc_final: 0.7621 (m110) REVERT: B 400 MET cc_start: 0.8282 (mtt) cc_final: 0.7911 (mtt) REVERT: B 429 MET cc_start: 0.8843 (ppp) cc_final: 0.8595 (ppp) REVERT: B 456 LEU cc_start: 0.9021 (mp) cc_final: 0.8535 (tp) REVERT: B 1031 ASP cc_start: 0.8986 (m-30) cc_final: 0.8647 (p0) REVERT: B 1068 PHE cc_start: 0.8039 (t80) cc_final: 0.7570 (t80) REVERT: B 1252 MET cc_start: 0.9184 (ttm) cc_final: 0.8931 (tpt) REVERT: B 1268 ILE cc_start: 0.8463 (tt) cc_final: 0.8206 (tt) REVERT: B 1287 TYR cc_start: 0.9189 (m-80) cc_final: 0.8731 (m-10) REVERT: B 1514 MET cc_start: 0.7279 (mtm) cc_final: 0.6933 (tpt) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1863 time to fit residues: 27.8923 Evaluate side-chains 81 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 210 optimal weight: 30.0000 chunk 564 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 367 optimal weight: 9.9990 chunk 154 optimal weight: 50.0000 chunk 626 optimal weight: 0.0050 chunk 520 optimal weight: 0.0060 chunk 290 optimal weight: 30.0000 chunk 52 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 329 optimal weight: 2.9990 overall best weight: 2.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 ASN C 152 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN ** F 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 51924 Z= 0.262 Angle : 0.842 16.893 70624 Z= 0.426 Chirality : 0.052 0.495 8540 Planarity : 0.007 0.076 8640 Dihedral : 8.916 145.466 7168 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.22 % Allowed : 3.69 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.09), residues: 6432 helix: -0.85 (0.07), residues: 3888 sheet: -1.78 (0.19), residues: 536 loop : -2.40 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.005 TRP A 90 HIS 0.031 0.003 HIS F 241 PHE 0.098 0.004 PHE H 583 TYR 0.043 0.004 TYR A 304 ARG 0.025 0.001 ARG D1096 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6430 Ramachandran restraints generated. 3215 Oldfield, 0 Emsley, 3215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6430 Ramachandran restraints generated. 3215 Oldfield, 0 Emsley, 3215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 77 MET cc_start: 0.8572 (tpp) cc_final: 0.7671 (tmm) REVERT: C 88 MET cc_start: 0.9407 (tpt) cc_final: 0.9010 (tmm) REVERT: C 91 TRP cc_start: 0.8984 (t60) cc_final: 0.8643 (t-100) REVERT: C 170 LYS cc_start: 0.9139 (mtpt) cc_final: 0.8527 (mttm) REVERT: C 209 MET cc_start: 0.8275 (ppp) cc_final: 0.8019 (ppp) outliers start: 3 outliers final: 3 residues processed: 50 average time/residue: 0.1300 time to fit residues: 8.1272 Evaluate side-chains 33 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.314 Evaluate side-chains 103 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 126 ASN cc_start: 0.8763 (m-40) cc_final: 0.8549 (t0) REVERT: F 257 MET cc_start: 0.8978 (mpp) cc_final: 0.8657 (mpp) REVERT: F 262 ASN cc_start: 0.7996 (m-40) cc_final: 0.7689 (m110) REVERT: F 400 MET cc_start: 0.8271 (mtt) cc_final: 0.7871 (mtt) REVERT: F 456 LEU cc_start: 0.9080 (mp) cc_final: 0.8477 (tp) REVERT: F 1031 ASP cc_start: 0.8978 (m-30) cc_final: 0.8622 (p0) REVERT: F 1068 PHE cc_start: 0.8059 (t80) cc_final: 0.7487 (t80) REVERT: F 1252 MET cc_start: 0.9143 (ttm) cc_final: 0.8910 (tpt) REVERT: F 1268 ILE cc_start: 0.8401 (tt) cc_final: 0.8143 (tt) REVERT: F 1287 TYR cc_start: 0.9188 (m-80) cc_final: 0.8726 (m-10) REVERT: F 1514 MET cc_start: 0.7267 (mtm) cc_final: 0.6905 (tpt) REVERT: F 1525 MET cc_start: 0.5460 (mpp) cc_final: 0.5101 (mpp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1954 time to fit residues: 31.4639 Evaluate side-chains 82 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 604 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 357 optimal weight: 0.6980 chunk 457 optimal weight: 0.0020 chunk 354 optimal weight: 40.0000 chunk 527 optimal weight: 0.3980 chunk 350 optimal weight: 0.2980 chunk 624 optimal weight: 0.7980 chunk 390 optimal weight: 0.0870 chunk 380 optimal weight: 0.3980 chunk 288 optimal weight: 0.9980 overall best weight: 0.2366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 392 GLN F 397 ASN ** F 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 51924 Z= 0.274 Angle : 0.867 11.866 70624 Z= 0.443 Chirality : 0.054 0.628 8540 Planarity : 0.007 0.073 8640 Dihedral : 8.877 144.657 7168 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.09), residues: 6432 helix: -0.94 (0.07), residues: 3896 sheet: -1.67 (0.19), residues: 536 loop : -2.46 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP G 90 HIS 0.031 0.002 HIS F 241 PHE 0.124 0.005 PHE F 363 TYR 0.043 0.004 TYR G 304 ARG 0.023 0.001 ARG B1096 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6430 Ramachandran restraints generated. 3215 Oldfield, 0 Emsley, 3215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6430 Ramachandran restraints generated. 3215 Oldfield, 0 Emsley, 3215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 MET cc_start: 0.8543 (tpp) cc_final: 0.7667 (tmm) REVERT: C 88 MET cc_start: 0.9407 (tpt) cc_final: 0.9005 (tmm) REVERT: C 91 TRP cc_start: 0.8960 (t60) cc_final: 0.8636 (t-100) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1267 time to fit residues: 7.2393 Evaluate side-chains 29 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.252 Evaluate side-chains 100 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 89 ILE cc_start: 0.9407 (mm) cc_final: 0.9109 (tt) REVERT: F 104 LEU cc_start: 0.8439 (tp) cc_final: 0.7856 (tp) REVERT: F 108 MET cc_start: 0.8829 (mmp) cc_final: 0.8280 (mmp) REVERT: F 126 ASN cc_start: 0.8814 (m-40) cc_final: 0.8550 (t0) REVERT: F 262 ASN cc_start: 0.8046 (m-40) cc_final: 0.7655 (m110) REVERT: F 400 MET cc_start: 0.8243 (mtt) cc_final: 0.7830 (mtt) REVERT: F 456 LEU cc_start: 0.9072 (mp) cc_final: 0.8451 (tp) REVERT: F 530 MET cc_start: 0.7412 (mmt) cc_final: 0.7076 (mmt) REVERT: F 1031 ASP cc_start: 0.8976 (m-30) cc_final: 0.8611 (p0) REVERT: F 1068 PHE cc_start: 0.8083 (t80) cc_final: 0.7532 (t80) REVERT: F 1268 ILE cc_start: 0.8355 (tt) cc_final: 0.8112 (tt) REVERT: F 1287 TYR cc_start: 0.9185 (m-80) cc_final: 0.8713 (m-10) REVERT: F 1514 MET cc_start: 0.7266 (mtm) cc_final: 0.6893 (tpt) REVERT: F 1550 MET cc_start: 0.5382 (tmm) cc_final: 0.5037 (tmm) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1897 time to fit residues: 29.2912 Evaluate side-chains 81 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 386 optimal weight: 8.9990 chunk 249 optimal weight: 0.4980 chunk 373 optimal weight: 0.3980 chunk 188 optimal weight: 0.4980 chunk 122 optimal weight: 30.0000 chunk 121 optimal weight: 20.0000 chunk 397 optimal weight: 0.0770 chunk 425 optimal weight: 40.0000 chunk 308 optimal weight: 50.0000 chunk 58 optimal weight: 40.0000 chunk 490 optimal weight: 3.9990 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 392 GLN F 397 ASN ** F 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 HIS F1234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 51924 Z= 0.270 Angle : 0.838 15.982 70624 Z= 0.424 Chirality : 0.052 0.508 8540 Planarity : 0.007 0.074 8640 Dihedral : 8.839 143.986 7168 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.07 % Allowed : 1.70 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.09), residues: 6432 helix: -0.96 (0.07), residues: 3932 sheet: -1.76 (0.19), residues: 536 loop : -2.51 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP E 90 HIS 0.067 0.003 HIS G 216 PHE 0.049 0.004 PHE A 35 TYR 0.043 0.004 TYR E 304 ARG 0.023 0.001 ARG B1096 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6430 Ramachandran restraints generated. 3215 Oldfield, 0 Emsley, 3215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6430 Ramachandran restraints generated. 3215 Oldfield, 0 Emsley, 3215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 MET cc_start: 0.8613 (tpp) cc_final: 0.7766 (tmm) REVERT: C 88 MET cc_start: 0.9387 (tpt) cc_final: 0.9013 (tmm) REVERT: C 91 TRP cc_start: 0.8966 (t60) cc_final: 0.8604 (t-100) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1479 time to fit residues: 8.3786 Evaluate side-chains 31 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.274 Evaluate side-chains 101 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 104 LEU cc_start: 0.8428 (tp) cc_final: 0.7795 (tp) REVERT: F 108 MET cc_start: 0.8833 (mmp) cc_final: 0.8191 (mmp) REVERT: F 126 ASN cc_start: 0.8832 (m-40) cc_final: 0.8578 (t0) REVERT: F 262 ASN cc_start: 0.7994 (m-40) cc_final: 0.7668 (m110) REVERT: F 400 MET cc_start: 0.8231 (mtt) cc_final: 0.7828 (mtt) REVERT: F 456 LEU cc_start: 0.9050 (mp) cc_final: 0.8457 (tp) REVERT: F 530 MET cc_start: 0.7595 (mmt) cc_final: 0.7257 (mmt) REVERT: F 1031 ASP cc_start: 0.8978 (m-30) cc_final: 0.8609 (p0) REVERT: F 1068 PHE cc_start: 0.8100 (t80) cc_final: 0.7525 (t80) REVERT: F 1268 ILE cc_start: 0.8350 (tt) cc_final: 0.8116 (tt) REVERT: F 1287 TYR cc_start: 0.9183 (m-80) cc_final: 0.8709 (m-10) REVERT: F 1514 MET cc_start: 0.7268 (mtm) cc_final: 0.6895 (tpt) REVERT: F 1550 MET cc_start: 0.5400 (tmm) cc_final: 0.5050 (tmm) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.1793 time to fit residues: 28.5141 Evaluate side-chains 82 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 568 optimal weight: 2.9990 chunk 598 optimal weight: 4.9990 chunk 545 optimal weight: 1.9990 chunk 582 optimal weight: 8.9990 chunk 350 optimal weight: 20.0000 chunk 253 optimal weight: 0.1980 chunk 457 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 chunk 525 optimal weight: 6.9990 chunk 550 optimal weight: 0.0060 chunk 579 optimal weight: 9.9990 overall best weight: 2.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 392 GLN F 397 ASN ** F 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 51924 Z= 0.270 Angle : 0.837 15.984 70624 Z= 0.424 Chirality : 0.052 0.507 8540 Planarity : 0.007 0.074 8640 Dihedral : 8.839 143.986 7168 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.09), residues: 6432 helix: -0.96 (0.07), residues: 3932 sheet: -1.76 (0.19), residues: 536 loop : -2.51 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP A 90 HIS 0.067 0.003 HIS C 216 PHE 0.049 0.004 PHE C 35 TYR 0.043 0.004 TYR A 304 ARG 0.023 0.001 ARG F1096 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6430 Ramachandran restraints generated. 3215 Oldfield, 0 Emsley, 3215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6430 Ramachandran restraints generated. 3215 Oldfield, 0 Emsley, 3215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 MET cc_start: 0.8628 (tpp) cc_final: 0.7767 (tmm) REVERT: C 88 MET cc_start: 0.9390 (tpt) cc_final: 0.9013 (tmm) REVERT: C 91 TRP cc_start: 0.8961 (t60) cc_final: 0.8604 (t-100) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1445 time to fit residues: 8.1370 Evaluate side-chains 31 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.309 Evaluate side-chains 98 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.224 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: F 104 LEU cc_start: 0.8426 (tp) cc_final: 0.7796 (tp) REVERT: F 108 MET cc_start: 0.8648 (mmp) cc_final: 0.8197 (mmp) REVERT: F 122 VAL cc_start: 0.9527 (t) cc_final: 0.9324 (t) REVERT: F 126 ASN cc_start: 0.8810 (m-40) cc_final: 0.8573 (t0) REVERT: F 262 ASN cc_start: 0.7992 (m-40) cc_final: 0.7669 (m110) REVERT: F 400 MET cc_start: 0.8225 (mtt) cc_final: 0.7824 (mtt) REVERT: F 456 LEU cc_start: 0.9044 (mp) cc_final: 0.8459 (tp) REVERT: F 530 MET cc_start: 0.7602 (mmt) cc_final: 0.7267 (mmt) REVERT: F 1031 ASP cc_start: 0.8977 (m-30) cc_final: 0.8614 (p0) REVERT: F 1068 PHE cc_start: 0.8086 (t80) cc_final: 0.7532 (t80) REVERT: F 1268 ILE cc_start: 0.8357 (tt) cc_final: 0.8115 (tt) REVERT: F 1287 TYR cc_start: 0.9177 (m-80) cc_final: 0.8693 (m-10) REVERT: F 1514 MET cc_start: 0.7269 (mtm) cc_final: 0.6894 (tpt) REVERT: F 1550 MET cc_start: 0.5401 (tmm) cc_final: 0.5052 (tmm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1820 time to fit residues: 27.9890 Evaluate side-chains 81 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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: 71.4104 > 50: distance: 0 - 1: 28.523 distance: 0 - 2: 39.574 distance: 3 - 4: 21.906 distance: 4 - 5: 19.037 distance: 4 - 7: 45.196 distance: 5 - 6: 15.639 distance: 5 - 10: 33.265 distance: 7 - 8: 30.741 distance: 7 - 9: 42.285 distance: 10 - 11: 4.890 distance: 11 - 14: 55.983 distance: 12 - 13: 31.206 distance: 15 - 16: 29.093 distance: 16 - 17: 34.411 distance: 16 - 19: 39.951 distance: 17 - 18: 31.824 distance: 17 - 22: 32.938 distance: 19 - 20: 49.737 distance: 20 - 21: 46.459 distance: 22 - 23: 17.585 distance: 23 - 24: 42.651 distance: 23 - 26: 14.511 distance: 24 - 25: 39.593 distance: 28 - 29: 33.635 distance: 28 - 31: 25.982 distance: 29 - 30: 17.189 distance: 29 - 35: 56.641 distance: 31 - 32: 13.323 distance: 31 - 33: 61.921 distance: 32 - 34: 56.925 distance: 37 - 38: 39.554 distance: 37 - 43: 24.928 distance: 39 - 40: 30.426 distance: 39 - 41: 31.350 distance: 40 - 42: 7.229 distance: 43 - 44: 42.139 distance: 44 - 47: 24.192 distance: 45 - 55: 13.695 distance: 47 - 48: 17.310 distance: 48 - 49: 4.633 distance: 48 - 50: 27.830 distance: 49 - 51: 29.050 distance: 50 - 52: 45.806 distance: 51 - 53: 23.876 distance: 52 - 53: 6.720 distance: 53 - 54: 29.756 distance: 55 - 56: 11.866 distance: 56 - 57: 16.931 distance: 56 - 59: 27.539 distance: 57 - 58: 5.984 distance: 57 - 65: 15.971 distance: 59 - 60: 11.337 distance: 60 - 61: 16.951 distance: 60 - 62: 6.644 distance: 62 - 64: 22.797 distance: 65 - 66: 12.597 distance: 66 - 67: 8.916 distance: 66 - 69: 19.602 distance: 67 - 68: 14.506 distance: 67 - 72: 15.471 distance: 69 - 70: 15.203 distance: 69 - 71: 6.341 distance: 72 - 73: 25.842 distance: 73 - 74: 13.797 distance: 73 - 76: 21.025 distance: 74 - 75: 41.626 distance: 74 - 80: 21.917 distance: 76 - 77: 25.111 distance: 76 - 78: 26.099 distance: 77 - 79: 21.043