Starting phenix.real_space_refine on Sat Jan 20 16:07:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnn_7538/01_2024/6cnn_7538_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnn_7538/01_2024/6cnn_7538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnn_7538/01_2024/6cnn_7538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnn_7538/01_2024/6cnn_7538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnn_7538/01_2024/6cnn_7538_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnn_7538/01_2024/6cnn_7538_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians Ca 12 9.91 5 K 4 8.98 5 P 4 5.49 5 S 108 5.16 5 C 10088 2.51 5 N 2744 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 17": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ARG 228": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 352": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 317": "NH1" <-> "NH2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ARG 352": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D ARG 228": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D ARG 331": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 15740 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1073 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 59 Chain: "F" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1073 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 59 Chain: "G" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1073 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 59 Chain: "H" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1073 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 81 Unusual residues: {' K': 4, 'LMT': 2, 'POV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'LMT': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'LMT': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'LMT': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.02, per 1000 atoms: 0.57 Number of scatterers: 15740 At special positions: 0 Unit cell: (139.05, 139.05, 109.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 12 19.99 K 4 19.00 S 108 16.00 P 4 15.00 O 2780 8.00 N 2744 7.00 C 10088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.95 Conformation dependent library (CDL) restraints added in 2.8 seconds 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 0 sheets defined 71.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'A' and resid 10 through 48 removed outlier: 3.716A pdb=" N ARG A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 90 removed outlier: 4.275A pdb=" N LEU A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 99 No H-bonds generated for 'chain 'A' and resid 96 through 99' Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.531A pdb=" N MET A 156 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU A 157 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 192 through 202 removed outlier: 3.518A pdb=" N LYS A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 226 removed outlier: 3.612A pdb=" N LEU A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA A 220 " --> pdb=" O TRP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 removed outlier: 4.416A pdb=" N TRP A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 261 through 288 removed outlier: 3.544A pdb=" N VAL A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 331 removed outlier: 4.037A pdb=" N HIS A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 368 removed outlier: 4.171A pdb=" N ARG A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 384 removed outlier: 3.848A pdb=" N GLN A 383 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASN A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 48 removed outlier: 3.717A pdb=" N ARG B 14 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 90 removed outlier: 4.277A pdb=" N LEU B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 99 No H-bonds generated for 'chain 'B' and resid 96 through 99' Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.532A pdb=" N MET B 156 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU B 157 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 170 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'B' and resid 192 through 202 removed outlier: 3.524A pdb=" N LYS B 197 " --> pdb=" O TRP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 226 removed outlier: 3.620A pdb=" N LEU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA B 220 " --> pdb=" O TRP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 248 removed outlier: 4.426A pdb=" N TRP B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) Proline residue: B 245 - end of helix Processing helix chain 'B' and resid 261 through 288 removed outlier: 3.546A pdb=" N VAL B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 271 " --> pdb=" O CYS B 267 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 331 removed outlier: 4.040A pdb=" N HIS B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET B 324 " --> pdb=" O GLN B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 368 removed outlier: 4.149A pdb=" N ARG B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 384 removed outlier: 3.854A pdb=" N GLN B 383 " --> pdb=" O TYR B 379 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 48 removed outlier: 3.721A pdb=" N ARG C 14 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ARG C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 90 removed outlier: 4.274A pdb=" N LEU C 72 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 99 No H-bonds generated for 'chain 'C' and resid 96 through 99' Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 153 through 158 removed outlier: 3.534A pdb=" N MET C 156 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU C 157 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 170 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 192 through 202 removed outlier: 3.522A pdb=" N LYS C 197 " --> pdb=" O TRP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 226 removed outlier: 3.622A pdb=" N LEU C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA C 220 " --> pdb=" O TRP C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 removed outlier: 4.415A pdb=" N TRP C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Proline residue: C 245 - end of helix Processing helix chain 'C' and resid 261 through 288 removed outlier: 3.545A pdb=" N VAL C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY C 271 " --> pdb=" O CYS C 267 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 331 removed outlier: 4.043A pdb=" N HIS C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 319 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET C 324 " --> pdb=" O GLN C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 368 removed outlier: 4.160A pdb=" N ARG C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 343 " --> pdb=" O ARG C 339 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 353 " --> pdb=" O ASN C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 384 removed outlier: 3.850A pdb=" N GLN C 383 " --> pdb=" O TYR C 379 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 48 removed outlier: 3.718A pdb=" N ARG D 14 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ARG D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 90 removed outlier: 4.272A pdb=" N LEU D 72 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 99 No H-bonds generated for 'chain 'D' and resid 96 through 99' Processing helix chain 'D' and resid 102 through 116 Processing helix chain 'D' and resid 153 through 158 removed outlier: 3.533A pdb=" N MET D 156 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU D 157 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 170 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 177 through 186 Processing helix chain 'D' and resid 192 through 202 removed outlier: 3.519A pdb=" N LYS D 197 " --> pdb=" O TRP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 226 removed outlier: 3.615A pdb=" N LEU D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY D 214 " --> pdb=" O GLY D 210 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR D 218 " --> pdb=" O GLY D 214 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA D 220 " --> pdb=" O TRP D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 4.414A pdb=" N TRP D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) Proline residue: D 245 - end of helix Processing helix chain 'D' and resid 261 through 288 removed outlier: 3.544A pdb=" N VAL D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY D 271 " --> pdb=" O CYS D 267 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 288 " --> pdb=" O VAL D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 331 removed outlier: 4.041A pdb=" N HIS D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS D 309 " --> pdb=" O ILE D 305 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 316 " --> pdb=" O LYS D 312 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 319 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET D 324 " --> pdb=" O GLN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 368 removed outlier: 4.173A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 353 " --> pdb=" O ASN D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 384 removed outlier: 3.845A pdb=" N GLN D 383 " --> pdb=" O TYR D 379 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN D 384 " --> pdb=" O ASP D 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 18 removed outlier: 4.365A pdb=" N GLU E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 38 removed outlier: 3.553A pdb=" N VAL E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 53 Processing helix chain 'E' and resid 65 through 74 removed outlier: 3.764A pdb=" N THR E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 removed outlier: 3.859A pdb=" N ALA E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 111 removed outlier: 3.992A pdb=" N THR E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN E 111 " --> pdb=" O HIS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 128 removed outlier: 3.653A pdb=" N GLU E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 145 Processing helix chain 'F' and resid 6 through 18 removed outlier: 4.364A pdb=" N GLU F 14 " --> pdb=" O ALA F 10 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 38 removed outlier: 3.552A pdb=" N VAL F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 53 Processing helix chain 'F' and resid 65 through 74 removed outlier: 3.760A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 removed outlier: 3.857A pdb=" N ALA F 88 " --> pdb=" O GLU F 84 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 111 removed outlier: 3.972A pdb=" N THR F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN F 111 " --> pdb=" O HIS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 128 removed outlier: 3.630A pdb=" N GLU F 123 " --> pdb=" O GLU F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'G' and resid 6 through 18 removed outlier: 4.358A pdb=" N GLU G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 38 removed outlier: 3.550A pdb=" N VAL G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 53 Processing helix chain 'G' and resid 65 through 74 removed outlier: 3.763A pdb=" N THR G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG G 74 " --> pdb=" O THR G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 92 removed outlier: 3.867A pdb=" N ALA G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 111 removed outlier: 4.004A pdb=" N THR G 110 " --> pdb=" O ARG G 106 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN G 111 " --> pdb=" O HIS G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 removed outlier: 3.660A pdb=" N GLU G 123 " --> pdb=" O GLU G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 145 Processing helix chain 'H' and resid 6 through 18 removed outlier: 4.361A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 38 removed outlier: 3.551A pdb=" N VAL H 35 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 53 Processing helix chain 'H' and resid 65 through 74 removed outlier: 3.766A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 92 removed outlier: 3.872A pdb=" N ALA H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 111 removed outlier: 3.980A pdb=" N THR H 110 " --> pdb=" O ARG H 106 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN H 111 " --> pdb=" O HIS H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 128 removed outlier: 3.651A pdb=" N GLU H 123 " --> pdb=" O GLU H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 145 880 hydrogen bonds defined for protein. 2628 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: 4.31 Time building geometry restraints manager: 6.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4757 1.34 - 1.45: 2265 1.45 - 1.57: 8786 1.57 - 1.69: 8 1.69 - 1.80: 188 Bond restraints: 16004 Sorted by residual: bond pdb=" C31 POV B1101 " pdb=" O31 POV B1101 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C31 POV A1101 " pdb=" O31 POV A1101 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C31 POV C1101 " pdb=" O31 POV C1101 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C31 POV D1101 " pdb=" O31 POV D1101 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C21 POV C1101 " pdb=" O21 POV C1101 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.87e+01 ... (remaining 15999 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.63: 211 105.63 - 112.73: 8540 112.73 - 119.83: 5938 119.83 - 126.93: 6737 126.93 - 134.03: 198 Bond angle restraints: 21624 Sorted by residual: angle pdb=" C2 LMT C1103 " pdb=" C3 LMT C1103 " pdb=" C4 LMT C1103 " ideal model delta sigma weight residual 117.09 107.29 9.80 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C2 LMT D1103 " pdb=" C3 LMT D1103 " pdb=" C4 LMT D1103 " ideal model delta sigma weight residual 117.09 107.32 9.77 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C2 LMT B1103 " pdb=" C3 LMT B1103 " pdb=" C4 LMT B1103 " ideal model delta sigma weight residual 117.09 107.32 9.77 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C2 LMT A1103 " pdb=" C3 LMT A1103 " pdb=" C4 LMT A1103 " ideal model delta sigma weight residual 117.09 107.32 9.77 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C32 POV C1101 " pdb=" C31 POV C1101 " pdb=" O31 POV C1101 " ideal model delta sigma weight residual 110.66 120.20 -9.54 3.00e+00 1.11e-01 1.01e+01 ... (remaining 21619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.59: 9385 20.59 - 41.18: 259 41.18 - 61.77: 72 61.77 - 82.36: 6 82.36 - 102.95: 30 Dihedral angle restraints: 9752 sinusoidal: 3944 harmonic: 5808 Sorted by residual: dihedral pdb=" CA PHE B 291 " pdb=" C PHE B 291 " pdb=" N ASN B 292 " pdb=" CA ASN B 292 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA PHE A 291 " pdb=" C PHE A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual 180.00 157.96 22.04 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA PHE C 291 " pdb=" C PHE C 291 " pdb=" N ASN C 292 " pdb=" CA ASN C 292 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 9749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1744 0.050 - 0.100: 646 0.100 - 0.149: 119 0.149 - 0.199: 23 0.199 - 0.249: 12 Chirality restraints: 2544 Sorted by residual: chirality pdb=" C5' LMT C1103 " pdb=" C4' LMT C1103 " pdb=" C6' LMT C1103 " pdb=" O5' LMT C1103 " both_signs ideal model delta sigma weight residual False -2.51 -2.26 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C5' LMT D1103 " pdb=" C4' LMT D1103 " pdb=" C6' LMT D1103 " pdb=" O5' LMT D1103 " both_signs ideal model delta sigma weight residual False -2.51 -2.26 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C5' LMT B1103 " pdb=" C4' LMT B1103 " pdb=" C6' LMT B1103 " pdb=" O5' LMT B1103 " both_signs ideal model delta sigma weight residual False -2.51 -2.26 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 2541 not shown) Planarity restraints: 2668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 189 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C ARG A 189 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG A 189 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE A 190 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 189 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" C ARG D 189 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG D 189 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE D 190 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 189 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" C ARG C 189 " -0.036 2.00e-02 2.50e+03 pdb=" O ARG C 189 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE C 190 " 0.012 2.00e-02 2.50e+03 ... (remaining 2665 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.64: 184 2.64 - 3.27: 16023 3.27 - 3.89: 29009 3.89 - 4.52: 38217 4.52 - 5.14: 59831 Nonbonded interactions: 143264 Sorted by model distance: nonbonded pdb=" OD1 ASP G 58 " pdb="CA CA G 202 " model vdw 2.016 2.510 nonbonded pdb=" OD1 ASP H 58 " pdb="CA CA H 202 " model vdw 2.016 2.510 nonbonded pdb=" OD1 ASP F 58 " pdb="CA CA F 202 " model vdw 2.019 2.510 nonbonded pdb=" OD1 ASP E 58 " pdb="CA CA E 202 " model vdw 2.020 2.510 nonbonded pdb=" OD1 ASP F 20 " pdb=" OD1 ASP F 24 " model vdw 2.129 3.040 ... (remaining 143259 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' and resid 9 through 386) selection = (chain 'B' and resid 9 through 386) selection = (chain 'C' and resid 9 through 386) selection = (chain 'D' and resid 9 through 386) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.030 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 44.360 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.008 0.128 16004 Z= 0.543 Angle : 1.070 9.797 21624 Z= 0.557 Chirality : 0.054 0.249 2544 Planarity : 0.006 0.050 2668 Dihedral : 12.899 102.947 5992 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.14), residues: 2000 helix: -2.92 (0.09), residues: 1560 sheet: None (None), residues: 0 loop : -1.45 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 221 HIS 0.006 0.002 HIS C 340 PHE 0.032 0.003 PHE D 291 TYR 0.013 0.003 TYR C 253 ARG 0.009 0.001 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 1.906 Fit side-chains REVERT: A 293 LYS cc_start: 0.8810 (tptt) cc_final: 0.8561 (tttt) REVERT: A 326 TYR cc_start: 0.8303 (t80) cc_final: 0.8064 (t80) REVERT: A 349 ASN cc_start: 0.8927 (t0) cc_final: 0.8638 (t0) REVERT: B 200 MET cc_start: 0.8186 (ttm) cc_final: 0.7957 (ttm) REVERT: B 293 LYS cc_start: 0.8804 (tptt) cc_final: 0.8550 (tttt) REVERT: B 320 GLN cc_start: 0.7828 (tt0) cc_final: 0.7606 (tt0) REVERT: B 326 TYR cc_start: 0.8269 (t80) cc_final: 0.7983 (t80) REVERT: B 349 ASN cc_start: 0.8913 (t0) cc_final: 0.8631 (t0) REVERT: C 200 MET cc_start: 0.8174 (ttm) cc_final: 0.7941 (ttm) REVERT: C 293 LYS cc_start: 0.8801 (tptt) cc_final: 0.8507 (tttt) REVERT: C 326 TYR cc_start: 0.8266 (t80) cc_final: 0.8024 (t80) REVERT: C 349 ASN cc_start: 0.8909 (t0) cc_final: 0.8624 (t0) REVERT: D 200 MET cc_start: 0.8183 (ttm) cc_final: 0.7938 (ttm) REVERT: D 293 LYS cc_start: 0.8807 (tptt) cc_final: 0.8554 (tttt) REVERT: D 320 GLN cc_start: 0.7866 (tt0) cc_final: 0.7426 (tt0) REVERT: D 326 TYR cc_start: 0.8312 (t80) cc_final: 0.8070 (t80) REVERT: D 349 ASN cc_start: 0.8919 (t0) cc_final: 0.8626 (t0) outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.3140 time to fit residues: 215.6702 Evaluate side-chains 266 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS A 320 GLN B 297 HIS C 297 HIS C 320 GLN D 297 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16004 Z= 0.198 Angle : 0.540 6.784 21624 Z= 0.280 Chirality : 0.038 0.196 2544 Planarity : 0.003 0.026 2668 Dihedral : 8.733 71.492 2600 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.24 % Allowed : 8.84 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.46 (0.18), residues: 2000 helix: -0.83 (0.12), residues: 1524 sheet: None (None), residues: 0 loop : -0.83 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 221 HIS 0.005 0.001 HIS A 328 PHE 0.011 0.001 PHE F 12 TYR 0.011 0.001 TYR B 179 ARG 0.007 0.001 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 353 time to evaluate : 1.500 Fit side-chains REVERT: A 213 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8454 (tt) REVERT: A 293 LYS cc_start: 0.8737 (tptt) cc_final: 0.8420 (tttt) REVERT: B 179 TYR cc_start: 0.8568 (m-80) cc_final: 0.8299 (m-80) REVERT: B 201 ASN cc_start: 0.8280 (m110) cc_final: 0.8038 (m-40) REVERT: B 213 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8447 (tt) REVERT: B 293 LYS cc_start: 0.8735 (tptt) cc_final: 0.8413 (tttt) REVERT: C 201 ASN cc_start: 0.8257 (m110) cc_final: 0.8025 (m-40) REVERT: C 213 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8426 (tt) REVERT: C 293 LYS cc_start: 0.8728 (tptt) cc_final: 0.8408 (tttt) REVERT: D 213 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8440 (tt) REVERT: D 293 LYS cc_start: 0.8763 (tptt) cc_final: 0.8440 (tttt) REVERT: E 17 SER cc_start: 0.8855 (m) cc_final: 0.8450 (t) REVERT: E 71 MET cc_start: 0.8808 (tpp) cc_final: 0.8569 (tpp) REVERT: F 17 SER cc_start: 0.8857 (m) cc_final: 0.8454 (t) REVERT: F 71 MET cc_start: 0.8807 (tpp) cc_final: 0.8557 (tpp) REVERT: G 17 SER cc_start: 0.8772 (m) cc_final: 0.8508 (t) REVERT: G 71 MET cc_start: 0.8806 (tpp) cc_final: 0.8576 (tpp) REVERT: H 17 SER cc_start: 0.8792 (m) cc_final: 0.8519 (t) REVERT: H 71 MET cc_start: 0.8804 (tpp) cc_final: 0.8574 (tpp) outliers start: 34 outliers final: 19 residues processed: 372 average time/residue: 0.2599 time to fit residues: 144.7423 Evaluate side-chains 318 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 295 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain H residue 9 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 196 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16004 Z= 0.184 Angle : 0.494 7.510 21624 Z= 0.252 Chirality : 0.037 0.138 2544 Planarity : 0.003 0.025 2668 Dihedral : 7.698 69.507 2600 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.03 % Allowed : 12.07 % Favored : 84.89 % 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: -0.00 (0.19), residues: 2000 helix: 0.26 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -0.41 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 221 HIS 0.004 0.001 HIS D 80 PHE 0.010 0.001 PHE A 291 TYR 0.009 0.001 TYR E 99 ARG 0.007 0.000 ARG G 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 291 time to evaluate : 1.868 Fit side-chains REVERT: A 206 ARG cc_start: 0.6580 (mtt180) cc_final: 0.6140 (tmm160) REVERT: A 293 LYS cc_start: 0.8729 (tptt) cc_final: 0.8504 (tttt) REVERT: B 206 ARG cc_start: 0.6592 (mtt180) cc_final: 0.5997 (ttp80) REVERT: B 293 LYS cc_start: 0.8730 (tptt) cc_final: 0.8498 (tttt) REVERT: C 206 ARG cc_start: 0.6618 (mtt180) cc_final: 0.5994 (ttp80) REVERT: C 293 LYS cc_start: 0.8728 (tptt) cc_final: 0.8453 (tttt) REVERT: D 206 ARG cc_start: 0.6588 (mtt180) cc_final: 0.6142 (tmm160) REVERT: D 293 LYS cc_start: 0.8749 (tptt) cc_final: 0.8479 (tttt) REVERT: E 17 SER cc_start: 0.8793 (m) cc_final: 0.8494 (t) REVERT: E 71 MET cc_start: 0.8791 (tpp) cc_final: 0.8573 (tpp) REVERT: F 17 SER cc_start: 0.8793 (m) cc_final: 0.8490 (t) REVERT: F 71 MET cc_start: 0.8793 (tpp) cc_final: 0.8550 (tpp) outliers start: 46 outliers final: 38 residues processed: 316 average time/residue: 0.2735 time to fit residues: 128.0886 Evaluate side-chains 313 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 275 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 91 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 94 optimal weight: 0.0770 chunk 20 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 193 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16004 Z= 0.147 Angle : 0.458 6.634 21624 Z= 0.234 Chirality : 0.035 0.146 2544 Planarity : 0.003 0.031 2668 Dihedral : 7.117 69.310 2600 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.17 % Allowed : 11.87 % Favored : 84.96 % 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: 0.84 (0.19), residues: 2000 helix: 0.88 (0.14), residues: 1516 sheet: None (None), residues: 0 loop : -0.17 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 221 HIS 0.004 0.001 HIS A 80 PHE 0.007 0.001 PHE B 291 TYR 0.010 0.001 TYR E 99 ARG 0.007 0.000 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 306 time to evaluate : 1.918 Fit side-chains REVERT: A 206 ARG cc_start: 0.6538 (mtt180) cc_final: 0.6199 (tmm160) REVERT: A 293 LYS cc_start: 0.8721 (tptt) cc_final: 0.8426 (tttt) REVERT: B 206 ARG cc_start: 0.6492 (mtt180) cc_final: 0.6194 (tmm160) REVERT: B 293 LYS cc_start: 0.8726 (tptt) cc_final: 0.8424 (tttt) REVERT: B 373 LYS cc_start: 0.7721 (tppt) cc_final: 0.7493 (ptmt) REVERT: C 206 ARG cc_start: 0.6538 (mtt180) cc_final: 0.6195 (tmm160) REVERT: C 293 LYS cc_start: 0.8722 (tptt) cc_final: 0.8418 (tttt) REVERT: D 206 ARG cc_start: 0.6530 (mtt180) cc_final: 0.6198 (tmm160) REVERT: D 293 LYS cc_start: 0.8757 (tptt) cc_final: 0.8484 (tttt) REVERT: D 326 TYR cc_start: 0.8060 (t80) cc_final: 0.7852 (t80) REVERT: D 374 MET cc_start: 0.7134 (tpp) cc_final: 0.6827 (tpp) REVERT: E 138 TYR cc_start: 0.8925 (t80) cc_final: 0.8322 (t80) REVERT: F 138 TYR cc_start: 0.8931 (t80) cc_final: 0.8405 (t80) REVERT: G 71 MET cc_start: 0.8827 (tpp) cc_final: 0.8598 (tpp) REVERT: G 138 TYR cc_start: 0.8943 (t80) cc_final: 0.8425 (t80) REVERT: H 71 MET cc_start: 0.8824 (tpp) cc_final: 0.8593 (tpp) REVERT: H 92 PHE cc_start: 0.7551 (m-10) cc_final: 0.7316 (m-80) REVERT: H 138 TYR cc_start: 0.8911 (t80) cc_final: 0.8294 (t80) REVERT: H 144 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6972 (tpp) outliers start: 48 outliers final: 33 residues processed: 325 average time/residue: 0.2742 time to fit residues: 131.5976 Evaluate side-chains 321 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 287 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 0.0030 chunk 173 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS B 358 HIS C 358 HIS D 358 HIS E 42 ASN F 42 ASN G 42 ASN H 42 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16004 Z= 0.143 Angle : 0.458 8.299 21624 Z= 0.235 Chirality : 0.035 0.154 2544 Planarity : 0.003 0.048 2668 Dihedral : 6.820 69.509 2600 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.10 % Allowed : 12.86 % Favored : 84.04 % 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: 1.44 (0.20), residues: 2000 helix: 1.33 (0.14), residues: 1508 sheet: None (None), residues: 0 loop : -0.02 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 221 HIS 0.004 0.001 HIS C 80 PHE 0.006 0.001 PHE C 291 TYR 0.010 0.001 TYR F 99 ARG 0.007 0.000 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 293 time to evaluate : 1.948 Fit side-chains REVERT: A 289 LEU cc_start: 0.7389 (mm) cc_final: 0.6820 (tt) REVERT: A 293 LYS cc_start: 0.8743 (tptt) cc_final: 0.8423 (tttt) REVERT: A 321 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7976 (mm-30) REVERT: B 289 LEU cc_start: 0.7394 (mm) cc_final: 0.6821 (tt) REVERT: B 293 LYS cc_start: 0.8748 (tptt) cc_final: 0.8431 (tttt) REVERT: B 373 LYS cc_start: 0.7651 (tppt) cc_final: 0.7442 (ptmt) REVERT: C 293 LYS cc_start: 0.8742 (tptt) cc_final: 0.8428 (tttt) REVERT: C 321 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8174 (mm-30) REVERT: D 289 LEU cc_start: 0.7446 (mm) cc_final: 0.6825 (tt) REVERT: D 293 LYS cc_start: 0.8765 (tptt) cc_final: 0.8479 (tttt) REVERT: E 138 TYR cc_start: 0.8943 (t80) cc_final: 0.8382 (t80) REVERT: F 138 TYR cc_start: 0.8932 (t80) cc_final: 0.8365 (t80) REVERT: G 82 GLU cc_start: 0.7907 (tp30) cc_final: 0.7692 (tp30) REVERT: G 138 TYR cc_start: 0.8958 (t80) cc_final: 0.8382 (t80) REVERT: H 138 TYR cc_start: 0.8915 (t80) cc_final: 0.8368 (t80) outliers start: 47 outliers final: 30 residues processed: 312 average time/residue: 0.2582 time to fit residues: 120.6067 Evaluate side-chains 315 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 285 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 137 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 42 ASN F 42 ASN G 42 ASN H 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16004 Z= 0.212 Angle : 0.495 7.224 21624 Z= 0.255 Chirality : 0.037 0.137 2544 Planarity : 0.003 0.037 2668 Dihedral : 6.914 70.841 2600 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.02 % Allowed : 12.07 % Favored : 83.91 % 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: 1.59 (0.20), residues: 2000 helix: 1.42 (0.14), residues: 1508 sheet: None (None), residues: 0 loop : 0.11 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 221 HIS 0.004 0.001 HIS D 80 PHE 0.013 0.001 PHE E 92 TYR 0.010 0.001 TYR E 99 ARG 0.006 0.001 ARG H 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 289 time to evaluate : 1.759 Fit side-chains revert: symmetry clash REVERT: A 213 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8114 (tt) REVERT: A 289 LEU cc_start: 0.7319 (mm) cc_final: 0.6754 (tt) REVERT: A 293 LYS cc_start: 0.8721 (tptt) cc_final: 0.8493 (tttt) REVERT: A 296 LYS cc_start: 0.8728 (tttp) cc_final: 0.8455 (tptm) REVERT: A 321 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8200 (mm-30) REVERT: B 213 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8109 (tt) REVERT: B 289 LEU cc_start: 0.7324 (mm) cc_final: 0.6751 (tt) REVERT: B 293 LYS cc_start: 0.8736 (tptt) cc_final: 0.8530 (tttt) REVERT: B 373 LYS cc_start: 0.7590 (tppt) cc_final: 0.7360 (ptmt) REVERT: C 289 LEU cc_start: 0.7382 (mm) cc_final: 0.6819 (tt) REVERT: C 293 LYS cc_start: 0.8729 (tptt) cc_final: 0.8502 (tttt) REVERT: C 296 LYS cc_start: 0.8730 (tttp) cc_final: 0.8455 (tptm) REVERT: D 213 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8113 (tt) REVERT: D 289 LEU cc_start: 0.7382 (mm) cc_final: 0.6796 (tt) REVERT: E 71 MET cc_start: 0.8841 (tpp) cc_final: 0.8599 (tpp) REVERT: E 138 TYR cc_start: 0.8953 (t80) cc_final: 0.8395 (t80) REVERT: F 71 MET cc_start: 0.8818 (tpp) cc_final: 0.8581 (tpp) REVERT: F 138 TYR cc_start: 0.8955 (t80) cc_final: 0.8360 (t80) REVERT: G 138 TYR cc_start: 0.8938 (t80) cc_final: 0.8342 (t80) REVERT: H 138 TYR cc_start: 0.8922 (t80) cc_final: 0.8368 (t80) outliers start: 61 outliers final: 51 residues processed: 316 average time/residue: 0.2537 time to fit residues: 120.9594 Evaluate side-chains 335 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 281 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 42 ASN Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 42 ASN Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 137 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 8.9990 chunk 21 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 42 ASN G 42 ASN H 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16004 Z= 0.157 Angle : 0.480 7.351 21624 Z= 0.246 Chirality : 0.036 0.163 2544 Planarity : 0.003 0.037 2668 Dihedral : 6.590 75.295 2600 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.43 % Allowed : 13.32 % Favored : 83.25 % 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: 1.92 (0.20), residues: 2000 helix: 1.65 (0.14), residues: 1516 sheet: None (None), residues: 0 loop : 0.27 (0.32), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 221 HIS 0.004 0.001 HIS C 80 PHE 0.008 0.001 PHE E 141 TYR 0.009 0.001 TYR G 99 ARG 0.006 0.000 ARG F 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 283 time to evaluate : 1.834 Fit side-chains revert: symmetry clash REVERT: A 289 LEU cc_start: 0.7330 (mm) cc_final: 0.6764 (tt) REVERT: A 293 LYS cc_start: 0.8741 (tptt) cc_final: 0.8508 (tttt) REVERT: A 296 LYS cc_start: 0.8641 (tttp) cc_final: 0.8376 (tptm) REVERT: A 321 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8205 (mm-30) REVERT: B 289 LEU cc_start: 0.7341 (mm) cc_final: 0.6772 (tt) REVERT: B 293 LYS cc_start: 0.8747 (tptt) cc_final: 0.8537 (tttt) REVERT: B 373 LYS cc_start: 0.7572 (tppt) cc_final: 0.7364 (ptmt) REVERT: C 91 ASN cc_start: 0.8977 (m-40) cc_final: 0.8773 (m-40) REVERT: C 289 LEU cc_start: 0.7348 (mm) cc_final: 0.6739 (tt) REVERT: C 293 LYS cc_start: 0.8736 (tptt) cc_final: 0.8512 (tttt) REVERT: C 296 LYS cc_start: 0.8618 (tttp) cc_final: 0.8366 (tptm) REVERT: D 289 LEU cc_start: 0.7349 (mm) cc_final: 0.6805 (tt) REVERT: D 296 LYS cc_start: 0.8612 (tttp) cc_final: 0.8360 (tptm) REVERT: E 71 MET cc_start: 0.8801 (tpp) cc_final: 0.8599 (tpp) REVERT: E 138 TYR cc_start: 0.8931 (t80) cc_final: 0.8437 (t80) REVERT: E 145 MET cc_start: 0.8505 (tpp) cc_final: 0.8272 (tpp) REVERT: F 71 MET cc_start: 0.8827 (tpp) cc_final: 0.8617 (tpp) REVERT: F 138 TYR cc_start: 0.8921 (t80) cc_final: 0.8415 (t80) REVERT: G 138 TYR cc_start: 0.8923 (t80) cc_final: 0.8414 (t80) REVERT: H 138 TYR cc_start: 0.8904 (t80) cc_final: 0.8353 (t80) outliers start: 52 outliers final: 39 residues processed: 301 average time/residue: 0.2629 time to fit residues: 118.5777 Evaluate side-chains 310 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 271 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 137 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 58 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 131 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16004 Z= 0.138 Angle : 0.460 7.760 21624 Z= 0.235 Chirality : 0.035 0.128 2544 Planarity : 0.003 0.046 2668 Dihedral : 6.316 83.899 2600 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.77 % Allowed : 14.45 % Favored : 82.78 % 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: 2.34 (0.20), residues: 2000 helix: 1.94 (0.14), residues: 1524 sheet: None (None), residues: 0 loop : 0.40 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 221 HIS 0.004 0.001 HIS D 80 PHE 0.008 0.001 PHE E 141 TYR 0.007 0.001 TYR G 99 ARG 0.006 0.000 ARG F 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 306 time to evaluate : 1.734 Fit side-chains revert: symmetry clash REVERT: A 289 LEU cc_start: 0.7454 (mm) cc_final: 0.6849 (tt) REVERT: A 293 LYS cc_start: 0.8750 (tptt) cc_final: 0.8515 (tttt) REVERT: A 296 LYS cc_start: 0.8578 (tttp) cc_final: 0.8336 (tptm) REVERT: A 321 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8178 (mm-30) REVERT: B 289 LEU cc_start: 0.7454 (mm) cc_final: 0.6875 (tt) REVERT: B 293 LYS cc_start: 0.8751 (tptt) cc_final: 0.8520 (tttt) REVERT: B 296 LYS cc_start: 0.8557 (tttp) cc_final: 0.8306 (tptm) REVERT: C 289 LEU cc_start: 0.7417 (mm) cc_final: 0.6783 (tt) REVERT: C 293 LYS cc_start: 0.8751 (tptt) cc_final: 0.8524 (tttt) REVERT: C 296 LYS cc_start: 0.8558 (tttp) cc_final: 0.8323 (tptm) REVERT: D 289 LEU cc_start: 0.7452 (mm) cc_final: 0.6858 (tt) REVERT: D 296 LYS cc_start: 0.8549 (tttp) cc_final: 0.8337 (tptm) REVERT: D 343 LYS cc_start: 0.8614 (mttt) cc_final: 0.8308 (mtmm) REVERT: E 71 MET cc_start: 0.8839 (tpp) cc_final: 0.8635 (tpp) REVERT: E 138 TYR cc_start: 0.8930 (t80) cc_final: 0.8383 (t80) REVERT: E 145 MET cc_start: 0.8465 (tpp) cc_final: 0.8164 (tpp) REVERT: F 71 MET cc_start: 0.8833 (tpp) cc_final: 0.8621 (tpp) REVERT: F 138 TYR cc_start: 0.8903 (t80) cc_final: 0.8425 (t80) REVERT: G 92 PHE cc_start: 0.7413 (m-10) cc_final: 0.7196 (m-80) REVERT: G 138 TYR cc_start: 0.8899 (t80) cc_final: 0.8369 (t80) REVERT: H 92 PHE cc_start: 0.7521 (m-10) cc_final: 0.7255 (m-80) REVERT: H 138 TYR cc_start: 0.8896 (t80) cc_final: 0.8350 (t80) outliers start: 42 outliers final: 35 residues processed: 320 average time/residue: 0.2533 time to fit residues: 121.3787 Evaluate side-chains 325 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 290 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 137 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 55 optimal weight: 0.2980 chunk 162 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 299 HIS ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16004 Z= 0.326 Angle : 0.604 7.001 21624 Z= 0.306 Chirality : 0.040 0.123 2544 Planarity : 0.004 0.052 2668 Dihedral : 7.295 89.515 2600 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.50 % Allowed : 14.38 % Favored : 82.12 % 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: 1.82 (0.19), residues: 2000 helix: 1.51 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : 0.42 (0.33), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 221 HIS 0.006 0.002 HIS C 340 PHE 0.014 0.002 PHE C 291 TYR 0.017 0.002 TYR D 179 ARG 0.011 0.001 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 280 time to evaluate : 1.668 Fit side-chains revert: symmetry clash REVERT: A 213 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8083 (tt) REVERT: A 289 LEU cc_start: 0.7322 (mm) cc_final: 0.6824 (tt) REVERT: A 293 LYS cc_start: 0.8791 (tptt) cc_final: 0.8570 (tttt) REVERT: A 296 LYS cc_start: 0.8867 (tttp) cc_final: 0.8653 (tptm) REVERT: B 213 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8079 (tt) REVERT: B 289 LEU cc_start: 0.7337 (mm) cc_final: 0.6819 (tt) REVERT: B 293 LYS cc_start: 0.8796 (tptt) cc_final: 0.8584 (tttt) REVERT: B 321 GLU cc_start: 0.8552 (tp30) cc_final: 0.8103 (mm-30) REVERT: B 373 LYS cc_start: 0.7613 (tppt) cc_final: 0.7331 (ptmt) REVERT: C 289 LEU cc_start: 0.7329 (mm) cc_final: 0.6765 (tt) REVERT: C 293 LYS cc_start: 0.8777 (tptt) cc_final: 0.8559 (tttt) REVERT: C 296 LYS cc_start: 0.8856 (tttp) cc_final: 0.8652 (tptm) REVERT: C 321 GLU cc_start: 0.8586 (tp30) cc_final: 0.8262 (mm-30) REVERT: D 213 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8105 (tt) REVERT: D 289 LEU cc_start: 0.7317 (mm) cc_final: 0.6835 (tt) REVERT: D 321 GLU cc_start: 0.8559 (tp30) cc_final: 0.8254 (mm-30) REVERT: E 71 MET cc_start: 0.8921 (tpp) cc_final: 0.8647 (tpp) REVERT: E 138 TYR cc_start: 0.8942 (t80) cc_final: 0.8394 (t80) REVERT: F 71 MET cc_start: 0.8905 (tpp) cc_final: 0.8605 (tpp) REVERT: F 138 TYR cc_start: 0.8939 (t80) cc_final: 0.8312 (t80) REVERT: G 138 TYR cc_start: 0.8962 (t80) cc_final: 0.8403 (t80) REVERT: H 138 TYR cc_start: 0.8941 (t80) cc_final: 0.8324 (t80) outliers start: 53 outliers final: 39 residues processed: 303 average time/residue: 0.2438 time to fit residues: 113.7178 Evaluate side-chains 311 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 269 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 137 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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: 56.8903 > 50: distance: 51 - 54: 18.906 distance: 54 - 55: 19.920 distance: 55 - 56: 14.404 distance: 55 - 58: 10.915 distance: 56 - 57: 15.416 distance: 59 - 60: 13.294 distance: 60 - 61: 9.550 distance: 61 - 62: 5.621 distance: 61 - 63: 13.296 distance: 63 - 64: 6.693 distance: 64 - 65: 8.455 distance: 64 - 67: 9.401 distance: 65 - 66: 8.809 distance: 65 - 68: 6.693 distance: 68 - 69: 9.399 distance: 69 - 70: 20.004 distance: 70 - 71: 11.545 distance: 70 - 72: 6.642 distance: 72 - 73: 5.847 distance: 73 - 74: 17.170 distance: 73 - 76: 4.660 distance: 74 - 75: 15.776 distance: 74 - 81: 5.374 distance: 76 - 77: 16.102 distance: 77 - 78: 6.874 distance: 78 - 79: 6.651 distance: 78 - 80: 7.330 distance: 81 - 82: 8.467 distance: 82 - 83: 5.857 distance: 82 - 85: 4.603 distance: 83 - 84: 9.384 distance: 83 - 88: 15.555 distance: 85 - 86: 10.510 distance: 85 - 87: 9.041 distance: 88 - 89: 13.597 distance: 89 - 90: 16.582 distance: 89 - 92: 9.648 distance: 90 - 91: 40.543 distance: 90 - 96: 21.418 distance: 92 - 93: 9.169 distance: 93 - 94: 8.026 distance: 93 - 95: 5.020 distance: 97 - 98: 22.287 distance: 97 - 100: 6.389 distance: 98 - 99: 7.962 distance: 98 - 108: 9.737 distance: 100 - 101: 12.902 distance: 101 - 102: 9.174 distance: 101 - 103: 10.375 distance: 102 - 104: 16.804 distance: 103 - 105: 14.957 distance: 104 - 106: 9.977 distance: 105 - 106: 14.932 distance: 106 - 107: 4.418 distance: 108 - 109: 11.554 distance: 109 - 110: 11.784 distance: 109 - 112: 7.309 distance: 110 - 111: 3.385 distance: 110 - 113: 5.705 distance: 111 - 131: 11.907 distance: 113 - 114: 9.726 distance: 114 - 115: 9.535 distance: 114 - 117: 19.055 distance: 115 - 116: 8.980 distance: 115 - 118: 6.201 distance: 116 - 140: 8.285