Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 19:41:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnn_7538/04_2023/6cnn_7538_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnn_7538/04_2023/6cnn_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_7538/04_2023/6cnn_7538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnn_7538/04_2023/6cnn_7538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnn_7538/04_2023/6cnn_7538_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnn_7538/04_2023/6cnn_7538_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 32 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: 32 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: 32 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: 32 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: 9.04, 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: 6.38 Conformation dependent library (CDL) restraints added in 2.6 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: 1.25 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: 4.03 Time building geometry restraints manager: 6.84 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 - 13.08: 8762 13.08 - 26.16: 478 26.16 - 39.25: 144 39.25 - 52.33: 36 52.33 - 65.41: 12 Dihedral angle restraints: 9432 sinusoidal: 3624 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 9429 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.370 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 42.460 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.560 ------------------------------------------------------------------------------- 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 : 10.143 65.411 5672 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 % 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 *********************** 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 : 1.951 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.3123 time to fit residues: 214.8107 Evaluate side-chains 266 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.859 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4501 ------------------------------------------------------------------------------- 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: 5.9990 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: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS B 297 HIS C 297 HIS C 320 GLN D 297 HIS D 320 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 16004 Z= 0.219 Angle : 0.554 6.808 21624 Z= 0.286 Chirality : 0.038 0.188 2544 Planarity : 0.003 0.025 2668 Dihedral : 7.373 58.104 2280 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.60 (0.17), residues: 2000 helix: -0.89 (0.12), residues: 1536 sheet: None (None), residues: 0 loop : -1.02 (0.28), residues: 464 *********************** 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 382 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 342 time to evaluate : 1.915 Fit side-chains outliers start: 40 outliers final: 23 residues processed: 361 average time/residue: 0.2705 time to fit residues: 147.1057 Evaluate side-chains 320 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 297 time to evaluate : 2.054 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1440 time to fit residues: 8.6454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 50 optimal weight: 0.0770 chunk 181 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 145 optimal weight: 0.5980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 16004 Z= 0.146 Angle : 0.485 7.649 21624 Z= 0.244 Chirality : 0.035 0.135 2544 Planarity : 0.003 0.026 2668 Dihedral : 6.305 54.714 2280 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 0.86 % 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: 0.10 (0.19), residues: 2000 helix: 0.32 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.36 (0.30), residues: 488 *********************** 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 330 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 317 time to evaluate : 1.918 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 321 average time/residue: 0.2746 time to fit residues: 130.0255 Evaluate side-chains 284 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 275 time to evaluate : 1.936 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1375 time to fit residues: 4.9110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 122 optimal weight: 0.0050 chunk 182 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 16004 Z= 0.148 Angle : 0.469 6.942 21624 Z= 0.237 Chirality : 0.035 0.141 2544 Planarity : 0.003 0.034 2668 Dihedral : 5.915 57.379 2280 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 1.65 % 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: 0.92 (0.19), residues: 2000 helix: 0.93 (0.14), residues: 1512 sheet: None (None), residues: 0 loop : -0.12 (0.31), residues: 488 *********************** 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 323 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 298 time to evaluate : 2.023 Fit side-chains outliers start: 25 outliers final: 15 residues processed: 312 average time/residue: 0.2758 time to fit residues: 132.8305 Evaluate side-chains 293 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 278 time to evaluate : 1.904 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1674 time to fit residues: 7.1599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 2 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 107 GLN D 80 HIS D 107 GLN E 42 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 ASN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 16004 Z= 0.220 Angle : 0.515 8.133 21624 Z= 0.264 Chirality : 0.038 0.155 2544 Planarity : 0.003 0.041 2668 Dihedral : 6.047 55.386 2280 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.72 % 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: 1.26 (0.19), residues: 2000 helix: 1.17 (0.14), residues: 1516 sheet: None (None), residues: 0 loop : 0.04 (0.31), residues: 484 *********************** 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 307 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 281 time to evaluate : 1.971 Fit side-chains outliers start: 26 outliers final: 10 residues processed: 291 average time/residue: 0.2527 time to fit residues: 112.1629 Evaluate side-chains 279 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 269 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1358 time to fit residues: 5.0964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 42 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 ASN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 16004 Z= 0.338 Angle : 0.621 7.868 21624 Z= 0.313 Chirality : 0.041 0.141 2544 Planarity : 0.004 0.044 2668 Dihedral : 6.623 55.808 2280 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 1.91 % 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: 1.10 (0.19), residues: 2000 helix: 1.00 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : 0.15 (0.32), residues: 476 *********************** 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 293 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 264 time to evaluate : 1.780 Fit side-chains outliers start: 29 outliers final: 22 residues processed: 269 average time/residue: 0.2511 time to fit residues: 104.6092 Evaluate side-chains 280 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 258 time to evaluate : 1.926 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1549 time to fit residues: 8.7670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 192 optimal weight: 0.0670 chunk 120 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 GLN C 364 GLN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 16004 Z= 0.196 Angle : 0.531 10.504 21624 Z= 0.259 Chirality : 0.036 0.117 2544 Planarity : 0.003 0.035 2668 Dihedral : 6.073 51.417 2280 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.53 % 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: 1.55 (0.20), residues: 2000 helix: 1.37 (0.14), residues: 1512 sheet: None (None), residues: 0 loop : 0.20 (0.32), residues: 488 *********************** 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 284 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 276 time to evaluate : 1.807 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 279 average time/residue: 0.2516 time to fit residues: 108.9803 Evaluate side-chains 261 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 258 time to evaluate : 1.807 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1434 time to fit residues: 3.2505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 122 optimal weight: 0.0170 chunk 131 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN D 349 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3845 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= 0.158 Angle : 0.521 10.062 21624 Z= 0.257 Chirality : 0.035 0.133 2544 Planarity : 0.003 0.051 2668 Dihedral : 5.724 48.697 2280 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 1.78 % 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: 1.94 (0.20), residues: 2000 helix: 1.63 (0.14), residues: 1520 sheet: None (None), residues: 0 loop : 0.38 (0.32), residues: 480 *********************** 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 308 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 281 time to evaluate : 2.012 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 287 average time/residue: 0.2616 time to fit residues: 114.8294 Evaluate side-chains 284 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 272 time to evaluate : 2.025 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1684 time to fit residues: 6.2750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 30.0000 chunk 168 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 162 optimal weight: 0.3980 chunk 169 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 299 HIS D 299 HIS ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 16004 Z= 0.203 Angle : 0.531 8.999 21624 Z= 0.266 Chirality : 0.036 0.120 2544 Planarity : 0.003 0.043 2668 Dihedral : 5.928 54.793 2280 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 0.13 % 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: 2.03 (0.19), residues: 2000 helix: 1.71 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.34 (0.32), residues: 480 *********************** 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 290 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 288 time to evaluate : 2.087 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 288 average time/residue: 0.2504 time to fit residues: 111.5869 Evaluate side-chains 281 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 279 time to evaluate : 1.956 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1401 time to fit residues: 3.0405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS C 364 GLN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 16004 Z= 0.197 Angle : 0.539 10.348 21624 Z= 0.268 Chirality : 0.036 0.121 2544 Planarity : 0.003 0.045 2668 Dihedral : 5.980 57.860 2280 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.33 % 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: 2.21 (0.19), residues: 2000 helix: 1.83 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.47 (0.32), residues: 480 ********************** REFINEMENT MACRO_CYCLE 10 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 294 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 289 time to evaluate : 2.087 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 289 average time/residue: 0.2497 time to fit residues: 111.9514 Evaluate side-chains 280 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 275 time to evaluate : 2.096 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3551 time to fit residues: 5.4148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 364 GLN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117484 restraints weight = 22776.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.116831 restraints weight = 15455.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117181 restraints weight = 13330.769| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 16004 Z= 0.264 Angle : 0.578 10.110 21624 Z= 0.287 Chirality : 0.038 0.123 2544 Planarity : 0.004 0.044 2668 Dihedral : 6.360 58.158 2280 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.40 % 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: 2.05 (0.19), residues: 2000 helix: 1.69 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : 0.44 (0.32), residues: 476 =============================================================================== Job complete usr+sys time: 2984.78 seconds wall clock time: 55 minutes 5.78 seconds (3305.78 seconds total)