Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 13:37:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnm_7537/04_2023/6cnm_7537_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnm_7537/04_2023/6cnm_7537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnm_7537/04_2023/6cnm_7537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnm_7537/04_2023/6cnm_7537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnm_7537/04_2023/6cnm_7537_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnm_7537/04_2023/6cnm_7537_updated.pdb" } resolution = 3.4 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 5 8.98 5 P 4 5.49 5 S 80 5.16 5 C 8096 2.51 5 N 2212 2.21 5 O 2144 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 103": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 317": "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 103": "NH1" <-> "NH2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B ARG 228": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 317": "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 103": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 317": "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 103": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "D ARG 228": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 317": "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" Residue "E TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12541 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2694 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2694 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2694 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 99 Chain: "D" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2694 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 99 Chain: "E" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 363 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 65} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "F" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 363 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 65} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "G" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 363 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 65} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "H" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 363 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 65} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 82 Unusual residues: {' K': 5, 'LMT': 2, 'POV': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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 Time building chain proxies: 7.19, per 1000 atoms: 0.57 Number of scatterers: 12541 At special positions: 0 Unit cell: (132.87, 132.87, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 5 19.00 S 80 16.00 P 4 15.00 O 2144 8.00 N 2212 7.00 C 8096 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: 5.47 Conformation dependent library (CDL) restraints added in 2.0 seconds 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 4 sheets defined 76.0% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 12 through 50 removed outlier: 3.649A pdb=" N LEU A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 91 removed outlier: 4.015A pdb=" N LYS A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 78 " --> pdb=" O CYS A 74 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 82 " --> pdb=" O ALA A 78 " (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 103 through 116 removed outlier: 3.807A pdb=" N VAL A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 170 removed outlier: 3.660A pdb=" N MET A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU A 160 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TYR A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.880A pdb=" N ILE A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 204 through 226 removed outlier: 3.947A pdb=" N THR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 removed outlier: 4.750A 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 289 removed outlier: 3.712A pdb=" N ILE A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 330 removed outlier: 3.517A pdb=" N GLN A 306 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 368 removed outlier: 3.733A pdb=" N LYS A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 385 removed outlier: 3.588A pdb=" N TYR A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 383 " --> pdb=" O TYR A 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 50 removed outlier: 3.648A pdb=" N LEU B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 21 " --> pdb=" O ARG B 17 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 91 removed outlier: 4.015A pdb=" N LYS B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 78 " --> pdb=" O CYS B 74 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 82 " --> pdb=" O ALA B 78 " (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 103 through 116 removed outlier: 3.789A pdb=" N VAL B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 170 removed outlier: 3.660A pdb=" N MET B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU B 160 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TYR B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL B 163 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.888A pdb=" N ILE B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 204 through 226 removed outlier: 3.946A pdb=" N THR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 248 removed outlier: 4.749A 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 289 removed outlier: 3.711A pdb=" N ILE B 265 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 271 " --> pdb=" O CYS B 267 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 330 removed outlier: 3.516A pdb=" N GLN B 306 " --> pdb=" O MET B 302 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 315 " --> pdb=" O MET B 311 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 368 removed outlier: 3.774A pdb=" N LYS B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 385 removed outlier: 3.590A pdb=" N TYR B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 383 " --> pdb=" O TYR B 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 50 removed outlier: 3.648A pdb=" N LEU C 19 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 91 removed outlier: 4.015A pdb=" N LYS C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 78 " --> pdb=" O CYS C 74 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 82 " --> pdb=" O ALA C 78 " (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 103 through 116 removed outlier: 3.788A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 170 removed outlier: 3.660A pdb=" N MET C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU C 160 " --> pdb=" O MET C 156 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TYR C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 177 through 186 removed outlier: 3.886A pdb=" N ILE C 182 " --> pdb=" O SER C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 204 through 226 removed outlier: 3.946A pdb=" N THR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 removed outlier: 4.750A 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 289 removed outlier: 3.711A pdb=" N ILE C 265 " --> pdb=" O MET C 261 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY C 271 " --> pdb=" O CYS C 267 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 330 removed outlier: 3.515A pdb=" N GLN C 306 " --> pdb=" O MET C 302 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 315 " --> pdb=" O MET C 311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 368 removed outlier: 3.741A pdb=" N LYS C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 361 " --> pdb=" O LYS C 357 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 362 " --> pdb=" O HIS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 385 removed outlier: 3.588A pdb=" N TYR C 379 " --> pdb=" O HIS C 375 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 383 " --> pdb=" O TYR C 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 50 removed outlier: 3.657A pdb=" N LEU D 19 " --> pdb=" O ARG D 15 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D 21 " --> pdb=" O ARG D 17 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 39 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 91 removed outlier: 4.019A pdb=" N LYS D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 78 " --> pdb=" O CYS D 74 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS D 82 " --> pdb=" O ALA D 78 " (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 103 through 116 removed outlier: 3.835A pdb=" N VAL D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 170 removed outlier: 3.657A pdb=" N MET D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU D 160 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TYR D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Proline residue: D 164 - end of helix Processing helix chain 'D' and resid 177 through 186 removed outlier: 3.880A pdb=" N ILE D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 204 through 226 removed outlier: 3.947A pdb=" N THR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 4.767A 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 289 removed outlier: 3.711A pdb=" N ILE D 265 " --> pdb=" O MET D 261 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY D 271 " --> pdb=" O CYS D 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET D 273 " --> pdb=" O CYS D 269 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 330 removed outlier: 3.518A pdb=" N GLN D 306 " --> pdb=" O MET D 302 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS D 309 " --> pdb=" O ILE D 305 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 315 " --> pdb=" O MET D 311 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU D 321 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 368 removed outlier: 3.733A pdb=" N LYS D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 361 " --> pdb=" O LYS D 357 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D 362 " --> pdb=" O HIS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 385 removed outlier: 3.581A pdb=" N TYR D 379 " --> pdb=" O HIS D 375 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN D 383 " --> pdb=" O TYR D 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 91 removed outlier: 3.555A pdb=" N VAL E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 111 removed outlier: 4.163A pdb=" N MET E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 128 Processing helix chain 'E' and resid 138 through 145 removed outlier: 3.780A pdb=" N GLN E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 91 removed outlier: 3.555A pdb=" N VAL F 91 " --> pdb=" O GLU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 111 removed outlier: 4.164A pdb=" N MET F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 128 Processing helix chain 'F' and resid 138 through 145 removed outlier: 3.780A pdb=" N GLN F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 91 removed outlier: 3.555A pdb=" N VAL G 91 " --> pdb=" O GLU G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 111 removed outlier: 4.164A pdb=" N MET G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 128 Processing helix chain 'G' and resid 138 through 145 removed outlier: 3.779A pdb=" N GLN G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 91 removed outlier: 3.555A pdb=" N VAL H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 111 removed outlier: 4.163A pdb=" N MET H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 128 Processing helix chain 'H' and resid 138 through 145 removed outlier: 3.780A pdb=" N GLN H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 99 through 101 Processing sheet with id= B, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= C, first strand: chain 'G' and resid 99 through 101 Processing sheet with id= D, first strand: chain 'H' and resid 99 through 101 796 hydrogen bonds defined for protein. 2388 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 5.84 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: 3947 1.34 - 1.46: 2547 1.46 - 1.58: 6138 1.58 - 1.70: 8 1.70 - 1.82: 128 Bond restraints: 12768 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 4.07e+01 bond pdb=" C31 POV D1101 " pdb=" O31 POV D1101 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C31 POV A1101 " pdb=" O31 POV A1101 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.04e+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 4.01e+01 bond pdb=" C21 POV A1101 " pdb=" O21 POV A1101 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.87e+01 ... (remaining 12763 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.92: 321 106.92 - 114.15: 7636 114.15 - 121.38: 6687 121.38 - 128.61: 2536 128.61 - 135.83: 148 Bond angle restraints: 17328 Sorted by residual: angle pdb=" C LEU B 249 " pdb=" N THR B 250 " pdb=" CA THR B 250 " ideal model delta sigma weight residual 122.07 128.25 -6.18 1.43e+00 4.89e-01 1.87e+01 angle pdb=" C LEU D 249 " pdb=" N THR D 250 " pdb=" CA THR D 250 " ideal model delta sigma weight residual 122.07 128.25 -6.18 1.43e+00 4.89e-01 1.87e+01 angle pdb=" C LEU A 249 " pdb=" N THR A 250 " pdb=" CA THR A 250 " ideal model delta sigma weight residual 122.07 128.24 -6.17 1.43e+00 4.89e-01 1.86e+01 angle pdb=" C LEU C 249 " pdb=" N THR C 250 " pdb=" CA THR C 250 " ideal model delta sigma weight residual 122.07 128.23 -6.16 1.43e+00 4.89e-01 1.86e+01 angle pdb=" CA PRO A 164 " pdb=" N PRO A 164 " pdb=" CD PRO A 164 " ideal model delta sigma weight residual 112.00 107.28 4.72 1.40e+00 5.10e-01 1.14e+01 ... (remaining 17323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 7090 16.57 - 33.13: 214 33.13 - 49.70: 68 49.70 - 66.27: 12 66.27 - 82.84: 8 Dihedral angle restraints: 7392 sinusoidal: 2516 harmonic: 4876 Sorted by residual: dihedral pdb=" CA LEU D 19 " pdb=" C LEU D 19 " pdb=" N GLU D 20 " pdb=" CA GLU D 20 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEU A 19 " pdb=" C LEU A 19 " pdb=" N GLU A 20 " pdb=" CA GLU A 20 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LEU B 19 " pdb=" C LEU B 19 " pdb=" N GLU B 20 " pdb=" CA GLU B 20 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 7389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1455 0.052 - 0.103: 526 0.103 - 0.155: 81 0.155 - 0.206: 18 0.206 - 0.258: 20 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CB VAL A 163 " pdb=" CA VAL A 163 " pdb=" CG1 VAL A 163 " pdb=" CG2 VAL A 163 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL B 163 " pdb=" CA VAL B 163 " pdb=" CG1 VAL B 163 " pdb=" CG2 VAL B 163 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL D 163 " pdb=" CA VAL D 163 " pdb=" CG1 VAL D 163 " pdb=" CG2 VAL D 163 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 2097 not shown) Planarity restraints: 2108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 157 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C LEU C 157 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU C 157 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU C 158 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 157 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C LEU D 157 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU D 157 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU D 158 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 157 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C LEU B 157 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU B 157 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 158 " -0.011 2.00e-02 2.50e+03 ... (remaining 2105 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.89: 4468 2.89 - 3.45: 13847 3.45 - 4.02: 21202 4.02 - 4.58: 31526 4.58 - 5.14: 42558 Nonbonded interactions: 113601 Sorted by model distance: nonbonded pdb=" OH TYR A 253 " pdb=" OG1 THR B 247 " model vdw 2.331 2.440 nonbonded pdb=" OH TYR B 253 " pdb=" OG1 THR C 247 " model vdw 2.332 2.440 nonbonded pdb=" OH TYR C 253 " pdb=" OG1 THR D 247 " model vdw 2.332 2.440 nonbonded pdb=" OG1 THR A 247 " pdb=" OH TYR D 253 " model vdw 2.332 2.440 nonbonded pdb=" O LEU B 356 " pdb=" NZ LYS B 360 " model vdw 2.429 2.520 ... (remaining 113596 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 10 through 386) selection = (chain 'B' and resid 10 through 386) selection = (chain 'C' and resid 10 through 386) selection = (chain 'D' and resid 10 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 7.050 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 35.260 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.080 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.010 0.128 12768 Z= 0.640 Angle : 1.114 10.833 17328 Z= 0.572 Chirality : 0.057 0.258 2100 Planarity : 0.006 0.042 2108 Dihedral : 10.533 82.836 4232 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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 (0.15), residues: 1676 helix: -2.82 (0.10), residues: 1292 sheet: None (None), residues: 0 loop : -1.92 (0.30), residues: 384 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2756 time to fit residues: 101.6433 Evaluate side-chains 171 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.517 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 0.1980 chunk 66 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 364 GLN B 320 GLN B 340 HIS B 364 GLN C 320 GLN C 340 HIS C 364 GLN D 340 HIS D 364 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 12768 Z= 0.144 Angle : 0.510 7.769 17328 Z= 0.258 Chirality : 0.037 0.154 2100 Planarity : 0.003 0.028 2108 Dihedral : 8.417 67.533 1912 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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: -1.54 (0.19), residues: 1676 helix: -0.79 (0.13), residues: 1296 sheet: None (None), residues: 0 loop : -1.23 (0.34), residues: 380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2134 time to fit residues: 73.0170 Evaluate side-chains 178 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.569 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 chunk 147 optimal weight: 0.2980 chunk 50 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 12768 Z= 0.265 Angle : 0.550 7.468 17328 Z= 0.277 Chirality : 0.040 0.134 2100 Planarity : 0.003 0.032 2108 Dihedral : 7.962 58.929 1912 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 1.88 % 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: -0.43 (0.21), residues: 1676 helix: 0.03 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -0.98 (0.36), residues: 368 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 19 residues processed: 182 average time/residue: 0.1688 time to fit residues: 49.9960 Evaluate side-chains 170 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 1.421 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1068 time to fit residues: 5.7254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.8215 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 12768 Z= 0.157 Angle : 0.466 7.365 17328 Z= 0.236 Chirality : 0.037 0.132 2100 Planarity : 0.002 0.023 2108 Dihedral : 7.200 57.641 1912 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.38 % 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: 0.35 (0.21), residues: 1676 helix: 0.64 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.90 (0.36), residues: 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 176 average time/residue: 0.1872 time to fit residues: 52.5640 Evaluate side-chains 173 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 1.551 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1110 time to fit residues: 2.4107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 135 optimal weight: 0.2980 chunk 109 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 12768 Z= 0.152 Angle : 0.468 7.371 17328 Z= 0.234 Chirality : 0.037 0.140 2100 Planarity : 0.002 0.022 2108 Dihedral : 6.890 59.591 1912 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 0.56 % 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: 0.90 (0.21), residues: 1676 helix: 1.06 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.82 (0.35), residues: 376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 164 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 169 average time/residue: 0.1894 time to fit residues: 51.4005 Evaluate side-chains 164 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1081 time to fit residues: 2.6614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 chunk 158 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 GLN ** C 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 12768 Z= 0.168 Angle : 0.470 7.344 17328 Z= 0.236 Chirality : 0.037 0.143 2100 Planarity : 0.002 0.022 2108 Dihedral : 6.655 59.111 1912 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.75 % 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: 1.17 (0.21), residues: 1676 helix: 1.27 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.78 (0.36), residues: 376 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 173 average time/residue: 0.1872 time to fit residues: 51.6510 Evaluate side-chains 166 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 159 time to evaluate : 1.628 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1122 time to fit residues: 3.5632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 0.2980 chunk 115 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 158 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 12768 Z= 0.128 Angle : 0.438 7.348 17328 Z= 0.224 Chirality : 0.036 0.153 2100 Planarity : 0.002 0.021 2108 Dihedral : 6.167 59.946 1912 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.28 % 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: 1.57 (0.21), residues: 1676 helix: 1.56 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.70 (0.35), residues: 376 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 174 average time/residue: 0.1970 time to fit residues: 54.3401 Evaluate side-chains 164 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 1.378 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1126 time to fit residues: 2.5494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 chunk 100 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 GLN D 320 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12768 Z= 0.212 Angle : 0.485 7.455 17328 Z= 0.248 Chirality : 0.038 0.121 2100 Planarity : 0.003 0.027 2108 Dihedral : 6.459 59.973 1912 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.21), residues: 1676 helix: 1.61 (0.14), residues: 1304 sheet: None (None), residues: 0 loop : -0.59 (0.37), residues: 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1878 time to fit residues: 47.6969 Evaluate side-chains 153 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 30.0000 chunk 151 optimal weight: 20.0000 chunk 138 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 115 optimal weight: 0.0870 chunk 45 optimal weight: 0.6980 chunk 133 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN B 320 GLN C 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 12768 Z= 0.158 Angle : 0.460 7.419 17328 Z= 0.235 Chirality : 0.036 0.117 2100 Planarity : 0.002 0.021 2108 Dihedral : 6.200 59.970 1912 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.21), residues: 1676 helix: 1.82 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.53 (0.36), residues: 380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1897 time to fit residues: 47.8943 Evaluate side-chains 154 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 0.9980 chunk 155 optimal weight: 30.0000 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 163 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 100 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN D 320 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 12768 Z= 0.142 Angle : 0.446 7.615 17328 Z= 0.229 Chirality : 0.036 0.118 2100 Planarity : 0.002 0.021 2108 Dihedral : 6.078 59.919 1912 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.19 % 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: 2.13 (0.21), residues: 1676 helix: 1.96 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 0.2069 time to fit residues: 53.4894 Evaluate side-chains 151 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.454 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.134942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.095041 restraints weight = 21083.070| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.99 r_work: 0.2960 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 12768 Z= 0.146 Angle : 0.447 7.604 17328 Z= 0.228 Chirality : 0.036 0.156 2100 Planarity : 0.002 0.021 2108 Dihedral : 6.056 59.855 1912 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.21), residues: 1676 helix: 2.03 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.41 (0.36), residues: 380 =============================================================================== Job complete usr+sys time: 2377.10 seconds wall clock time: 44 minutes 4.49 seconds (2644.49 seconds total)