Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 03:58:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/04_2023/6z7q_11112.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/04_2023/6z7q_11112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/04_2023/6z7q_11112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/04_2023/6z7q_11112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/04_2023/6z7q_11112.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/04_2023/6z7q_11112.pdb" } resolution = 3.8 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= 0.003 sd= 0.975 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 10575 2.51 5 N 2880 2.21 5 O 3150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "B TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 158": "NH1" <-> "NH2" Residue "D ARG 212": "NH1" <-> "NH2" Residue "D TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D GLU 415": "OE1" <-> "OE2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "E TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 158": "NH1" <-> "NH2" Residue "E ARG 212": "NH1" <-> "NH2" Residue "E TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 258": "NH1" <-> "NH2" Residue "E GLU 265": "OE1" <-> "OE2" Residue "E GLU 415": "OE1" <-> "OE2" Residue "E ARG 469": "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: 16665 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3333 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3333 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3333 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3333 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3333 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 8.91, per 1000 atoms: 0.53 Number of scatterers: 16665 At special positions: 0 Unit cell: (121.797, 122.838, 111.387, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 3150 8.00 N 2880 7.00 C 10575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 2.2 seconds 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3950 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 35 sheets defined 7.7% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 172 through 190 removed outlier: 3.503A pdb=" N ILE A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 296 removed outlier: 3.502A pdb=" N GLU A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 292 " --> pdb=" O TYR A 288 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLN A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 190 removed outlier: 3.503A pdb=" N ILE B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 185 " --> pdb=" O ASN B 181 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 296 removed outlier: 3.502A pdb=" N GLU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 292 " --> pdb=" O TYR B 288 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLN B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 190 removed outlier: 3.504A pdb=" N ILE C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL C 185 " --> pdb=" O ASN C 181 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 296 removed outlier: 3.502A pdb=" N GLU C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 292 " --> pdb=" O TYR C 288 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN C 293 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS C 294 " --> pdb=" O ALA C 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 190 removed outlier: 3.504A pdb=" N ILE D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP D 178 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR D 188 " --> pdb=" O ILE D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 296 removed outlier: 3.502A pdb=" N GLU D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ALA D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 292 " --> pdb=" O TYR D 288 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLN D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 190 removed outlier: 3.503A pdb=" N ILE E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP E 178 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR E 188 " --> pdb=" O ILE E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 296 removed outlier: 3.501A pdb=" N GLU E 289 " --> pdb=" O VAL E 285 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA E 290 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE E 292 " --> pdb=" O TYR E 288 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLN E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS E 294 " --> pdb=" O ALA E 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 143 removed outlier: 3.654A pdb=" N PHE A 141 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 164 " --> pdb=" O PHE A 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 322 removed outlier: 4.355A pdb=" N ASP A 322 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 399 through 404 removed outlier: 4.396A pdb=" N TRP A 376 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL A 402 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL A 374 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.567A pdb=" N VAL A 453 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AA9, first strand: chain 'B' and resid 125 through 126 Processing sheet with id=AB1, first strand: chain 'B' and resid 140 through 143 removed outlier: 3.655A pdb=" N PHE B 141 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B 164 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 148 Processing sheet with id=AB3, first strand: chain 'B' and resid 321 through 322 removed outlier: 4.354A pdb=" N ASP B 322 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 326 " --> pdb=" O ASP B 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 399 through 404 removed outlier: 4.396A pdb=" N TRP B 376 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL B 402 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL B 374 " --> pdb=" O VAL B 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 410 through 413 removed outlier: 3.567A pdb=" N VAL B 453 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AB7, first strand: chain 'C' and resid 125 through 126 Processing sheet with id=AB8, first strand: chain 'C' and resid 140 through 143 removed outlier: 3.655A pdb=" N PHE C 141 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE C 164 " --> pdb=" O PHE C 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 146 through 148 Processing sheet with id=AC1, first strand: chain 'C' and resid 321 through 322 removed outlier: 4.355A pdb=" N ASP C 322 " --> pdb=" O ARG C 326 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG C 326 " --> pdb=" O ASP C 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 399 through 404 removed outlier: 4.396A pdb=" N TRP C 376 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL C 402 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL C 374 " --> pdb=" O VAL C 402 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 410 through 413 removed outlier: 3.568A pdb=" N VAL C 453 " --> pdb=" O LYS C 410 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 67 through 68 Processing sheet with id=AC5, first strand: chain 'D' and resid 125 through 126 Processing sheet with id=AC6, first strand: chain 'D' and resid 140 through 143 removed outlier: 3.655A pdb=" N PHE D 141 " --> pdb=" O PHE D 164 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE D 164 " --> pdb=" O PHE D 141 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 146 through 148 Processing sheet with id=AC8, first strand: chain 'D' and resid 321 through 322 removed outlier: 4.356A pdb=" N ASP D 322 " --> pdb=" O ARG D 326 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 399 through 404 removed outlier: 4.396A pdb=" N TRP D 376 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL D 402 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL D 374 " --> pdb=" O VAL D 402 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 410 through 413 removed outlier: 3.568A pdb=" N VAL D 453 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AD3, first strand: chain 'E' and resid 125 through 126 Processing sheet with id=AD4, first strand: chain 'E' and resid 140 through 143 removed outlier: 3.654A pdb=" N PHE E 141 " --> pdb=" O PHE E 164 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE E 164 " --> pdb=" O PHE E 141 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 146 through 148 Processing sheet with id=AD6, first strand: chain 'E' and resid 321 through 322 removed outlier: 4.355A pdb=" N ASP E 322 " --> pdb=" O ARG E 326 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 399 through 404 removed outlier: 4.396A pdb=" N TRP E 376 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL E 402 " --> pdb=" O VAL E 374 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL E 374 " --> pdb=" O VAL E 402 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 410 through 413 removed outlier: 3.567A pdb=" N VAL E 453 " --> pdb=" O LYS E 410 " (cutoff:3.500A) 180 hydrogen bonds defined for protein. 420 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: 3.73 Time building geometry restraints manager: 6.85 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: 5490 1.34 - 1.46: 3821 1.46 - 1.58: 7624 1.58 - 1.70: 0 1.70 - 1.81: 105 Bond restraints: 17040 Sorted by residual: bond pdb=" C PHE E 232 " pdb=" N HIS E 233 " ideal model delta sigma weight residual 1.333 1.294 0.039 2.74e-02 1.33e+03 2.00e+00 bond pdb=" C PHE D 232 " pdb=" N HIS D 233 " ideal model delta sigma weight residual 1.333 1.294 0.039 2.74e-02 1.33e+03 1.98e+00 bond pdb=" C PHE B 232 " pdb=" N HIS B 233 " ideal model delta sigma weight residual 1.333 1.294 0.038 2.74e-02 1.33e+03 1.97e+00 bond pdb=" C PHE A 232 " pdb=" N HIS A 233 " ideal model delta sigma weight residual 1.333 1.294 0.038 2.74e-02 1.33e+03 1.96e+00 bond pdb=" C PHE C 232 " pdb=" N HIS C 233 " ideal model delta sigma weight residual 1.333 1.295 0.038 2.74e-02 1.33e+03 1.91e+00 ... (remaining 17035 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.49: 606 106.49 - 113.36: 9356 113.36 - 120.22: 5750 120.22 - 127.09: 7239 127.09 - 133.96: 224 Bond angle restraints: 23175 Sorted by residual: angle pdb=" N LEU C 80 " pdb=" CA LEU C 80 " pdb=" C LEU C 80 " ideal model delta sigma weight residual 112.97 110.14 2.83 1.06e+00 8.90e-01 7.14e+00 angle pdb=" N LEU B 80 " pdb=" CA LEU B 80 " pdb=" C LEU B 80 " ideal model delta sigma weight residual 112.97 110.14 2.83 1.06e+00 8.90e-01 7.13e+00 angle pdb=" N LEU E 80 " pdb=" CA LEU E 80 " pdb=" C LEU E 80 " ideal model delta sigma weight residual 112.97 110.16 2.81 1.06e+00 8.90e-01 7.01e+00 angle pdb=" N LEU A 80 " pdb=" CA LEU A 80 " pdb=" C LEU A 80 " ideal model delta sigma weight residual 112.97 110.17 2.80 1.06e+00 8.90e-01 6.98e+00 angle pdb=" N LEU D 80 " pdb=" CA LEU D 80 " pdb=" C LEU D 80 " ideal model delta sigma weight residual 112.97 110.18 2.79 1.06e+00 8.90e-01 6.93e+00 ... (remaining 23170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 9116 17.00 - 34.00: 976 34.00 - 51.01: 128 51.01 - 68.01: 20 68.01 - 85.01: 35 Dihedral angle restraints: 10275 sinusoidal: 4180 harmonic: 6095 Sorted by residual: dihedral pdb=" CA PHE B 89 " pdb=" C PHE B 89 " pdb=" N GLN B 90 " pdb=" CA GLN B 90 " ideal model delta harmonic sigma weight residual 180.00 155.05 24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA PHE A 89 " pdb=" C PHE A 89 " pdb=" N GLN A 90 " pdb=" CA GLN A 90 " ideal model delta harmonic sigma weight residual 180.00 155.05 24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA PHE C 89 " pdb=" C PHE C 89 " pdb=" N GLN C 90 " pdb=" CA GLN C 90 " ideal model delta harmonic sigma weight residual 180.00 155.06 24.94 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 10272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1350 0.028 - 0.057: 740 0.057 - 0.085: 270 0.085 - 0.114: 195 0.114 - 0.142: 40 Chirality restraints: 2595 Sorted by residual: chirality pdb=" CA ILE A 257 " pdb=" N ILE A 257 " pdb=" C ILE A 257 " pdb=" CB ILE A 257 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE E 257 " pdb=" N ILE E 257 " pdb=" C ILE E 257 " pdb=" CB ILE E 257 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE C 257 " pdb=" N ILE C 257 " pdb=" C ILE C 257 " pdb=" CB ILE C 257 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 2592 not shown) Planarity restraints: 3015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 279 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO D 280 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 280 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 280 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 279 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO B 280 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 280 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 280 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 279 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.63e+00 pdb=" N PRO C 280 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 280 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 280 " 0.026 5.00e-02 4.00e+02 ... (remaining 3012 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1473 2.72 - 3.27: 18501 3.27 - 3.81: 25600 3.81 - 4.36: 32484 4.36 - 4.90: 52739 Nonbonded interactions: 130797 Sorted by model distance: nonbonded pdb=" NZ LYS C 205 " pdb=" O ILE C 441 " model vdw 2.176 2.520 nonbonded pdb=" NZ LYS B 205 " pdb=" O ILE B 441 " model vdw 2.176 2.520 nonbonded pdb=" NZ LYS D 205 " pdb=" O ILE D 441 " model vdw 2.176 2.520 nonbonded pdb=" NZ LYS A 205 " pdb=" O ILE A 441 " model vdw 2.177 2.520 nonbonded pdb=" NZ LYS E 205 " pdb=" O ILE E 441 " model vdw 2.177 2.520 ... (remaining 130792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.860 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 39.920 Find NCS groups from input model: 1.030 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.006 0.039 17040 Z= 0.378 Angle : 0.771 5.618 23175 Z= 0.425 Chirality : 0.046 0.142 2595 Planarity : 0.005 0.048 3015 Dihedral : 14.472 85.010 6325 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.74 % Allowed : 28.57 % Favored : 70.69 % 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: -6.49 (0.14), residues: 2030 helix: -5.04 (0.14), residues: 145 sheet: -5.28 (0.13), residues: 485 loop : -4.12 (0.14), residues: 1400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.2883 time to fit residues: 155.7484 Evaluate side-chains 227 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.961 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 186 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 GLN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 17040 Z= 0.365 Angle : 0.794 7.423 23175 Z= 0.401 Chirality : 0.048 0.206 2595 Planarity : 0.005 0.044 3015 Dihedral : 7.119 28.957 2265 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 20.89 % Favored : 78.87 % Rotamer Outliers : 4.17 % 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: -5.73 (0.15), residues: 2030 helix: -3.86 (0.31), residues: 160 sheet: -4.74 (0.16), residues: 485 loop : -3.66 (0.15), residues: 1385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 298 time to evaluate : 2.171 Fit side-chains revert: symmetry clash outliers start: 78 outliers final: 54 residues processed: 353 average time/residue: 0.2555 time to fit residues: 142.0259 Evaluate side-chains 291 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 237 time to evaluate : 2.308 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.1687 time to fit residues: 20.1244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN E 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 17040 Z= 0.239 Angle : 0.734 8.183 23175 Z= 0.365 Chirality : 0.048 0.208 2595 Planarity : 0.005 0.041 3015 Dihedral : 6.372 28.348 2265 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.08 % Favored : 78.92 % Rotamer Outliers : 3.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.36 (0.16), residues: 2030 helix: -3.57 (0.33), residues: 155 sheet: -4.39 (0.18), residues: 440 loop : -3.52 (0.15), residues: 1435 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 306 time to evaluate : 1.975 Fit side-chains revert: symmetry clash outliers start: 74 outliers final: 34 residues processed: 367 average time/residue: 0.2399 time to fit residues: 140.1588 Evaluate side-chains 289 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 255 time to evaluate : 2.071 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1519 time to fit residues: 12.4487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 8.9990 chunk 140 optimal weight: 0.6980 chunk 96 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 17040 Z= 0.379 Angle : 0.772 8.403 23175 Z= 0.387 Chirality : 0.048 0.178 2595 Planarity : 0.005 0.044 3015 Dihedral : 6.546 28.323 2265 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.79 % Favored : 79.21 % Rotamer Outliers : 4.17 % 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: -5.18 (0.16), residues: 2030 helix: -3.26 (0.34), residues: 155 sheet: -4.20 (0.18), residues: 465 loop : -3.41 (0.15), residues: 1410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 272 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 50 residues processed: 330 average time/residue: 0.2515 time to fit residues: 132.8676 Evaluate side-chains 292 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 242 time to evaluate : 2.060 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.1577 time to fit residues: 17.4961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 147 optimal weight: 0.0020 chunk 81 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 overall best weight: 1.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 ASN D 396 ASN E 83 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 17040 Z= 0.200 Angle : 0.723 8.655 23175 Z= 0.356 Chirality : 0.045 0.165 2595 Planarity : 0.005 0.043 3015 Dihedral : 6.094 26.703 2265 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.50 % Favored : 83.50 % Rotamer Outliers : 2.09 % 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: -4.89 (0.17), residues: 2030 helix: -2.81 (0.34), residues: 155 sheet: -3.97 (0.19), residues: 465 loop : -3.24 (0.15), residues: 1410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 306 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 21 residues processed: 335 average time/residue: 0.2412 time to fit residues: 129.8209 Evaluate side-chains 275 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 254 time to evaluate : 2.103 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1574 time to fit residues: 9.1686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 0.0980 chunk 48 optimal weight: 8.9990 chunk 198 optimal weight: 0.0770 chunk 164 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.8344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN C 333 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 17040 Z= 0.169 Angle : 0.714 12.500 23175 Z= 0.346 Chirality : 0.045 0.201 2595 Planarity : 0.005 0.044 3015 Dihedral : 5.801 25.299 2265 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.31 % Favored : 83.69 % Rotamer Outliers : 2.51 % 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: -4.63 (0.17), residues: 2030 helix: -2.49 (0.35), residues: 160 sheet: -3.73 (0.20), residues: 485 loop : -3.08 (0.16), residues: 1385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 295 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 25 residues processed: 326 average time/residue: 0.2538 time to fit residues: 132.2784 Evaluate side-chains 302 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 277 time to evaluate : 2.134 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1587 time to fit residues: 10.3422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 91 optimal weight: 0.0030 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 17040 Z= 0.251 Angle : 0.734 13.247 23175 Z= 0.358 Chirality : 0.045 0.186 2595 Planarity : 0.005 0.046 3015 Dihedral : 5.849 25.637 2265 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 18.03 % Favored : 81.92 % Rotamer Outliers : 2.09 % 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: -4.59 (0.17), residues: 2030 helix: -2.02 (0.35), residues: 180 sheet: -3.66 (0.20), residues: 485 loop : -3.13 (0.16), residues: 1365 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 283 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 23 residues processed: 310 average time/residue: 0.2563 time to fit residues: 129.1026 Evaluate side-chains 284 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 261 time to evaluate : 2.097 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1852 time to fit residues: 11.0774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 179 optimal weight: 0.0980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN A 396 ASN B 96 ASN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN D 396 ASN E 83 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 ASN ** E 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 17040 Z= 0.259 Angle : 0.752 13.737 23175 Z= 0.365 Chirality : 0.046 0.218 2595 Planarity : 0.005 0.043 3015 Dihedral : 5.870 25.631 2265 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 17.29 % Favored : 82.66 % Rotamer Outliers : 1.76 % 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: -4.56 (0.17), residues: 2030 helix: -1.83 (0.36), residues: 180 sheet: -3.67 (0.20), residues: 485 loop : -3.12 (0.16), residues: 1365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 259 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 279 average time/residue: 0.2484 time to fit residues: 111.4545 Evaluate side-chains 263 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 246 time to evaluate : 2.081 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1590 time to fit residues: 7.9192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 144 optimal weight: 0.0270 chunk 56 optimal weight: 0.0870 chunk 166 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 97 ASN A 396 ASN B 128 ASN B 492 HIS ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN E 83 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN E 396 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 17040 Z= 0.171 Angle : 0.733 13.239 23175 Z= 0.349 Chirality : 0.045 0.208 2595 Planarity : 0.005 0.043 3015 Dihedral : 5.566 24.083 2265 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.04 % Favored : 85.91 % 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: -4.32 (0.17), residues: 2030 helix: -1.87 (0.34), residues: 195 sheet: -3.44 (0.20), residues: 485 loop : -2.95 (0.16), residues: 1350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 318 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 326 average time/residue: 0.2594 time to fit residues: 134.2635 Evaluate side-chains 284 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 274 time to evaluate : 2.128 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1571 time to fit residues: 5.7716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN D 96 ASN ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN E 95 GLN E 396 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 17040 Z= 0.264 Angle : 0.774 14.312 23175 Z= 0.374 Chirality : 0.047 0.230 2595 Planarity : 0.005 0.044 3015 Dihedral : 5.717 24.568 2265 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 16.16 % Favored : 83.79 % 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: -4.27 (0.17), residues: 2030 helix: -1.37 (0.35), residues: 200 sheet: -3.41 (0.21), residues: 465 loop : -3.03 (0.16), residues: 1365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 269 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 278 average time/residue: 0.2664 time to fit residues: 118.0086 Evaluate side-chains 265 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 255 time to evaluate : 2.435 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1930 time to fit residues: 6.4437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN E 83 GLN E 396 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.128229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113567 restraints weight = 27815.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116847 restraints weight = 14263.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119014 restraints weight = 8824.690| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 17040 Z= 0.323 Angle : 0.803 14.197 23175 Z= 0.393 Chirality : 0.048 0.263 2595 Planarity : 0.005 0.045 3015 Dihedral : 6.007 26.030 2265 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 17.34 % Favored : 82.61 % Rotamer Outliers : 0.91 % 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: -4.35 (0.17), residues: 2030 helix: -1.34 (0.35), residues: 205 sheet: -3.42 (0.20), residues: 485 loop : -3.11 (0.16), residues: 1340 =============================================================================== Job complete usr+sys time: 3154.23 seconds wall clock time: 58 minutes 36.25 seconds (3516.25 seconds total)