Starting phenix.real_space_refine on Sun Mar 17 03:52:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/03_2024/6z7q_11112.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/03_2024/6z7q_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_11112/03_2024/6z7q_11112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/03_2024/6z7q_11112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/03_2024/6z7q_11112.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z7q_11112/03_2024/6z7q_11112.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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-dev-5265/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: 8.74, per 1000 atoms: 0.52 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: 6.41 Conformation dependent library (CDL) restraints added in 3.0 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: 1.49 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: 3.98 Time building geometry restraints manager: 7.00 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: 0.250 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: 2.280 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 43.120 Find NCS groups from input model: 0.800 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.690 ------------------------------------------------------------------------------- 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 % Allowed : 11.50 % Favored : 88.50 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 161 HIS 0.003 0.001 HIS B 86 PHE 0.010 0.001 PHE B 412 TYR 0.012 0.002 TYR D 55 ARG 0.002 0.000 ARG D 116 *********************** 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 : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8811 (t0) cc_final: 0.8556 (t0) REVERT: A 146 MET cc_start: 0.8487 (ttt) cc_final: 0.7449 (ttm) REVERT: B 117 TRP cc_start: 0.9447 (m100) cc_final: 0.9217 (m100) REVERT: B 146 MET cc_start: 0.8517 (ttt) cc_final: 0.8028 (ttm) REVERT: B 171 TYR cc_start: 0.9149 (m-10) cc_final: 0.8890 (m-80) REVERT: B 239 LEU cc_start: 0.8801 (tp) cc_final: 0.8418 (tp) REVERT: C 63 ASP cc_start: 0.8618 (t0) cc_final: 0.8266 (t0) REVERT: C 146 MET cc_start: 0.8373 (ttt) cc_final: 0.7577 (ttm) REVERT: C 239 LEU cc_start: 0.9006 (tp) cc_final: 0.8547 (tp) REVERT: D 63 ASP cc_start: 0.8710 (t0) cc_final: 0.8367 (t0) REVERT: D 64 THR cc_start: 0.9310 (p) cc_final: 0.9098 (t) REVERT: D 81 ASN cc_start: 0.8888 (t0) cc_final: 0.8667 (t0) REVERT: D 125 LEU cc_start: 0.9137 (tp) cc_final: 0.8930 (tp) REVERT: D 133 ASN cc_start: 0.9393 (p0) cc_final: 0.9097 (p0) REVERT: D 146 MET cc_start: 0.8493 (ttt) cc_final: 0.7757 (ttm) REVERT: D 239 LEU cc_start: 0.8752 (tp) cc_final: 0.8281 (tp) REVERT: D 484 ARG cc_start: 0.7930 (mtm180) cc_final: 0.7618 (mtm180) REVERT: E 116 ARG cc_start: 0.8839 (tpt170) cc_final: 0.8618 (tpt90) REVERT: E 133 ASN cc_start: 0.9425 (p0) cc_final: 0.9175 (p0) REVERT: E 146 MET cc_start: 0.8646 (ttt) cc_final: 0.8149 (ttm) REVERT: E 317 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7968 (mm-30) REVERT: E 455 GLU cc_start: 0.8634 (tp30) cc_final: 0.8331 (mm-30) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.2897 time to fit residues: 156.8896 Evaluate side-chains 233 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.835 ------------------------------------------------------------------------------- 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: 0.2980 chunk 86 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 186 optimal weight: 3.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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 416 GLN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17040 Z= 0.253 Angle : 0.756 7.135 23175 Z= 0.378 Chirality : 0.047 0.187 2595 Planarity : 0.005 0.043 3015 Dihedral : 6.847 28.385 2265 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 19.61 % Favored : 80.15 % Rotamer: Outliers : 3.42 % Allowed : 18.82 % Favored : 77.75 % 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: -5.69 (0.15), residues: 2030 helix: -3.53 (0.35), residues: 155 sheet: -4.66 (0.16), residues: 485 loop : -3.69 (0.15), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 215 HIS 0.007 0.001 HIS D 86 PHE 0.011 0.001 PHE D 344 TYR 0.021 0.001 TYR D 82 ARG 0.003 0.000 ARG B 66 *********************** 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 380 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 316 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.8172 (ttt) cc_final: 0.7362 (ttm) REVERT: A 201 ASP cc_start: 0.8202 (t0) cc_final: 0.7181 (t0) REVERT: A 223 MET cc_start: 0.8758 (mmp) cc_final: 0.8394 (mmm) REVERT: B 117 TRP cc_start: 0.9423 (m100) cc_final: 0.9182 (m100) REVERT: B 146 MET cc_start: 0.8207 (ttt) cc_final: 0.7439 (ttm) REVERT: B 168 GLU cc_start: 0.7949 (mp0) cc_final: 0.7643 (mp0) REVERT: B 201 ASP cc_start: 0.8492 (t0) cc_final: 0.7530 (t0) REVERT: B 289 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7654 (mt-10) REVERT: B 383 GLN cc_start: 0.7448 (tp40) cc_final: 0.6931 (tp40) REVERT: C 146 MET cc_start: 0.8202 (ttt) cc_final: 0.7335 (ttm) REVERT: C 201 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7728 (t70) REVERT: D 63 ASP cc_start: 0.8649 (t0) cc_final: 0.8341 (t0) REVERT: D 64 THR cc_start: 0.9357 (p) cc_final: 0.9114 (t) REVERT: D 81 ASN cc_start: 0.8570 (t0) cc_final: 0.8337 (t0) REVERT: D 133 ASN cc_start: 0.9284 (p0) cc_final: 0.8975 (p0) REVERT: D 146 MET cc_start: 0.8234 (ttt) cc_final: 0.7515 (ttm) REVERT: D 178 ASP cc_start: 0.8599 (t0) cc_final: 0.8303 (t0) REVERT: D 201 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7566 (t70) REVERT: D 284 ASP cc_start: 0.8379 (t0) cc_final: 0.7817 (t0) REVERT: D 484 ARG cc_start: 0.7646 (mtm180) cc_final: 0.7360 (mtm180) REVERT: E 57 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7441 (mt-10) REVERT: E 133 ASN cc_start: 0.9359 (p0) cc_final: 0.9111 (p0) REVERT: E 146 MET cc_start: 0.8385 (ttt) cc_final: 0.7671 (ttm) REVERT: E 201 ASP cc_start: 0.8361 (t0) cc_final: 0.7650 (t0) REVERT: E 223 MET cc_start: 0.8532 (mmp) cc_final: 0.8229 (mmm) REVERT: E 455 GLU cc_start: 0.8586 (tp30) cc_final: 0.8282 (mm-30) REVERT: E 460 LEU cc_start: 0.8781 (tt) cc_final: 0.8576 (tt) outliers start: 64 outliers final: 40 residues processed: 353 average time/residue: 0.2518 time to fit residues: 139.1859 Evaluate side-chains 294 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 252 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 330 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 0.0270 chunk 57 optimal weight: 10.0000 chunk 154 optimal weight: 0.0020 chunk 126 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 overall best weight: 2.8052 ------------------------------------------------------------------------------- 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 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN C 329 ASN ** 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 181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17040 Z= 0.266 Angle : 0.730 8.096 23175 Z= 0.364 Chirality : 0.048 0.210 2595 Planarity : 0.005 0.038 3015 Dihedral : 6.352 27.911 2265 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.08 % Favored : 78.92 % Rotamer: Outliers : 6.26 % Allowed : 18.34 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.42 (0.16), residues: 2030 helix: -3.40 (0.30), residues: 185 sheet: -4.39 (0.17), residues: 465 loop : -3.55 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 215 HIS 0.011 0.001 HIS B 492 PHE 0.009 0.001 PHE D 412 TYR 0.023 0.002 TYR C 82 ARG 0.004 0.000 ARG E 66 *********************** 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 407 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 290 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.8202 (ttt) cc_final: 0.7441 (ttm) REVERT: A 201 ASP cc_start: 0.8282 (t0) cc_final: 0.7289 (t0) REVERT: A 223 MET cc_start: 0.8838 (mmp) cc_final: 0.8387 (mmm) REVERT: A 289 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7764 (mt-10) REVERT: B 146 MET cc_start: 0.8217 (ttt) cc_final: 0.7406 (ttm) REVERT: B 171 TYR cc_start: 0.8841 (m-80) cc_final: 0.8591 (m-10) REVERT: B 181 ASN cc_start: 0.8519 (p0) cc_final: 0.8284 (t0) REVERT: B 201 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7662 (t70) REVERT: C 146 MET cc_start: 0.8183 (ttt) cc_final: 0.7580 (ttm) REVERT: C 201 ASP cc_start: 0.8251 (t0) cc_final: 0.7662 (t0) REVERT: C 251 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8670 (tt) REVERT: C 327 SER cc_start: 0.9155 (m) cc_final: 0.8774 (t) REVERT: C 380 ASP cc_start: 0.7930 (t0) cc_final: 0.7620 (t0) REVERT: D 81 ASN cc_start: 0.8541 (t0) cc_final: 0.8299 (t0) REVERT: D 133 ASN cc_start: 0.9312 (p0) cc_final: 0.8943 (p0) REVERT: D 146 MET cc_start: 0.8340 (ttt) cc_final: 0.7775 (ttm) REVERT: D 178 ASP cc_start: 0.8615 (t0) cc_final: 0.8311 (t0) REVERT: D 201 ASP cc_start: 0.8398 (t0) cc_final: 0.7697 (t0) REVERT: D 223 MET cc_start: 0.8786 (mmm) cc_final: 0.8530 (mmm) REVERT: D 284 ASP cc_start: 0.8352 (t0) cc_final: 0.7769 (t0) REVERT: D 484 ARG cc_start: 0.7727 (mtm180) cc_final: 0.7369 (mtm180) REVERT: E 133 ASN cc_start: 0.9382 (p0) cc_final: 0.9120 (p0) REVERT: E 146 MET cc_start: 0.8260 (ttt) cc_final: 0.7651 (ttm) REVERT: E 201 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7867 (t0) REVERT: E 383 GLN cc_start: 0.7442 (tp40) cc_final: 0.7161 (tp40) REVERT: E 460 LEU cc_start: 0.8773 (tt) cc_final: 0.8541 (tt) outliers start: 117 outliers final: 78 residues processed: 378 average time/residue: 0.2303 time to fit residues: 139.8684 Evaluate side-chains 338 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 257 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 461 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 198 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 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 E 83 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN E 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17040 Z= 0.284 Angle : 0.716 8.127 23175 Z= 0.357 Chirality : 0.046 0.168 2595 Planarity : 0.005 0.043 3015 Dihedral : 6.248 27.356 2265 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.13 % Favored : 81.87 % Rotamer: Outliers : 7.22 % Allowed : 20.64 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.17 (0.16), residues: 2030 helix: -3.19 (0.30), residues: 185 sheet: -4.18 (0.18), residues: 465 loop : -3.40 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 215 HIS 0.010 0.001 HIS B 492 PHE 0.011 0.001 PHE C 232 TYR 0.024 0.002 TYR C 82 ARG 0.003 0.000 ARG E 66 *********************** 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 415 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 280 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.8160 (ttt) cc_final: 0.7407 (ttm) REVERT: A 148 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7260 (mt-10) REVERT: A 201 ASP cc_start: 0.8274 (t0) cc_final: 0.7281 (t0) REVERT: A 223 MET cc_start: 0.8854 (mmp) cc_final: 0.8360 (mmm) REVERT: A 257 ILE cc_start: 0.9362 (mm) cc_final: 0.8963 (mt) REVERT: B 146 MET cc_start: 0.8176 (ttt) cc_final: 0.7405 (ttm) REVERT: B 168 GLU cc_start: 0.7877 (mp0) cc_final: 0.7673 (mp0) REVERT: B 171 TYR cc_start: 0.8889 (m-80) cc_final: 0.8605 (m-10) REVERT: B 181 ASN cc_start: 0.8397 (p0) cc_final: 0.8076 (t0) REVERT: B 201 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.7658 (t70) REVERT: B 223 MET cc_start: 0.8708 (mmm) cc_final: 0.8414 (mmm) REVERT: C 146 MET cc_start: 0.8178 (ttt) cc_final: 0.7586 (ttm) REVERT: C 201 ASP cc_start: 0.8347 (t0) cc_final: 0.7982 (t0) REVERT: C 251 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8698 (tt) REVERT: C 327 SER cc_start: 0.9149 (m) cc_final: 0.8770 (t) REVERT: C 380 ASP cc_start: 0.7943 (t0) cc_final: 0.7601 (t0) REVERT: D 81 ASN cc_start: 0.8535 (t0) cc_final: 0.8305 (t0) REVERT: D 133 ASN cc_start: 0.9303 (p0) cc_final: 0.9018 (p0) REVERT: D 146 MET cc_start: 0.8288 (ttt) cc_final: 0.7675 (ttm) REVERT: D 201 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7935 (t0) REVERT: D 223 MET cc_start: 0.8866 (mmm) cc_final: 0.8595 (mmm) REVERT: D 484 ARG cc_start: 0.7660 (mtm180) cc_final: 0.7262 (mtm180) REVERT: E 133 ASN cc_start: 0.9362 (p0) cc_final: 0.9105 (p0) REVERT: E 146 MET cc_start: 0.8248 (ttt) cc_final: 0.7654 (ttm) REVERT: E 201 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7728 (t0) REVERT: E 239 LEU cc_start: 0.8626 (tp) cc_final: 0.8320 (tp) REVERT: E 289 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7441 (mt-10) REVERT: E 460 LEU cc_start: 0.8756 (tt) cc_final: 0.8467 (tt) outliers start: 135 outliers final: 97 residues processed: 381 average time/residue: 0.2262 time to fit residues: 140.0703 Evaluate side-chains 356 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 255 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 495 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 147 optimal weight: 0.0070 chunk 81 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 177 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 overall best weight: 2.1004 ------------------------------------------------------------------------------- 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 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** C 333 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN D 333 ASN E 83 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN E 333 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17040 Z= 0.218 Angle : 0.696 7.944 23175 Z= 0.343 Chirality : 0.045 0.154 2595 Planarity : 0.005 0.041 3015 Dihedral : 6.012 26.194 2265 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.73 % Favored : 82.27 % Rotamer: Outliers : 6.63 % Allowed : 22.62 % Favored : 70.75 % 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: -4.94 (0.16), residues: 2030 helix: -2.90 (0.31), residues: 185 sheet: -3.99 (0.19), residues: 465 loop : -3.27 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 376 HIS 0.010 0.001 HIS B 492 PHE 0.008 0.001 PHE D 412 TYR 0.020 0.001 TYR E 62 ARG 0.004 0.000 ARG A 66 *********************** 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 432 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 308 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.8755 (mmp) cc_final: 0.8219 (mmm) REVERT: B 71 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7922 (t70) REVERT: B 146 MET cc_start: 0.8081 (ttt) cc_final: 0.7136 (ttm) REVERT: B 168 GLU cc_start: 0.7904 (mp0) cc_final: 0.7614 (mp0) REVERT: B 171 TYR cc_start: 0.8869 (m-80) cc_final: 0.8584 (m-10) REVERT: B 201 ASP cc_start: 0.8367 (t0) cc_final: 0.7768 (t70) REVERT: C 146 MET cc_start: 0.8077 (ttt) cc_final: 0.7520 (ttm) REVERT: C 201 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7998 (t0) REVERT: C 327 SER cc_start: 0.9122 (m) cc_final: 0.8799 (t) REVERT: D 133 ASN cc_start: 0.9206 (p0) cc_final: 0.8947 (p0) REVERT: D 146 MET cc_start: 0.8220 (ttt) cc_final: 0.7516 (ttm) REVERT: D 201 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8081 (t70) REVERT: D 227 TYR cc_start: 0.8982 (m-80) cc_final: 0.8531 (m-80) REVERT: D 284 ASP cc_start: 0.8357 (t0) cc_final: 0.7949 (t0) REVERT: D 484 ARG cc_start: 0.7646 (mtm180) cc_final: 0.7262 (mtm180) REVERT: E 133 ASN cc_start: 0.9286 (p0) cc_final: 0.9010 (p0) REVERT: E 146 MET cc_start: 0.8198 (ttt) cc_final: 0.7565 (ttm) REVERT: E 201 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7675 (t0) REVERT: E 223 MET cc_start: 0.8657 (mmm) cc_final: 0.8250 (mmm) REVERT: E 239 LEU cc_start: 0.8517 (tp) cc_final: 0.8161 (tp) REVERT: E 289 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7393 (mt-10) REVERT: E 460 LEU cc_start: 0.8747 (tt) cc_final: 0.8514 (tt) REVERT: E 471 SER cc_start: 0.9023 (t) cc_final: 0.8718 (m) outliers start: 124 outliers final: 98 residues processed: 395 average time/residue: 0.2339 time to fit residues: 148.2706 Evaluate side-chains 370 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 268 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 161 TRP Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 466 LEU 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: 2.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 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 329 ASN E 396 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 17040 Z= 0.445 Angle : 0.794 8.919 23175 Z= 0.398 Chirality : 0.048 0.162 2595 Planarity : 0.005 0.055 3015 Dihedral : 6.573 27.404 2265 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.34 % Favored : 79.66 % Rotamer: Outliers : 8.07 % Allowed : 22.51 % Favored : 69.41 % 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: -5.06 (0.16), residues: 2030 helix: -2.91 (0.30), residues: 185 sheet: -4.06 (0.19), residues: 465 loop : -3.37 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 343 HIS 0.011 0.002 HIS B 492 PHE 0.017 0.002 PHE D 232 TYR 0.025 0.002 TYR C 82 ARG 0.005 0.000 ARG A 66 *********************** 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 403 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 252 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7060 (mt-10) REVERT: A 223 MET cc_start: 0.8864 (mmp) cc_final: 0.8641 (mmm) REVERT: B 146 MET cc_start: 0.8264 (ttt) cc_final: 0.7591 (ttm) REVERT: B 171 TYR cc_start: 0.8985 (m-80) cc_final: 0.8779 (m-10) REVERT: B 178 ASP cc_start: 0.8698 (t0) cc_final: 0.8464 (t0) REVERT: B 201 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8233 (t70) REVERT: B 383 GLN cc_start: 0.7325 (tp40) cc_final: 0.6919 (tp40) REVERT: C 146 MET cc_start: 0.8239 (ttt) cc_final: 0.7612 (ttm) REVERT: C 201 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7836 (t0) REVERT: C 223 MET cc_start: 0.8747 (mmm) cc_final: 0.8245 (mmm) REVERT: C 327 SER cc_start: 0.9155 (m) cc_final: 0.8761 (t) REVERT: D 133 ASN cc_start: 0.9258 (p0) cc_final: 0.8991 (p0) REVERT: D 146 MET cc_start: 0.8296 (ttt) cc_final: 0.7868 (ttm) REVERT: D 178 ASP cc_start: 0.8735 (t0) cc_final: 0.8153 (t0) REVERT: D 201 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8147 (t0) REVERT: D 274 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8127 (mm) REVERT: D 455 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8263 (mm-30) REVERT: D 484 ARG cc_start: 0.7722 (mtm180) cc_final: 0.7318 (mtm180) REVERT: E 133 ASN cc_start: 0.9334 (p0) cc_final: 0.9072 (p0) REVERT: E 146 MET cc_start: 0.8285 (ttt) cc_final: 0.7414 (ttm) REVERT: E 178 ASP cc_start: 0.8651 (t0) cc_final: 0.8373 (t0) REVERT: E 201 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7695 (t0) REVERT: E 289 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7454 (mt-10) REVERT: E 460 LEU cc_start: 0.8871 (tt) cc_final: 0.8667 (tt) outliers start: 151 outliers final: 110 residues processed: 375 average time/residue: 0.2308 time to fit residues: 139.3312 Evaluate side-chains 349 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 234 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 161 TRP Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 495 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 113 optimal weight: 0.0060 chunk 144 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 chunk 123 optimal weight: 0.0470 chunk 120 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 128 ASN ** 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 396 ASN E 83 GLN E 95 GLN ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3195 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= 0.167 Angle : 0.698 9.958 23175 Z= 0.340 Chirality : 0.044 0.207 2595 Planarity : 0.005 0.044 3015 Dihedral : 5.890 25.177 2265 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.42 % Favored : 84.58 % Rotamer: Outliers : 6.36 % Allowed : 25.35 % Favored : 68.29 % 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: -4.70 (0.17), residues: 2030 helix: -2.28 (0.33), residues: 185 sheet: -3.88 (0.19), residues: 465 loop : -3.15 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 376 HIS 0.011 0.001 HIS B 492 PHE 0.013 0.001 PHE D 232 TYR 0.025 0.001 TYR E 82 ARG 0.002 0.000 ARG E 66 *********************** 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 427 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 308 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.7965 (OUTLIER) cc_final: 0.7544 (t0) REVERT: A 148 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6902 (mt-10) REVERT: A 223 MET cc_start: 0.8744 (mmp) cc_final: 0.8395 (mmm) REVERT: A 368 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7827 (t) REVERT: B 145 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8907 (mt) REVERT: B 146 MET cc_start: 0.7952 (ttt) cc_final: 0.7247 (ttm) REVERT: B 171 TYR cc_start: 0.8838 (m-80) cc_final: 0.8533 (m-10) REVERT: B 201 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8006 (t0) REVERT: C 61 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7518 (pt) REVERT: C 146 MET cc_start: 0.7945 (ttt) cc_final: 0.6806 (ttm) REVERT: C 201 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7917 (t70) REVERT: C 223 MET cc_start: 0.8647 (mmm) cc_final: 0.8280 (mmm) REVERT: C 227 TYR cc_start: 0.8925 (m-80) cc_final: 0.8539 (m-80) REVERT: C 327 SER cc_start: 0.9074 (m) cc_final: 0.8773 (t) REVERT: D 146 MET cc_start: 0.8125 (ttt) cc_final: 0.7438 (ttm) REVERT: D 223 MET cc_start: 0.8629 (mmm) cc_final: 0.8280 (mmm) REVERT: D 227 TYR cc_start: 0.8911 (m-80) cc_final: 0.8527 (m-80) REVERT: D 284 ASP cc_start: 0.8313 (t0) cc_final: 0.7924 (t0) REVERT: D 381 MET cc_start: 0.7152 (mtp) cc_final: 0.6872 (ttt) REVERT: D 484 ARG cc_start: 0.7598 (mtm180) cc_final: 0.7299 (mtm180) REVERT: E 133 ASN cc_start: 0.9252 (p0) cc_final: 0.8901 (p0) REVERT: E 146 MET cc_start: 0.8106 (ttt) cc_final: 0.7357 (ttt) REVERT: E 201 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7496 (t0) REVERT: E 223 MET cc_start: 0.8400 (mmm) cc_final: 0.8039 (mmm) REVERT: E 289 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7217 (mt-10) REVERT: E 327 SER cc_start: 0.8761 (m) cc_final: 0.8447 (t) REVERT: E 460 LEU cc_start: 0.8677 (tt) cc_final: 0.8423 (tt) REVERT: E 471 SER cc_start: 0.8919 (t) cc_final: 0.8652 (m) outliers start: 119 outliers final: 79 residues processed: 392 average time/residue: 0.2398 time to fit residues: 152.2263 Evaluate side-chains 363 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 277 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 481 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 118 optimal weight: 0.0040 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 125 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 128 ASN ** 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 ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN D 329 ASN D 396 ASN E 83 GLN E 96 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17040 Z= 0.187 Angle : 0.702 13.498 23175 Z= 0.342 Chirality : 0.045 0.218 2595 Planarity : 0.005 0.043 3015 Dihedral : 5.713 24.939 2265 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.12 % Favored : 84.88 % Rotamer: Outliers : 5.61 % Allowed : 26.68 % Favored : 67.70 % 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: -4.50 (0.17), residues: 2030 helix: -2.05 (0.34), residues: 185 sheet: -3.58 (0.20), residues: 485 loop : -3.06 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 343 HIS 0.011 0.001 HIS B 492 PHE 0.026 0.001 PHE B 232 TYR 0.030 0.002 TYR B 227 ARG 0.004 0.000 ARG E 126 *********************** 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 413 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 308 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.7567 (OUTLIER) cc_final: 0.7273 (m110) REVERT: A 148 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6916 (mt-10) REVERT: A 223 MET cc_start: 0.8677 (mmp) cc_final: 0.8292 (mmm) REVERT: A 327 SER cc_start: 0.8778 (m) cc_final: 0.8419 (t) REVERT: B 145 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8966 (mt) REVERT: B 146 MET cc_start: 0.8031 (ttt) cc_final: 0.7176 (ttt) REVERT: B 171 TYR cc_start: 0.8855 (m-80) cc_final: 0.8593 (m-10) REVERT: B 201 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8016 (t0) REVERT: B 223 MET cc_start: 0.8330 (mmm) cc_final: 0.7951 (mmm) REVERT: B 284 ASP cc_start: 0.8420 (t0) cc_final: 0.7925 (t0) REVERT: C 146 MET cc_start: 0.7956 (ttt) cc_final: 0.7207 (ttm) REVERT: C 327 SER cc_start: 0.9060 (m) cc_final: 0.8783 (t) REVERT: D 133 ASN cc_start: 0.9163 (p0) cc_final: 0.8883 (p0) REVERT: D 146 MET cc_start: 0.8286 (ttt) cc_final: 0.7932 (ttm) REVERT: D 201 ASP cc_start: 0.8136 (t70) cc_final: 0.7740 (t0) REVERT: D 223 MET cc_start: 0.8602 (mmm) cc_final: 0.8322 (mmm) REVERT: D 227 TYR cc_start: 0.8912 (m-80) cc_final: 0.8545 (m-80) REVERT: D 284 ASP cc_start: 0.8338 (t0) cc_final: 0.7955 (t0) REVERT: D 289 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6911 (mt-10) REVERT: D 484 ARG cc_start: 0.7600 (mtm180) cc_final: 0.7300 (mtm180) REVERT: E 133 ASN cc_start: 0.9288 (p0) cc_final: 0.8918 (p0) REVERT: E 146 MET cc_start: 0.8103 (ttt) cc_final: 0.7459 (ttt) REVERT: E 201 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7599 (t0) REVERT: E 223 MET cc_start: 0.8443 (mmm) cc_final: 0.8202 (mmm) REVERT: E 327 SER cc_start: 0.8813 (m) cc_final: 0.8480 (t) REVERT: E 460 LEU cc_start: 0.8721 (tt) cc_final: 0.8492 (tt) REVERT: E 471 SER cc_start: 0.8881 (t) cc_final: 0.8589 (m) outliers start: 105 outliers final: 86 residues processed: 375 average time/residue: 0.2319 time to fit residues: 139.5345 Evaluate side-chains 375 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 285 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 495 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 174 optimal weight: 0.8980 chunk 183 optimal weight: 0.2980 chunk 120 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN B 96 ASN ** 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 ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN D 396 ASN E 83 GLN E 396 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17040 Z= 0.172 Angle : 0.704 13.134 23175 Z= 0.341 Chirality : 0.045 0.317 2595 Planarity : 0.005 0.046 3015 Dihedral : 5.574 24.333 2265 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.65 % Favored : 86.35 % Rotamer: Outliers : 4.76 % Allowed : 27.65 % Favored : 67.59 % 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: -4.37 (0.17), residues: 2030 helix: -2.10 (0.34), residues: 185 sheet: -3.41 (0.21), residues: 485 loop : -2.98 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 376 HIS 0.011 0.001 HIS B 492 PHE 0.015 0.001 PHE B 232 TYR 0.029 0.001 TYR B 227 ARG 0.003 0.000 ARG B 126 *********************** 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 403 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 314 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6937 (mt-10) REVERT: A 171 TYR cc_start: 0.8757 (m-10) cc_final: 0.8510 (m-80) REVERT: A 223 MET cc_start: 0.8646 (mmp) cc_final: 0.8281 (mmm) REVERT: A 239 LEU cc_start: 0.8093 (tp) cc_final: 0.7819 (tt) REVERT: A 327 SER cc_start: 0.8752 (m) cc_final: 0.8414 (t) REVERT: A 471 SER cc_start: 0.8667 (t) cc_final: 0.8395 (m) REVERT: B 145 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8952 (mt) REVERT: B 146 MET cc_start: 0.7876 (ttt) cc_final: 0.6974 (ttt) REVERT: B 201 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7588 (t70) REVERT: B 223 MET cc_start: 0.8351 (mmm) cc_final: 0.8001 (mmm) REVERT: C 146 MET cc_start: 0.7990 (ttt) cc_final: 0.7389 (ttm) REVERT: C 201 ASP cc_start: 0.7990 (t0) cc_final: 0.7420 (t0) REVERT: C 223 MET cc_start: 0.8284 (mmm) cc_final: 0.7935 (mmm) REVERT: C 327 SER cc_start: 0.9049 (m) cc_final: 0.8711 (t) REVERT: D 146 MET cc_start: 0.8250 (ttt) cc_final: 0.7800 (ttm) REVERT: D 201 ASP cc_start: 0.8180 (t70) cc_final: 0.7790 (t0) REVERT: D 223 MET cc_start: 0.8595 (mmm) cc_final: 0.8344 (mmm) REVERT: D 227 TYR cc_start: 0.8867 (m-80) cc_final: 0.8633 (m-80) REVERT: D 484 ARG cc_start: 0.7554 (mtm180) cc_final: 0.7214 (mtm180) REVERT: E 146 MET cc_start: 0.8069 (ttt) cc_final: 0.7221 (ttt) REVERT: E 201 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7518 (t0) REVERT: E 327 SER cc_start: 0.8784 (m) cc_final: 0.8491 (t) REVERT: E 471 SER cc_start: 0.8742 (t) cc_final: 0.8511 (m) outliers start: 89 outliers final: 72 residues processed: 368 average time/residue: 0.2386 time to fit residues: 139.8607 Evaluate side-chains 359 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 284 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 481 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 396 ASN ** 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 194 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN ** 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: 0.7904 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17040 Z= 0.210 Angle : 0.723 12.370 23175 Z= 0.351 Chirality : 0.047 0.349 2595 Planarity : 0.005 0.043 3015 Dihedral : 5.579 25.331 2265 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.17 % Favored : 84.83 % Rotamer: Outliers : 4.65 % Allowed : 28.29 % Favored : 67.06 % 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: -4.22 (0.17), residues: 2030 helix: -1.61 (0.36), residues: 185 sheet: -3.20 (0.21), residues: 460 loop : -3.01 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 376 HIS 0.011 0.001 HIS B 492 PHE 0.022 0.001 PHE C 232 TYR 0.026 0.002 TYR B 227 ARG 0.004 0.000 ARG C 66 ********************** 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 374 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 287 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.7494 (OUTLIER) cc_final: 0.7131 (m110) REVERT: A 148 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6805 (mt-10) REVERT: A 223 MET cc_start: 0.8673 (mmp) cc_final: 0.8313 (mmm) REVERT: A 239 LEU cc_start: 0.8066 (tp) cc_final: 0.7836 (tt) REVERT: A 327 SER cc_start: 0.8726 (m) cc_final: 0.8382 (t) REVERT: B 71 ASP cc_start: 0.7304 (t70) cc_final: 0.6990 (t70) REVERT: B 145 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8994 (mt) REVERT: B 146 MET cc_start: 0.7958 (ttt) cc_final: 0.7078 (ttt) REVERT: B 201 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7836 (t70) REVERT: B 223 MET cc_start: 0.8419 (mmm) cc_final: 0.8060 (mmm) REVERT: B 322 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6607 (p0) REVERT: C 146 MET cc_start: 0.8052 (ttt) cc_final: 0.7431 (ttm) REVERT: C 201 ASP cc_start: 0.8046 (t0) cc_final: 0.7457 (t0) REVERT: C 223 MET cc_start: 0.8305 (mmm) cc_final: 0.7936 (mmm) REVERT: C 327 SER cc_start: 0.9042 (m) cc_final: 0.8682 (t) REVERT: D 133 ASN cc_start: 0.9211 (p0) cc_final: 0.8863 (p0) REVERT: D 146 MET cc_start: 0.8278 (ttt) cc_final: 0.7815 (ttm) REVERT: D 201 ASP cc_start: 0.8204 (t70) cc_final: 0.7814 (t0) REVERT: D 223 MET cc_start: 0.8659 (mmm) cc_final: 0.8397 (mmm) REVERT: D 227 TYR cc_start: 0.8925 (m-80) cc_final: 0.8609 (m-80) REVERT: D 484 ARG cc_start: 0.7589 (mtm180) cc_final: 0.7247 (mtm180) REVERT: E 71 ASP cc_start: 0.7901 (t70) cc_final: 0.7580 (t70) REVERT: E 146 MET cc_start: 0.8126 (ttt) cc_final: 0.7422 (ttt) REVERT: E 201 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7738 (t70) REVERT: E 471 SER cc_start: 0.8795 (t) cc_final: 0.8527 (m) outliers start: 87 outliers final: 78 residues processed: 343 average time/residue: 0.2480 time to fit residues: 134.4925 Evaluate side-chains 352 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 269 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 495 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 162 optimal weight: 0.0770 chunk 68 optimal weight: 0.0170 chunk 167 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 overall best weight: 1.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 396 ASN ** 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 83 GLN D 95 GLN D 329 ASN D 396 ASN E 83 GLN ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121090 restraints weight = 26818.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.124453 restraints weight = 14171.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126681 restraints weight = 8906.121| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17040 Z= 0.221 Angle : 0.731 14.103 23175 Z= 0.354 Chirality : 0.046 0.320 2595 Planarity : 0.005 0.044 3015 Dihedral : 5.594 26.350 2265 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.57 % Favored : 84.43 % Rotamer: Outliers : 4.92 % Allowed : 27.81 % Favored : 67.27 % 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: -4.15 (0.17), residues: 2030 helix: -1.39 (0.37), residues: 185 sheet: -3.11 (0.22), residues: 460 loop : -3.01 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 376 HIS 0.011 0.001 HIS B 492 PHE 0.018 0.001 PHE C 232 TYR 0.026 0.002 TYR B 227 ARG 0.004 0.000 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3371.36 seconds wall clock time: 61 minutes 55.37 seconds (3715.37 seconds total)