Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 05:22:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgk_11209/04_2023/6zgk_11209.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgk_11209/04_2023/6zgk_11209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgk_11209/04_2023/6zgk_11209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgk_11209/04_2023/6zgk_11209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgk_11209/04_2023/6zgk_11209.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgk_11209/04_2023/6zgk_11209.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 20 5.16 5 C 7710 2.51 5 N 1875 2.21 5 O 2025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 293": "NH1" <-> "NH2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 293": "NH1" <-> "NH2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 293": "NH1" <-> "NH2" Residue "D PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 243": "OE1" <-> "OE2" Residue "E TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11630 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2326 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2326 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 127 Chain: "C" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2326 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 127 Chain: "D" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2326 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 127 Chain: "E" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2326 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 127 Time building chain proxies: 6.36, per 1000 atoms: 0.55 Number of scatterers: 11630 At special positions: 0 Unit cell: (92.66, 91.02, 115.62, 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 20 16.00 O 2025 8.00 N 1875 7.00 C 7710 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: 4.44 Conformation dependent library (CDL) restraints added in 1.9 seconds 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3010 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 34.2% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 201 through 214 removed outlier: 3.744A pdb=" N MET A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 209 " --> pdb=" O MET A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 243 removed outlier: 4.027A pdb=" N THR A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 282 removed outlier: 3.674A pdb=" N PHE A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.984A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 201 through 214 removed outlier: 3.744A pdb=" N MET B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 209 " --> pdb=" O MET B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 243 removed outlier: 4.027A pdb=" N THR B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 282 removed outlier: 3.673A pdb=" N PHE B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 315 removed outlier: 3.985A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 201 through 214 removed outlier: 3.744A pdb=" N MET C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 209 " --> pdb=" O MET C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 243 removed outlier: 4.027A pdb=" N THR C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 282 removed outlier: 3.673A pdb=" N PHE C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 315 removed outlier: 3.985A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 196 through 201 Processing helix chain 'D' and resid 201 through 214 removed outlier: 3.744A pdb=" N MET D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 209 " --> pdb=" O MET D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 243 removed outlier: 4.028A pdb=" N THR D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 282 removed outlier: 3.673A pdb=" N PHE D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 315 removed outlier: 3.985A pdb=" N ILE D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing helix chain 'E' and resid 196 through 201 Processing helix chain 'E' and resid 201 through 214 removed outlier: 3.743A pdb=" N MET E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 209 " --> pdb=" O MET E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 243 removed outlier: 4.028A pdb=" N THR E 226 " --> pdb=" O GLU E 222 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 282 removed outlier: 3.673A pdb=" N PHE E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 315 removed outlier: 3.984A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 95 removed outlier: 4.900A pdb=" N ALA A 87 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER A 107 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A 36 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU A 30 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS A 38 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU A 24 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER A 44 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE A 22 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N SER A 46 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR A 20 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LYS A 48 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL A 18 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU A 16 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA A 143 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A 18 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.685A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 86 through 95 removed outlier: 4.900A pdb=" N ALA B 87 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER B 107 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR B 36 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU B 30 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS B 38 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE B 42 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU B 24 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER B 44 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE B 22 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N SER B 46 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR B 20 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N LYS B 48 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL B 18 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA B 143 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.686A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 86 through 95 removed outlier: 4.899A pdb=" N ALA C 87 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER C 107 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR C 36 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU C 30 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS C 38 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE C 42 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU C 24 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER C 44 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE C 22 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N SER C 46 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR C 20 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N LYS C 48 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL C 18 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.685A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 86 through 95 removed outlier: 4.899A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR D 36 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU D 30 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS D 38 " --> pdb=" O TYR D 28 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE D 42 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU D 24 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER D 44 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE D 22 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N SER D 46 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR D 20 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LYS D 48 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL D 18 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA D 143 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL D 18 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.684A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 95 removed outlier: 4.899A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR E 36 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU E 30 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS E 38 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE E 42 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU E 24 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER E 44 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE E 22 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N SER E 46 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR E 20 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LYS E 48 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL E 18 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.685A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1620 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: 3.00 Time building geometry restraints manager: 4.83 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: 3570 1.34 - 1.46: 2515 1.46 - 1.58: 5820 1.58 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 11940 Sorted by residual: bond pdb=" N THR B 158 " pdb=" CA THR B 158 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.27e-02 6.20e+03 6.02e+00 bond pdb=" N THR D 158 " pdb=" CA THR D 158 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.27e-02 6.20e+03 5.83e+00 bond pdb=" N THR A 158 " pdb=" CA THR A 158 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.27e-02 6.20e+03 5.81e+00 bond pdb=" N THR E 158 " pdb=" CA THR E 158 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.27e-02 6.20e+03 5.70e+00 bond pdb=" N TRP A 160 " pdb=" CA TRP A 160 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.29e-02 6.01e+03 5.66e+00 ... (remaining 11935 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.98: 425 106.98 - 113.78: 6830 113.78 - 120.58: 4687 120.58 - 127.38: 4333 127.38 - 134.18: 120 Bond angle restraints: 16395 Sorted by residual: angle pdb=" CA LEU E 157 " pdb=" C LEU E 157 " pdb=" O LEU E 157 " ideal model delta sigma weight residual 122.44 118.20 4.24 1.32e+00 5.74e-01 1.03e+01 angle pdb=" CA LEU B 157 " pdb=" C LEU B 157 " pdb=" O LEU B 157 " ideal model delta sigma weight residual 122.44 118.21 4.23 1.32e+00 5.74e-01 1.03e+01 angle pdb=" CA LEU C 157 " pdb=" C LEU C 157 " pdb=" O LEU C 157 " ideal model delta sigma weight residual 122.44 118.21 4.23 1.32e+00 5.74e-01 1.03e+01 angle pdb=" CA LEU D 157 " pdb=" C LEU D 157 " pdb=" O LEU D 157 " ideal model delta sigma weight residual 122.44 118.23 4.21 1.32e+00 5.74e-01 1.02e+01 angle pdb=" CA LEU A 157 " pdb=" C LEU A 157 " pdb=" O LEU A 157 " ideal model delta sigma weight residual 122.44 118.25 4.19 1.32e+00 5.74e-01 1.01e+01 ... (remaining 16390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.88: 6011 10.88 - 21.77: 639 21.77 - 32.65: 245 32.65 - 43.53: 105 43.53 - 54.42: 20 Dihedral angle restraints: 7020 sinusoidal: 2415 harmonic: 4605 Sorted by residual: dihedral pdb=" CA CYS D 27 " pdb=" C CYS D 27 " pdb=" N TYR D 28 " pdb=" CA TYR D 28 " ideal model delta harmonic sigma weight residual -180.00 -154.38 -25.62 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA CYS B 27 " pdb=" C CYS B 27 " pdb=" N TYR B 28 " pdb=" CA TYR B 28 " ideal model delta harmonic sigma weight residual -180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA CYS A 27 " pdb=" C CYS A 27 " pdb=" N TYR A 28 " pdb=" CA TYR A 28 " ideal model delta harmonic sigma weight residual -180.00 -154.40 -25.60 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 7017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1162 0.034 - 0.068: 520 0.068 - 0.102: 237 0.102 - 0.135: 67 0.135 - 0.169: 14 Chirality restraints: 2000 Sorted by residual: chirality pdb=" CA THR B 158 " pdb=" N THR B 158 " pdb=" C THR B 158 " pdb=" CB THR B 158 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA THR C 158 " pdb=" N THR C 158 " pdb=" C THR C 158 " pdb=" CB THR C 158 " both_signs ideal model delta sigma weight residual False 2.53 2.69 -0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA THR E 158 " pdb=" N THR E 158 " pdb=" C THR E 158 " pdb=" CB THR E 158 " both_signs ideal model delta sigma weight residual False 2.53 2.69 -0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 1997 not shown) Planarity restraints: 2035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 73 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO E 74 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 73 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO D 74 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 74 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 74 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 73 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO A 74 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.027 5.00e-02 4.00e+02 ... (remaining 2032 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 173 2.67 - 3.23: 11401 3.23 - 3.78: 17409 3.78 - 4.34: 22585 4.34 - 4.90: 37951 Nonbonded interactions: 89519 Sorted by model distance: nonbonded pdb=" O VAL A 90 " pdb=" NH1 ARG B 133 " model vdw 2.111 2.520 nonbonded pdb=" O VAL B 90 " pdb=" NH1 ARG C 133 " model vdw 2.186 2.520 nonbonded pdb=" O VAL C 90 " pdb=" NH1 ARG D 133 " model vdw 2.198 2.520 nonbonded pdb=" O VAL D 90 " pdb=" NH1 ARG E 133 " model vdw 2.204 2.520 nonbonded pdb=" NH1 ARG A 133 " pdb=" O VAL E 90 " model vdw 2.212 2.520 ... (remaining 89514 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: 1.370 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: 4.550 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 30.750 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5282 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 0.049 11940 Z= 0.398 Angle : 0.681 5.483 16395 Z= 0.389 Chirality : 0.047 0.169 2000 Planarity : 0.005 0.049 2035 Dihedral : 12.304 54.417 4010 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1515 helix: 0.81 (0.22), residues: 480 sheet: -0.76 (0.27), residues: 420 loop : -0.95 (0.26), residues: 615 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.217 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2711 time to fit residues: 80.9620 Evaluate side-chains 151 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.331 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 11940 Z= 0.359 Angle : 0.808 9.603 16395 Z= 0.413 Chirality : 0.053 0.370 2000 Planarity : 0.007 0.095 2035 Dihedral : 5.111 26.679 1660 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer Outliers : 4.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1515 helix: 1.07 (0.22), residues: 510 sheet: -0.79 (0.27), residues: 390 loop : -1.40 (0.25), residues: 615 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 189 time to evaluate : 1.226 Fit side-chains outliers start: 49 outliers final: 18 residues processed: 223 average time/residue: 0.2756 time to fit residues: 83.9542 Evaluate side-chains 143 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1049 time to fit residues: 5.4015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 0.0060 chunk 92 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 chunk 147 optimal weight: 7.9990 chunk 121 optimal weight: 0.2980 chunk 135 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS C 127 HIS D 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 11940 Z= 0.275 Angle : 0.596 5.821 16395 Z= 0.312 Chirality : 0.045 0.149 2000 Planarity : 0.005 0.048 2035 Dihedral : 4.539 31.089 1660 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1515 helix: 1.46 (0.22), residues: 510 sheet: -0.41 (0.28), residues: 390 loop : -1.50 (0.25), residues: 615 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 1.213 Fit side-chains outliers start: 28 outliers final: 20 residues processed: 173 average time/residue: 0.2641 time to fit residues: 63.4838 Evaluate side-chains 147 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.331 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1079 time to fit residues: 5.8888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 0.1980 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS C 127 HIS D 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.7791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 11940 Z= 0.343 Angle : 0.666 10.478 16395 Z= 0.340 Chirality : 0.046 0.141 2000 Planarity : 0.006 0.063 2035 Dihedral : 4.527 28.940 1660 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1515 helix: 1.39 (0.22), residues: 510 sheet: -0.44 (0.28), residues: 390 loop : -1.75 (0.24), residues: 615 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 1.208 Fit side-chains outliers start: 34 outliers final: 18 residues processed: 193 average time/residue: 0.2225 time to fit residues: 62.7218 Evaluate side-chains 154 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1081 time to fit residues: 5.2752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 130 optimal weight: 0.0670 chunk 36 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS B 127 HIS D 235 HIS E 127 HIS E 235 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.8035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11940 Z= 0.176 Angle : 0.551 8.803 16395 Z= 0.281 Chirality : 0.042 0.148 2000 Planarity : 0.005 0.047 2035 Dihedral : 4.384 31.415 1660 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.22), residues: 1515 helix: 1.76 (0.21), residues: 510 sheet: -0.79 (0.26), residues: 430 loop : -1.62 (0.25), residues: 575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 1.297 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 152 average time/residue: 0.2298 time to fit residues: 51.3109 Evaluate side-chains 137 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1031 time to fit residues: 3.9804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 139 optimal weight: 0.4980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.8714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 11940 Z= 0.288 Angle : 0.593 8.012 16395 Z= 0.307 Chirality : 0.044 0.173 2000 Planarity : 0.006 0.117 2035 Dihedral : 4.349 28.879 1660 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.22), residues: 1515 helix: 1.58 (0.21), residues: 510 sheet: -0.69 (0.26), residues: 420 loop : -1.74 (0.25), residues: 585 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.301 Fit side-chains outliers start: 28 outliers final: 18 residues processed: 147 average time/residue: 0.2220 time to fit residues: 48.3499 Evaluate side-chains 133 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1096 time to fit residues: 5.4871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.9055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 11940 Z= 0.271 Angle : 0.565 7.474 16395 Z= 0.293 Chirality : 0.043 0.127 2000 Planarity : 0.005 0.060 2035 Dihedral : 4.355 31.572 1660 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.22), residues: 1515 helix: 1.72 (0.22), residues: 490 sheet: -0.60 (0.26), residues: 420 loop : -1.64 (0.25), residues: 605 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.356 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 130 average time/residue: 0.2452 time to fit residues: 46.1691 Evaluate side-chains 124 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1079 time to fit residues: 3.4432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 113 optimal weight: 0.0470 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.9245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11940 Z= 0.196 Angle : 0.542 6.815 16395 Z= 0.276 Chirality : 0.042 0.131 2000 Planarity : 0.005 0.056 2035 Dihedral : 4.206 28.888 1660 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1515 helix: 1.89 (0.22), residues: 485 sheet: -0.51 (0.26), residues: 420 loop : -1.66 (0.25), residues: 610 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.314 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 110 average time/residue: 0.2491 time to fit residues: 39.7332 Evaluate side-chains 103 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1245 time to fit residues: 2.2184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 121 optimal weight: 0.0370 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.9387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11940 Z= 0.173 Angle : 0.524 6.390 16395 Z= 0.267 Chirality : 0.042 0.135 2000 Planarity : 0.005 0.067 2035 Dihedral : 4.173 31.241 1660 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.22), residues: 1515 helix: 2.05 (0.22), residues: 485 sheet: -0.41 (0.26), residues: 420 loop : -1.62 (0.24), residues: 610 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 1.242 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 106 average time/residue: 0.2463 time to fit residues: 38.0504 Evaluate side-chains 102 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.441 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1068 time to fit residues: 2.3005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 149 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 0.0470 chunk 94 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.9776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 11940 Z= 0.353 Angle : 0.614 6.155 16395 Z= 0.323 Chirality : 0.044 0.135 2000 Planarity : 0.005 0.048 2035 Dihedral : 4.355 29.607 1660 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.22), residues: 1515 helix: 1.57 (0.22), residues: 485 sheet: -0.33 (0.28), residues: 395 loop : -1.59 (0.24), residues: 635 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 1.348 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 147 average time/residue: 0.2465 time to fit residues: 53.7221 Evaluate side-chains 137 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.435 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1318 time to fit residues: 2.1955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 49 optimal weight: 0.0770 chunk 122 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.193776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.148575 restraints weight = 12919.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.137727 restraints weight = 12791.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140134 restraints weight = 10793.104| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.9881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11940 Z= 0.182 Angle : 0.541 6.291 16395 Z= 0.277 Chirality : 0.042 0.137 2000 Planarity : 0.004 0.041 2035 Dihedral : 4.300 30.780 1660 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.22), residues: 1515 helix: 1.92 (0.22), residues: 485 sheet: -0.38 (0.27), residues: 420 loop : -1.62 (0.24), residues: 610 =============================================================================== Job complete usr+sys time: 2026.53 seconds wall clock time: 37 minutes 50.44 seconds (2270.44 seconds total)