Starting phenix.real_space_refine on Fri Mar 15 12:09:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgk_11209/03_2024/6zgk_11209.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgk_11209/03_2024/6zgk_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_11209/03_2024/6zgk_11209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgk_11209/03_2024/6zgk_11209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgk_11209/03_2024/6zgk_11209.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgk_11209/03_2024/6zgk_11209.pdb" } resolution = 3.6 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= 0.000 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-dev-5265/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: 6.55, per 1000 atoms: 0.56 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: 4.75 Conformation dependent library (CDL) restraints added in 2.4 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: 1.29 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: 3.07 Time building geometry restraints manager: 5.13 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: 0.010 Normalize map: mean=0, sd=1: 0.850 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: 4.160 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 33.950 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.960 ------------------------------------------------------------------------------- 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 % Allowed : 0.43 % Favored : 99.57 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 160 HIS 0.002 0.001 HIS C 235 PHE 0.014 0.002 PHE C 121 TYR 0.012 0.002 TYR D 102 ARG 0.009 0.001 ARG E 287 *********************** 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 : 1.431 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2619 time to fit residues: 78.1642 Evaluate side-chains 151 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 % Allowed : 10.99 % Favored : 84.81 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP C 160 HIS 0.010 0.003 HIS C 235 PHE 0.018 0.002 PHE A 207 TYR 0.029 0.003 TYR C 23 ARG 0.006 0.001 ARG A 105 *********************** 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 : 1.275 Fit side-chains REVERT: A 23 TYR cc_start: 0.6487 (t80) cc_final: 0.6273 (t80) REVERT: A 115 ASP cc_start: 0.7349 (p0) cc_final: 0.6854 (p0) REVERT: B 115 ASP cc_start: 0.7088 (p0) cc_final: 0.6514 (p0) REVERT: B 309 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8111 (mm) REVERT: C 115 ASP cc_start: 0.7369 (p0) cc_final: 0.6964 (p0) REVERT: D 115 ASP cc_start: 0.7024 (p0) cc_final: 0.6549 (p0) REVERT: E 115 ASP cc_start: 0.7200 (p0) cc_final: 0.6657 (p0) REVERT: E 185 ASP cc_start: 0.6286 (OUTLIER) cc_final: 0.5828 (t0) outliers start: 49 outliers final: 18 residues processed: 223 average time/residue: 0.2723 time to fit residues: 82.7653 Evaluate side-chains 150 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 185 ASP 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: 5.9990 chunk 113 optimal weight: 0.0270 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: 1.9990 chunk 46 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 overall best weight: 1.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS C 127 HIS D 127 HIS E 127 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.6198 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= 0.253 Angle : 0.576 5.426 16395 Z= 0.301 Chirality : 0.045 0.152 2000 Planarity : 0.005 0.047 2035 Dihedral : 4.506 31.095 1660 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.83 % Allowed : 16.74 % Favored : 80.43 % 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: -0.28 (0.22), residues: 1515 helix: 1.49 (0.22), residues: 510 sheet: -0.40 (0.28), residues: 390 loop : -1.46 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 160 HIS 0.004 0.001 HIS E 277 PHE 0.016 0.002 PHE E 216 TYR 0.012 0.001 TYR A 102 ARG 0.009 0.001 ARG B 77 *********************** 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 191 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 1.240 Fit side-chains REVERT: A 23 TYR cc_start: 0.6723 (t80) cc_final: 0.6441 (t80) REVERT: A 75 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6669 (mm-30) REVERT: A 77 ARG cc_start: 0.7745 (mtt-85) cc_final: 0.7440 (mtt-85) REVERT: A 115 ASP cc_start: 0.7451 (p0) cc_final: 0.7169 (p0) REVERT: A 185 ASP cc_start: 0.7067 (t0) cc_final: 0.6651 (t70) REVERT: A 187 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.7080 (pt0) REVERT: A 214 THR cc_start: 0.9138 (p) cc_final: 0.8902 (t) REVERT: A 217 TRP cc_start: 0.7474 (m-10) cc_final: 0.7213 (m-10) REVERT: B 75 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6701 (mm-30) REVERT: B 77 ARG cc_start: 0.7451 (mtt-85) cc_final: 0.7115 (mtt-85) REVERT: B 115 ASP cc_start: 0.7336 (p0) cc_final: 0.7041 (p0) REVERT: B 130 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6851 (mp) REVERT: B 214 THR cc_start: 0.9095 (p) cc_final: 0.8880 (t) REVERT: B 309 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8242 (mp) REVERT: C 105 ARG cc_start: 0.7521 (ptm-80) cc_final: 0.7217 (ptm-80) REVERT: C 185 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.6297 (t0) REVERT: D 115 ASP cc_start: 0.7254 (p0) cc_final: 0.6935 (p0) REVERT: D 185 ASP cc_start: 0.6710 (OUTLIER) cc_final: 0.6284 (t70) REVERT: E 77 ARG cc_start: 0.7826 (mtt-85) cc_final: 0.7496 (mtt-85) REVERT: E 115 ASP cc_start: 0.7383 (p0) cc_final: 0.7017 (p0) outliers start: 33 outliers final: 20 residues processed: 178 average time/residue: 0.2405 time to fit residues: 61.0007 Evaluate side-chains 158 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 284 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 30.0000 chunk 102 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 129 optimal weight: 0.0370 chunk 39 optimal weight: 10.0000 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.7898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11940 Z= 0.366 Angle : 0.678 9.774 16395 Z= 0.349 Chirality : 0.046 0.141 2000 Planarity : 0.006 0.069 2035 Dihedral : 4.527 28.965 1660 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.24 % Allowed : 18.03 % Favored : 76.74 % 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: 1.30 (0.22), residues: 510 sheet: -0.50 (0.28), residues: 395 loop : -1.76 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 160 HIS 0.007 0.002 HIS D 235 PHE 0.016 0.002 PHE C 116 TYR 0.016 0.002 TYR A 102 ARG 0.010 0.001 ARG D 192 *********************** 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 222 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 161 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 126 LEU cc_start: 0.8431 (mt) cc_final: 0.8066 (mt) REVERT: A 185 ASP cc_start: 0.7332 (t0) cc_final: 0.7057 (t0) REVERT: A 214 THR cc_start: 0.9246 (p) cc_final: 0.9041 (t) REVERT: B 77 ARG cc_start: 0.7883 (mtt-85) cc_final: 0.7651 (mtt-85) REVERT: B 130 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7549 (mp) REVERT: B 309 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8365 (mp) REVERT: C 75 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6760 (mm-30) REVERT: D 126 LEU cc_start: 0.8485 (mt) cc_final: 0.8242 (mt) REVERT: D 130 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7589 (mp) REVERT: D 185 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6998 (t70) REVERT: E 185 ASP cc_start: 0.7012 (t70) cc_final: 0.6771 (t0) outliers start: 61 outliers final: 39 residues processed: 207 average time/residue: 0.2318 time to fit residues: 69.0049 Evaluate side-chains 170 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 127 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 292 THR 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: 9.9990 chunk 59 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 130 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 C 235 HIS D 235 HIS E 127 HIS E 235 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.8147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11940 Z= 0.182 Angle : 0.563 8.733 16395 Z= 0.288 Chirality : 0.043 0.141 2000 Planarity : 0.005 0.047 2035 Dihedral : 4.405 31.410 1660 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.43 % Allowed : 20.17 % Favored : 76.39 % 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: -0.26 (0.22), residues: 1515 helix: 1.72 (0.21), residues: 510 sheet: -0.20 (0.28), residues: 395 loop : -1.84 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 160 HIS 0.002 0.001 HIS B 277 PHE 0.014 0.001 PHE E 42 TYR 0.018 0.001 TYR A 23 ARG 0.007 0.001 ARG C 105 *********************** 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 175 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 135 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: B 77 ARG cc_start: 0.7812 (mtt-85) cc_final: 0.7565 (mtt-85) REVERT: B 130 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7545 (mp) REVERT: B 187 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7271 (mt0) REVERT: B 309 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8250 (mt) REVERT: D 130 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7471 (mp) REVERT: E 75 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6978 (mm-30) outliers start: 40 outliers final: 25 residues processed: 167 average time/residue: 0.1946 time to fit residues: 49.3757 Evaluate side-chains 150 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 281 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.0770 chunk 130 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 0.0670 chunk 145 optimal weight: 0.5980 chunk 120 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.8318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11940 Z= 0.147 Angle : 0.525 7.633 16395 Z= 0.264 Chirality : 0.042 0.137 2000 Planarity : 0.005 0.043 2035 Dihedral : 4.148 27.986 1660 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.61 % Allowed : 20.60 % Favored : 75.79 % 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: -0.16 (0.22), residues: 1515 helix: 2.02 (0.21), residues: 510 sheet: -0.61 (0.26), residues: 430 loop : -1.66 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 213 HIS 0.003 0.001 HIS A 127 PHE 0.011 0.001 PHE B 265 TYR 0.018 0.001 TYR A 23 ARG 0.009 0.001 ARG D 77 *********************** 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 161 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 119 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: B 309 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8213 (mt) REVERT: D 75 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6070 (mm-30) outliers start: 42 outliers final: 31 residues processed: 150 average time/residue: 0.2007 time to fit residues: 46.1840 Evaluate side-chains 141 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 281 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN B 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.8596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11940 Z= 0.224 Angle : 0.546 7.018 16395 Z= 0.281 Chirality : 0.043 0.133 2000 Planarity : 0.004 0.043 2035 Dihedral : 4.175 30.968 1660 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.86 % Allowed : 20.34 % Favored : 75.79 % 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: -0.19 (0.22), residues: 1515 helix: 2.01 (0.22), residues: 490 sheet: -0.49 (0.26), residues: 420 loop : -1.66 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 213 HIS 0.003 0.001 HIS A 277 PHE 0.010 0.001 PHE A 265 TYR 0.019 0.001 TYR A 23 ARG 0.004 0.000 ARG B 105 *********************** 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 152 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 107 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7578 (p90) REVERT: B 185 ASP cc_start: 0.7452 (t0) cc_final: 0.7159 (t0) REVERT: B 187 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7427 (mt0) REVERT: B 309 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8243 (mt) outliers start: 45 outliers final: 29 residues processed: 142 average time/residue: 0.2516 time to fit residues: 53.5451 Evaluate side-chains 133 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 281 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.1455 > 50: distance: 11 - 14: 5.495 distance: 14 - 15: 3.528 distance: 15 - 16: 13.063 distance: 15 - 18: 26.502 distance: 16 - 17: 14.677 distance: 16 - 19: 8.992 distance: 19 - 20: 15.391 distance: 19 - 25: 22.720 distance: 20 - 21: 20.720 distance: 20 - 23: 11.466 distance: 21 - 22: 21.425 distance: 21 - 26: 7.363 distance: 23 - 24: 23.038 distance: 24 - 25: 30.898 distance: 26 - 27: 9.604 distance: 27 - 28: 16.629 distance: 27 - 30: 19.716 distance: 28 - 29: 36.130 distance: 28 - 34: 32.559 distance: 30 - 31: 31.485 distance: 31 - 32: 28.557 distance: 31 - 33: 35.712 distance: 34 - 35: 14.765 distance: 35 - 36: 19.964 distance: 35 - 38: 12.601 distance: 36 - 37: 3.398 distance: 36 - 41: 17.040 distance: 38 - 39: 24.525 distance: 38 - 40: 24.375 distance: 41 - 42: 26.790 distance: 42 - 43: 28.116 distance: 42 - 45: 14.589 distance: 43 - 44: 31.104 distance: 43 - 48: 40.718 distance: 45 - 46: 26.761 distance: 45 - 47: 26.120 distance: 48 - 49: 17.420 distance: 49 - 50: 26.398 distance: 49 - 52: 30.200 distance: 50 - 51: 32.880 distance: 50 - 53: 13.924 distance: 53 - 54: 20.049 distance: 54 - 55: 7.997 distance: 54 - 57: 22.059 distance: 55 - 56: 35.109 distance: 55 - 60: 32.474 distance: 57 - 58: 24.523 distance: 57 - 59: 11.471 distance: 60 - 61: 21.702 distance: 61 - 62: 38.088 distance: 62 - 63: 28.057 distance: 62 - 64: 33.816 distance: 64 - 65: 12.475 distance: 65 - 66: 15.249 distance: 65 - 68: 22.529 distance: 66 - 67: 32.534 distance: 66 - 72: 39.046 distance: 68 - 69: 28.630 distance: 68 - 70: 12.377 distance: 69 - 71: 25.122 distance: 72 - 73: 16.590 distance: 73 - 74: 16.477 distance: 73 - 76: 32.479 distance: 74 - 75: 27.702 distance: 74 - 84: 18.792 distance: 76 - 77: 9.717 distance: 77 - 78: 7.154 distance: 77 - 79: 23.447 distance: 78 - 80: 16.043 distance: 79 - 81: 18.113 distance: 80 - 82: 13.872 distance: 81 - 82: 8.548 distance: 82 - 83: 16.586