Starting phenix.real_space_refine on Fri Mar 15 00:07:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgd_11202/03_2024/6zgd_11202.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgd_11202/03_2024/6zgd_11202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgd_11202/03_2024/6zgd_11202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgd_11202/03_2024/6zgd_11202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgd_11202/03_2024/6zgd_11202.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgd_11202/03_2024/6zgd_11202.pdb" } resolution = 4.1 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= 0.003 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 6745 2.51 5 N 1685 2.21 5 O 1725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 189": "NH1" <-> "NH2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 181": "OE1" <-> "OE2" Residue "E TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 189": "NH1" <-> "NH2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10175 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2035 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 17, 'TRANS': 270} Chain breaks: 3 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 166 Chain: "B" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2035 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 17, 'TRANS': 270} Chain breaks: 3 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 166 Chain: "C" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2035 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 17, 'TRANS': 270} Chain breaks: 3 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 166 Chain: "D" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2035 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 17, 'TRANS': 270} Chain breaks: 3 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 166 Chain: "E" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2035 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 17, 'TRANS': 270} Chain breaks: 3 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 166 Time building chain proxies: 5.75, per 1000 atoms: 0.57 Number of scatterers: 10175 At special positions: 0 Unit cell: (89.38, 87.74, 112.34, 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 1725 8.00 N 1685 7.00 C 6745 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: 4.09 Conformation dependent library (CDL) restraints added in 2.0 seconds 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2840 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 38.5% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 201 through 214 removed outlier: 3.714A pdb=" N MET A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 244 removed outlier: 4.300A pdb=" N THR A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 282 removed outlier: 3.887A pdb=" N PHE A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 314 Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 201 through 214 removed outlier: 3.714A pdb=" N MET B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 244 removed outlier: 4.299A pdb=" N THR B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 282 removed outlier: 3.887A pdb=" N PHE B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 314 Proline residue: B 300 - end of helix Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 201 through 214 removed outlier: 3.714A pdb=" N MET C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 244 removed outlier: 4.300A pdb=" N THR C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 282 removed outlier: 3.887A pdb=" N PHE C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 314 Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 152 through 156 Processing helix chain 'D' and resid 196 through 201 Processing helix chain 'D' and resid 201 through 214 removed outlier: 3.714A pdb=" N MET D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 244 removed outlier: 4.299A pdb=" N THR D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 282 removed outlier: 3.887A pdb=" N PHE D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 314 Proline residue: D 300 - end of helix Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'E' and resid 196 through 201 Processing helix chain 'E' and resid 201 through 214 removed outlier: 3.714A pdb=" N MET E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 244 removed outlier: 4.299A pdb=" N THR E 226 " --> pdb=" O GLU E 222 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 282 removed outlier: 3.887A pdb=" N PHE E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 314 Proline residue: E 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 94 removed outlier: 5.265A pdb=" N ALA A 87 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER A 107 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 37 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR A 36 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N SER A 29 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N CYS A 27 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASN A 40 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE A 25 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 42 " --> pdb=" O TYR A 23 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 18 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 128 removed outlier: 6.472A pdb=" N LYS A 183 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL A 169 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 94 removed outlier: 5.265A pdb=" N ALA B 87 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER B 107 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 37 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N THR B 36 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N SER B 29 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 25 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 42 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 18 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 128 removed outlier: 6.473A pdb=" N LYS B 183 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL B 169 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 86 through 94 removed outlier: 5.265A pdb=" N ALA C 87 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER C 107 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 37 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR C 36 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N SER C 29 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N CYS C 27 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASN C 40 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE C 25 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 42 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL C 18 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78 Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 128 removed outlier: 6.472A pdb=" N LYS C 183 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL C 169 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 94 removed outlier: 5.265A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 37 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N THR D 36 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N SER D 29 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N CYS D 27 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASN D 40 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 25 " --> pdb=" O ASN D 40 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE D 42 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL D 18 " --> pdb=" O VAL D 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AB3, first strand: chain 'D' and resid 125 through 128 removed outlier: 6.472A pdb=" N LYS D 183 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL D 169 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 86 through 94 removed outlier: 5.265A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE E 37 " --> pdb=" O VAL E 110 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR E 36 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER E 29 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE E 25 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE E 42 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL E 18 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78 Processing sheet with id=AB6, first strand: chain 'E' and resid 125 through 128 removed outlier: 6.472A pdb=" N LYS E 183 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL E 169 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1635 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: 2.85 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3180 1.34 - 1.46: 2421 1.46 - 1.57: 4819 1.57 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 10455 Sorted by residual: bond pdb=" CG1 ILE A 233 " pdb=" CD1 ILE A 233 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.78e+00 bond pdb=" CG1 ILE C 233 " pdb=" CD1 ILE C 233 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.74e+00 bond pdb=" CG1 ILE E 233 " pdb=" CD1 ILE E 233 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.74e+00 bond pdb=" CG1 ILE B 233 " pdb=" CD1 ILE B 233 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.71e+00 bond pdb=" CG1 ILE D 233 " pdb=" CD1 ILE D 233 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.68e+00 ... (remaining 10450 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.01: 407 107.01 - 113.79: 5806 113.79 - 120.56: 4190 120.56 - 127.33: 3906 127.33 - 134.10: 111 Bond angle restraints: 14420 Sorted by residual: angle pdb=" N VAL D 155 " pdb=" CA VAL D 155 " pdb=" C VAL D 155 " ideal model delta sigma weight residual 111.91 109.26 2.65 8.90e-01 1.26e+00 8.90e+00 angle pdb=" N VAL B 155 " pdb=" CA VAL B 155 " pdb=" C VAL B 155 " ideal model delta sigma weight residual 111.91 109.27 2.64 8.90e-01 1.26e+00 8.82e+00 angle pdb=" N VAL C 155 " pdb=" CA VAL C 155 " pdb=" C VAL C 155 " ideal model delta sigma weight residual 111.91 109.28 2.63 8.90e-01 1.26e+00 8.75e+00 angle pdb=" N VAL E 155 " pdb=" CA VAL E 155 " pdb=" C VAL E 155 " ideal model delta sigma weight residual 111.91 109.30 2.61 8.90e-01 1.26e+00 8.58e+00 angle pdb=" N VAL A 155 " pdb=" CA VAL A 155 " pdb=" C VAL A 155 " ideal model delta sigma weight residual 111.91 109.31 2.60 8.90e-01 1.26e+00 8.56e+00 ... (remaining 14415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.11: 5273 10.11 - 20.23: 491 20.23 - 30.34: 226 30.34 - 40.46: 35 40.46 - 50.57: 25 Dihedral angle restraints: 6050 sinusoidal: 1730 harmonic: 4320 Sorted by residual: dihedral pdb=" CA PRO E 9 " pdb=" C PRO E 9 " pdb=" N PRO E 10 " pdb=" CA PRO E 10 " ideal model delta harmonic sigma weight residual 180.00 -159.38 -20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA PRO A 9 " pdb=" C PRO A 9 " pdb=" N PRO A 10 " pdb=" CA PRO A 10 " ideal model delta harmonic sigma weight residual -180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA PRO C 9 " pdb=" C PRO C 9 " pdb=" N PRO C 10 " pdb=" CA PRO C 10 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 6047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1285 0.046 - 0.092: 333 0.092 - 0.137: 132 0.137 - 0.183: 5 0.183 - 0.229: 5 Chirality restraints: 1760 Sorted by residual: chirality pdb=" CA PHE A 299 " pdb=" N PHE A 299 " pdb=" C PHE A 299 " pdb=" CB PHE A 299 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PHE B 299 " pdb=" N PHE B 299 " pdb=" C PHE B 299 " pdb=" CB PHE B 299 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA PHE C 299 " pdb=" N PHE C 299 " pdb=" C PHE C 299 " pdb=" CB PHE C 299 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1757 not shown) Planarity restraints: 1825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 198 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO B 199 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 199 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 199 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 198 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO D 199 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 199 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 199 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 198 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO A 199 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " -0.038 5.00e-02 4.00e+02 ... (remaining 1822 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 182 2.69 - 3.24: 10400 3.24 - 3.79: 15383 3.79 - 4.35: 17375 4.35 - 4.90: 30233 Nonbonded interactions: 73573 Sorted by model distance: nonbonded pdb=" O LEU E 209 " pdb=" OG SER E 212 " model vdw 2.137 2.440 nonbonded pdb=" O LEU D 209 " pdb=" OG SER D 212 " model vdw 2.137 2.440 nonbonded pdb=" O LEU C 209 " pdb=" OG SER C 212 " model vdw 2.137 2.440 nonbonded pdb=" O LEU B 209 " pdb=" OG SER B 212 " model vdw 2.138 2.440 nonbonded pdb=" O LEU A 209 " pdb=" OG SER A 212 " model vdw 2.138 2.440 ... (remaining 73568 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: 1.170 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: 3.960 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 30.000 Find NCS groups from input model: 0.610 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 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 0.065 10455 Z= 0.391 Angle : 0.622 5.723 14420 Z= 0.352 Chirality : 0.048 0.229 1760 Planarity : 0.006 0.069 1825 Dihedral : 10.928 50.574 3210 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.61 % Allowed : 0.00 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1400 helix: 0.93 (0.21), residues: 515 sheet: -1.41 (0.26), residues: 335 loop : -1.88 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 160 HIS 0.005 0.002 HIS A 235 PHE 0.025 0.002 PHE E 299 TYR 0.011 0.002 TYR D 251 ARG 0.007 0.001 ARG C 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 284 time to evaluate : 1.163 Fit side-chains REVERT: A 38 LYS cc_start: 0.7893 (mttm) cc_final: 0.7588 (ttmm) REVERT: A 117 ARG cc_start: 0.7693 (mtm180) cc_final: 0.7303 (mmm-85) REVERT: A 287 ARG cc_start: 0.8701 (mtp85) cc_final: 0.8472 (mmm-85) REVERT: B 117 ARG cc_start: 0.7648 (mtm180) cc_final: 0.7333 (mmm-85) REVERT: B 238 PHE cc_start: 0.9275 (t80) cc_final: 0.8904 (t80) REVERT: B 287 ARG cc_start: 0.8783 (mtp85) cc_final: 0.8487 (mmm-85) REVERT: C 117 ARG cc_start: 0.7847 (mtm180) cc_final: 0.7432 (mmm-85) REVERT: C 287 ARG cc_start: 0.8755 (mtp85) cc_final: 0.8492 (mmm-85) REVERT: D 38 LYS cc_start: 0.7831 (mttm) cc_final: 0.7578 (ttmm) REVERT: D 187 GLN cc_start: 0.7847 (mt0) cc_final: 0.7621 (tt0) REVERT: D 239 ASN cc_start: 0.8713 (t0) cc_final: 0.8485 (t0) REVERT: E 287 ARG cc_start: 0.8734 (mtp85) cc_final: 0.8465 (mmm-85) outliers start: 5 outliers final: 0 residues processed: 284 average time/residue: 0.2337 time to fit residues: 89.8924 Evaluate side-chains 202 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 0.0470 chunk 36 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 42 optimal weight: 30.0000 chunk 66 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 overall best weight: 2.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN B 80 ASN B 245 ASN C 245 ASN D 80 ASN D 245 ASN E 245 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10455 Z= 0.391 Angle : 0.603 5.649 14420 Z= 0.330 Chirality : 0.048 0.192 1760 Planarity : 0.006 0.050 1825 Dihedral : 4.488 19.328 1525 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.22), residues: 1400 helix: 1.07 (0.22), residues: 495 sheet: -0.98 (0.27), residues: 320 loop : -2.17 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 160 HIS 0.006 0.002 HIS D 235 PHE 0.022 0.002 PHE C 238 TYR 0.008 0.001 TYR A 251 ARG 0.004 0.001 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8348 (mttm) cc_final: 0.7916 (ttmm) REVERT: B 238 PHE cc_start: 0.9260 (t80) cc_final: 0.9014 (t80) REVERT: B 239 ASN cc_start: 0.8684 (t0) cc_final: 0.8387 (t0) REVERT: C 200 ASN cc_start: 0.8383 (t0) cc_final: 0.8066 (t0) REVERT: C 287 ARG cc_start: 0.8795 (mtp85) cc_final: 0.8582 (mmm-85) REVERT: D 38 LYS cc_start: 0.8230 (mttm) cc_final: 0.7938 (ttmm) REVERT: E 287 ARG cc_start: 0.8800 (mtp85) cc_final: 0.8519 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.2135 time to fit residues: 74.0234 Evaluate side-chains 196 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.0010 chunk 39 optimal weight: 20.0000 chunk 105 optimal weight: 0.5980 chunk 86 optimal weight: 0.0980 chunk 35 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 137 optimal weight: 0.2980 chunk 113 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 102 optimal weight: 0.5980 overall best weight: 0.3186 ------------------------------------------------------------------------------- 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: 0.8047 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10455 Z= 0.179 Angle : 0.544 5.589 14420 Z= 0.284 Chirality : 0.045 0.152 1760 Planarity : 0.005 0.040 1825 Dihedral : 4.148 17.730 1525 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.22), residues: 1400 helix: 1.52 (0.22), residues: 500 sheet: -0.82 (0.26), residues: 360 loop : -2.22 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 213 HIS 0.004 0.001 HIS D 235 PHE 0.014 0.001 PHE C 37 TYR 0.008 0.001 TYR D 221 ARG 0.006 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8310 (mttm) cc_final: 0.7951 (ttmm) REVERT: C 38 LYS cc_start: 0.8371 (ttmm) cc_final: 0.8168 (ttmm) REVERT: C 200 ASN cc_start: 0.8081 (t0) cc_final: 0.7819 (t0) REVERT: C 274 THR cc_start: 0.9326 (p) cc_final: 0.9119 (m) REVERT: C 287 ARG cc_start: 0.8799 (mtp85) cc_final: 0.8455 (mmm-85) REVERT: D 38 LYS cc_start: 0.8242 (mttm) cc_final: 0.7893 (ttmm) REVERT: D 239 ASN cc_start: 0.8666 (t0) cc_final: 0.8294 (t0) REVERT: D 274 THR cc_start: 0.9241 (p) cc_final: 0.9016 (m) REVERT: E 287 ARG cc_start: 0.8763 (mtp85) cc_final: 0.8466 (mmm-85) REVERT: E 310 LEU cc_start: 0.8710 (mm) cc_final: 0.8476 (mm) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2134 time to fit residues: 82.1978 Evaluate side-chains 212 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 14 optimal weight: 30.0000 chunk 60 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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: 0.8360 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.083 10455 Z= 0.746 Angle : 0.799 7.916 14420 Z= 0.447 Chirality : 0.052 0.185 1760 Planarity : 0.007 0.055 1825 Dihedral : 5.167 19.530 1525 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.22), residues: 1400 helix: 0.64 (0.22), residues: 490 sheet: -1.08 (0.25), residues: 345 loop : -2.39 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 160 HIS 0.009 0.004 HIS A 235 PHE 0.030 0.003 PHE E 238 TYR 0.030 0.003 TYR D 278 ARG 0.005 0.001 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8409 (mttm) cc_final: 0.7752 (mtpp) REVERT: A 42 PHE cc_start: 0.7052 (p90) cc_final: 0.6842 (p90) REVERT: A 200 ASN cc_start: 0.8527 (t0) cc_final: 0.8281 (t0) REVERT: B 200 ASN cc_start: 0.8709 (t0) cc_final: 0.8414 (t0) REVERT: B 239 ASN cc_start: 0.9064 (t0) cc_final: 0.8718 (t0) REVERT: C 42 PHE cc_start: 0.7010 (p90) cc_final: 0.6797 (p90) REVERT: C 200 ASN cc_start: 0.8551 (t0) cc_final: 0.8242 (t0) REVERT: C 287 ARG cc_start: 0.8905 (mtp85) cc_final: 0.8638 (mmm-85) REVERT: D 38 LYS cc_start: 0.8338 (mttm) cc_final: 0.7728 (mtpp) REVERT: D 200 ASN cc_start: 0.8619 (t0) cc_final: 0.8219 (t0) REVERT: D 312 PHE cc_start: 0.8625 (t80) cc_final: 0.8283 (t80) REVERT: E 42 PHE cc_start: 0.6892 (p90) cc_final: 0.6662 (p90) REVERT: E 200 ASN cc_start: 0.8591 (t0) cc_final: 0.8341 (t0) REVERT: E 287 ARG cc_start: 0.8857 (mtp85) cc_final: 0.8574 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2108 time to fit residues: 65.3749 Evaluate side-chains 185 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 45 optimal weight: 0.0570 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10455 Z= 0.215 Angle : 0.572 6.185 14420 Z= 0.302 Chirality : 0.047 0.184 1760 Planarity : 0.006 0.053 1825 Dihedral : 4.448 18.246 1525 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.22), residues: 1400 helix: 1.23 (0.22), residues: 495 sheet: -1.21 (0.25), residues: 350 loop : -2.15 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 213 HIS 0.005 0.001 HIS C 235 PHE 0.012 0.001 PHE B 37 TYR 0.009 0.001 TYR E 221 ARG 0.006 0.000 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.150 Fit side-chains REVERT: A 38 LYS cc_start: 0.8377 (mttm) cc_final: 0.7732 (mtpp) REVERT: A 200 ASN cc_start: 0.8256 (t0) cc_final: 0.8047 (t0) REVERT: B 200 ASN cc_start: 0.8443 (t0) cc_final: 0.8230 (t0) REVERT: B 239 ASN cc_start: 0.8674 (t0) cc_final: 0.8400 (t0) REVERT: B 274 THR cc_start: 0.9347 (p) cc_final: 0.8848 (t) REVERT: C 200 ASN cc_start: 0.8190 (t0) cc_final: 0.7963 (t0) REVERT: C 287 ARG cc_start: 0.8840 (mtp85) cc_final: 0.8515 (mmm-85) REVERT: D 38 LYS cc_start: 0.8310 (mttm) cc_final: 0.7722 (mtpp) REVERT: D 117 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7209 (mmm-85) REVERT: D 200 ASN cc_start: 0.8202 (t0) cc_final: 0.7849 (t0) REVERT: E 200 ASN cc_start: 0.8458 (t0) cc_final: 0.8159 (t0) REVERT: E 274 THR cc_start: 0.9403 (p) cc_final: 0.8843 (t) REVERT: E 287 ARG cc_start: 0.8857 (mtp85) cc_final: 0.8560 (mmm-85) REVERT: E 310 LEU cc_start: 0.8757 (mm) cc_final: 0.8553 (mm) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2261 time to fit residues: 77.4665 Evaluate side-chains 206 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 0.0020 chunk 11 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 71 optimal weight: 30.0000 chunk 130 optimal weight: 0.8980 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10455 Z= 0.203 Angle : 0.552 6.259 14420 Z= 0.288 Chirality : 0.045 0.163 1760 Planarity : 0.005 0.048 1825 Dihedral : 4.221 17.394 1525 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.22), residues: 1400 helix: 1.41 (0.22), residues: 495 sheet: -0.93 (0.26), residues: 350 loop : -2.09 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 213 HIS 0.006 0.002 HIS E 235 PHE 0.017 0.001 PHE A 238 TYR 0.008 0.001 TYR D 221 ARG 0.006 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 1.164 Fit side-chains REVERT: A 38 LYS cc_start: 0.8403 (mttm) cc_final: 0.7759 (mtpp) REVERT: A 243 GLU cc_start: 0.6376 (mm-30) cc_final: 0.6129 (mm-30) REVERT: B 239 ASN cc_start: 0.8779 (t0) cc_final: 0.8357 (t0) REVERT: C 200 ASN cc_start: 0.8285 (t0) cc_final: 0.7921 (t0) REVERT: C 274 THR cc_start: 0.9264 (p) cc_final: 0.9039 (m) REVERT: C 287 ARG cc_start: 0.8793 (mtp85) cc_final: 0.8499 (mmm-85) REVERT: D 38 LYS cc_start: 0.8287 (mttm) cc_final: 0.7716 (mtpp) REVERT: D 239 ASN cc_start: 0.8643 (t0) cc_final: 0.8379 (t0) REVERT: D 243 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6000 (mm-30) REVERT: D 274 THR cc_start: 0.9265 (p) cc_final: 0.9021 (m) REVERT: E 187 GLN cc_start: 0.7841 (mt0) cc_final: 0.7535 (tt0) REVERT: E 200 ASN cc_start: 0.8422 (t0) cc_final: 0.8051 (t0) REVERT: E 243 GLU cc_start: 0.6832 (mm-30) cc_final: 0.5516 (mm-30) REVERT: E 287 ARG cc_start: 0.8849 (mtp85) cc_final: 0.8566 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2155 time to fit residues: 76.9225 Evaluate side-chains 206 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 20.0000 chunk 77 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 30.0000 chunk 75 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10455 Z= 0.269 Angle : 0.564 7.680 14420 Z= 0.298 Chirality : 0.046 0.164 1760 Planarity : 0.005 0.060 1825 Dihedral : 4.252 17.389 1525 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.22), residues: 1400 helix: 1.47 (0.23), residues: 495 sheet: -0.91 (0.27), residues: 350 loop : -2.10 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 213 HIS 0.006 0.002 HIS A 235 PHE 0.020 0.001 PHE A 238 TYR 0.010 0.001 TYR D 278 ARG 0.006 0.000 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.222 Fit side-chains REVERT: A 38 LYS cc_start: 0.8380 (mttm) cc_final: 0.7751 (mtpp) REVERT: A 200 ASN cc_start: 0.8412 (t0) cc_final: 0.8105 (t0) REVERT: B 200 ASN cc_start: 0.8498 (t0) cc_final: 0.8163 (t0) REVERT: B 239 ASN cc_start: 0.8889 (t0) cc_final: 0.8525 (t0) REVERT: B 243 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6418 (mm-30) REVERT: B 274 THR cc_start: 0.9276 (p) cc_final: 0.8750 (t) REVERT: C 200 ASN cc_start: 0.8366 (t0) cc_final: 0.7977 (t0) REVERT: C 287 ARG cc_start: 0.8810 (mtp85) cc_final: 0.8517 (mmm-85) REVERT: D 38 LYS cc_start: 0.8285 (mttm) cc_final: 0.7703 (mtpp) REVERT: D 117 ARG cc_start: 0.7756 (mtp180) cc_final: 0.7264 (mmm-85) REVERT: D 200 ASN cc_start: 0.8350 (t0) cc_final: 0.8065 (t0) REVERT: D 243 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6614 (mm-30) REVERT: D 274 THR cc_start: 0.9326 (p) cc_final: 0.9086 (m) REVERT: E 200 ASN cc_start: 0.8497 (t0) cc_final: 0.8074 (t0) REVERT: E 287 ARG cc_start: 0.8856 (mtp85) cc_final: 0.8618 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.2091 time to fit residues: 70.3729 Evaluate side-chains 199 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 GLN E 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10455 Z= 0.379 Angle : 0.609 7.186 14420 Z= 0.328 Chirality : 0.047 0.215 1760 Planarity : 0.006 0.067 1825 Dihedral : 4.460 17.699 1525 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.22), residues: 1400 helix: 1.38 (0.22), residues: 490 sheet: -1.05 (0.27), residues: 350 loop : -2.12 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 213 HIS 0.006 0.003 HIS C 235 PHE 0.017 0.002 PHE A 299 TYR 0.014 0.002 TYR D 278 ARG 0.007 0.000 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8379 (mttm) cc_final: 0.7741 (mtpp) REVERT: A 200 ASN cc_start: 0.8367 (t0) cc_final: 0.8134 (t0) REVERT: B 200 ASN cc_start: 0.8621 (t0) cc_final: 0.8238 (t0) REVERT: B 239 ASN cc_start: 0.8880 (t0) cc_final: 0.8489 (t0) REVERT: B 274 THR cc_start: 0.9315 (p) cc_final: 0.9069 (m) REVERT: C 200 ASN cc_start: 0.8448 (t0) cc_final: 0.8049 (t0) REVERT: C 287 ARG cc_start: 0.8867 (mtp85) cc_final: 0.8593 (mmm-85) REVERT: D 38 LYS cc_start: 0.8306 (mttm) cc_final: 0.7717 (mtpp) REVERT: D 117 ARG cc_start: 0.7813 (mtp180) cc_final: 0.7342 (mmm-85) REVERT: D 200 ASN cc_start: 0.8383 (t0) cc_final: 0.8087 (t0) REVERT: D 274 THR cc_start: 0.9333 (p) cc_final: 0.9082 (m) REVERT: E 200 ASN cc_start: 0.8436 (t0) cc_final: 0.8118 (t0) REVERT: E 243 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6729 (mt-10) REVERT: E 287 ARG cc_start: 0.8868 (mtp85) cc_final: 0.8630 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.2231 time to fit residues: 74.3599 Evaluate side-chains 199 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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: 0.8161 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10455 Z= 0.290 Angle : 0.575 6.368 14420 Z= 0.306 Chirality : 0.047 0.210 1760 Planarity : 0.006 0.067 1825 Dihedral : 4.400 17.335 1525 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.23), residues: 1400 helix: 1.42 (0.23), residues: 490 sheet: -0.96 (0.27), residues: 350 loop : -2.14 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 213 HIS 0.006 0.002 HIS C 235 PHE 0.019 0.002 PHE C 299 TYR 0.011 0.001 TYR D 278 ARG 0.007 0.000 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8356 (mttm) cc_final: 0.7734 (mtpp) REVERT: A 200 ASN cc_start: 0.8244 (t0) cc_final: 0.8016 (t0) REVERT: A 239 ASN cc_start: 0.8759 (t0) cc_final: 0.8037 (t0) REVERT: B 200 ASN cc_start: 0.8471 (t0) cc_final: 0.8226 (t0) REVERT: B 239 ASN cc_start: 0.8795 (t0) cc_final: 0.8440 (t0) REVERT: B 274 THR cc_start: 0.9306 (p) cc_final: 0.8793 (t) REVERT: C 200 ASN cc_start: 0.8324 (t0) cc_final: 0.7956 (t0) REVERT: C 287 ARG cc_start: 0.8858 (mtp85) cc_final: 0.8571 (mmm-85) REVERT: D 38 LYS cc_start: 0.8324 (mttm) cc_final: 0.7711 (mtpp) REVERT: D 117 ARG cc_start: 0.7764 (mtp180) cc_final: 0.7245 (mmm-85) REVERT: D 200 ASN cc_start: 0.8336 (t0) cc_final: 0.8082 (t0) REVERT: D 274 THR cc_start: 0.9336 (p) cc_final: 0.9121 (m) REVERT: E 200 ASN cc_start: 0.8420 (t0) cc_final: 0.8156 (t0) REVERT: E 287 ARG cc_start: 0.8862 (mtp85) cc_final: 0.8628 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.2099 time to fit residues: 70.4739 Evaluate side-chains 203 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.3980 chunk 63 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN E 187 GLN ** E 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 10455 Z= 0.510 Angle : 0.678 8.598 14420 Z= 0.373 Chirality : 0.049 0.217 1760 Planarity : 0.006 0.062 1825 Dihedral : 4.805 18.332 1525 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.23), residues: 1400 helix: 0.99 (0.22), residues: 495 sheet: -0.99 (0.28), residues: 325 loop : -2.28 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 160 HIS 0.007 0.003 HIS D 235 PHE 0.030 0.002 PHE D 299 TYR 0.021 0.002 TYR D 278 ARG 0.008 0.001 ARG D 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8380 (mttm) cc_final: 0.7733 (mtpp) REVERT: A 200 ASN cc_start: 0.8463 (t0) cc_final: 0.8258 (t0) REVERT: A 274 THR cc_start: 0.9418 (m) cc_final: 0.8725 (t) REVERT: B 200 ASN cc_start: 0.8661 (t0) cc_final: 0.8323 (t0) REVERT: B 239 ASN cc_start: 0.8933 (t0) cc_final: 0.8554 (t0) REVERT: B 274 THR cc_start: 0.9353 (p) cc_final: 0.8822 (t) REVERT: C 200 ASN cc_start: 0.8485 (t0) cc_final: 0.8153 (t0) REVERT: C 287 ARG cc_start: 0.8889 (mtp85) cc_final: 0.8612 (mmm-85) REVERT: D 38 LYS cc_start: 0.8336 (mttm) cc_final: 0.7727 (mtpp) REVERT: D 117 ARG cc_start: 0.7775 (mtp180) cc_final: 0.7327 (mmm-85) REVERT: D 200 ASN cc_start: 0.8484 (t0) cc_final: 0.8272 (t0) REVERT: D 274 THR cc_start: 0.9372 (p) cc_final: 0.9156 (m) REVERT: E 42 PHE cc_start: 0.6841 (p90) cc_final: 0.6563 (p90) REVERT: E 200 ASN cc_start: 0.8566 (t0) cc_final: 0.8295 (t0) REVERT: E 287 ARG cc_start: 0.8882 (mtp85) cc_final: 0.8647 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2162 time to fit residues: 70.1457 Evaluate side-chains 189 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 114 optimal weight: 30.0000 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 187 GLN ** E 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.156209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117586 restraints weight = 17415.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120947 restraints weight = 9817.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123205 restraints weight = 6776.747| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10455 Z= 0.210 Angle : 0.570 6.451 14420 Z= 0.297 Chirality : 0.047 0.192 1760 Planarity : 0.005 0.053 1825 Dihedral : 4.410 17.158 1525 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.23), residues: 1400 helix: 1.20 (0.23), residues: 500 sheet: -0.98 (0.27), residues: 350 loop : -2.17 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 213 HIS 0.005 0.001 HIS B 235 PHE 0.020 0.001 PHE C 299 TYR 0.009 0.001 TYR D 221 ARG 0.007 0.000 ARG D 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2191.94 seconds wall clock time: 39 minutes 52.58 seconds (2392.58 seconds total)