Starting phenix.real_space_refine (version: dev) on Sat May 14 07:19:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmt_0919/05_2022/6lmt_0919_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmt_0919/05_2022/6lmt_0919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmt_0919/05_2022/6lmt_0919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmt_0919/05_2022/6lmt_0919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmt_0919/05_2022/6lmt_0919_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmt_0919/05_2022/6lmt_0919_updated.pdb" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 17552 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 175 Unusual residues: {'Y01': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'Y01': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'Y01': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'Y01': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'Y01': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'Y01': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'Y01': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.29, per 1000 atoms: 0.59 Number of scatterers: 17552 At special positions: 0 Unit cell: (123.67, 123.67, 100.43, 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 192 16.00 O 2976 8.00 N 2696 7.00 C 11688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 160 " distance=2.01 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 160 " distance=2.01 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 160 " distance=2.01 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 160 " distance=2.01 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 160 " distance=2.01 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 160 " distance=2.01 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.04 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 160 " distance=2.01 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 160 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.99 Conformation dependent library (CDL) restraints added in 2.4 seconds 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 0 sheets defined 77.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 48 through 70 removed outlier: 3.682A pdb=" N LEU A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 74 through 82 Processing helix chain 'A' and resid 92 through 120 removed outlier: 4.358A pdb=" N ILE A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 122 through 131 removed outlier: 3.559A pdb=" N SER A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE A 130 " --> pdb=" O CYS A 126 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ASN A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 148 through 157 removed outlier: 3.722A pdb=" N ARG A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 167 through 205 Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 210 through 258 removed outlier: 3.761A pdb=" N PHE A 239 " --> pdb=" O HIS A 235 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 21 through 36 Processing helix chain 'B' and resid 48 through 70 removed outlier: 3.682A pdb=" N LEU B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 74 through 82 Processing helix chain 'B' and resid 92 through 120 removed outlier: 4.359A pdb=" N ILE B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 122 through 131 removed outlier: 3.560A pdb=" N SER B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE B 130 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 148 through 157 removed outlier: 3.723A pdb=" N ARG B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 167 through 205 Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 210 through 258 removed outlier: 3.760A pdb=" N PHE B 239 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN B 250 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 21 through 36 Processing helix chain 'C' and resid 48 through 70 removed outlier: 3.681A pdb=" N LEU C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 74 through 82 Processing helix chain 'C' and resid 92 through 120 removed outlier: 4.358A pdb=" N ILE C 108 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 122 through 131 removed outlier: 3.559A pdb=" N SER C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE C 130 " --> pdb=" O CYS C 126 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 148 through 157 removed outlier: 3.722A pdb=" N ARG C 157 " --> pdb=" O LYS C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 167 through 205 Proline residue: C 204 - end of helix Processing helix chain 'C' and resid 210 through 258 removed outlier: 3.761A pdb=" N PHE C 239 " --> pdb=" O HIS C 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN C 250 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 13 Processing helix chain 'D' and resid 21 through 36 Processing helix chain 'D' and resid 48 through 70 removed outlier: 3.682A pdb=" N LEU D 56 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 74 through 82 Processing helix chain 'D' and resid 92 through 120 removed outlier: 4.359A pdb=" N ILE D 108 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 122 through 131 removed outlier: 3.560A pdb=" N SER D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE D 130 " --> pdb=" O CYS D 126 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 148 through 157 removed outlier: 3.723A pdb=" N ARG D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 167 through 205 Proline residue: D 204 - end of helix Processing helix chain 'D' and resid 210 through 258 removed outlier: 3.760A pdb=" N PHE D 239 " --> pdb=" O HIS D 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN D 250 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 13 Processing helix chain 'E' and resid 21 through 36 Processing helix chain 'E' and resid 48 through 70 removed outlier: 3.682A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 74 through 82 Processing helix chain 'E' and resid 92 through 120 removed outlier: 4.358A pdb=" N ILE E 108 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 122 through 131 removed outlier: 3.560A pdb=" N SER E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE E 130 " --> pdb=" O CYS E 126 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ASN E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 148 through 157 removed outlier: 3.723A pdb=" N ARG E 157 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 167 through 205 Proline residue: E 204 - end of helix Processing helix chain 'E' and resid 210 through 258 removed outlier: 3.759A pdb=" N PHE E 239 " --> pdb=" O HIS E 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN E 250 " --> pdb=" O GLN E 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 13 Processing helix chain 'F' and resid 21 through 36 Processing helix chain 'F' and resid 48 through 70 removed outlier: 3.682A pdb=" N LEU F 56 " --> pdb=" O GLY F 52 " (cutoff:3.500A) Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 74 through 82 Processing helix chain 'F' and resid 92 through 120 removed outlier: 4.359A pdb=" N ILE F 108 " --> pdb=" O GLN F 104 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 122 through 131 removed outlier: 3.560A pdb=" N SER F 129 " --> pdb=" O LEU F 125 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE F 130 " --> pdb=" O CYS F 126 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN F 131 " --> pdb=" O ALA F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 148 through 157 removed outlier: 3.723A pdb=" N ARG F 157 " --> pdb=" O LYS F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 167 through 205 Proline residue: F 204 - end of helix Processing helix chain 'F' and resid 210 through 258 removed outlier: 3.760A pdb=" N PHE F 239 " --> pdb=" O HIS F 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN F 250 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY F 253 " --> pdb=" O GLU F 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 21 through 36 Processing helix chain 'G' and resid 48 through 70 removed outlier: 3.682A pdb=" N LEU G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 92 through 120 removed outlier: 4.358A pdb=" N ILE G 108 " --> pdb=" O GLN G 104 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA G 109 " --> pdb=" O ARG G 105 " (cutoff:3.500A) Proline residue: G 110 - end of helix Processing helix chain 'G' and resid 122 through 131 removed outlier: 3.559A pdb=" N SER G 129 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE G 130 " --> pdb=" O CYS G 126 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ASN G 131 " --> pdb=" O ALA G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 136 No H-bonds generated for 'chain 'G' and resid 134 through 136' Processing helix chain 'G' and resid 148 through 157 removed outlier: 3.722A pdb=" N ARG G 157 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 163 No H-bonds generated for 'chain 'G' and resid 161 through 163' Processing helix chain 'G' and resid 167 through 205 Proline residue: G 204 - end of helix Processing helix chain 'G' and resid 210 through 258 removed outlier: 3.761A pdb=" N PHE G 239 " --> pdb=" O HIS G 235 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN G 250 " --> pdb=" O GLN G 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN G 257 " --> pdb=" O GLY G 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 13 Processing helix chain 'H' and resid 21 through 36 Processing helix chain 'H' and resid 48 through 70 removed outlier: 3.682A pdb=" N LEU H 56 " --> pdb=" O GLY H 52 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 92 through 120 removed outlier: 4.359A pdb=" N ILE H 108 " --> pdb=" O GLN H 104 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 122 through 131 removed outlier: 3.560A pdb=" N SER H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE H 130 " --> pdb=" O CYS H 126 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'H' and resid 148 through 157 removed outlier: 3.723A pdb=" N ARG H 157 " --> pdb=" O LYS H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 167 through 205 Proline residue: H 204 - end of helix Processing helix chain 'H' and resid 210 through 258 removed outlier: 3.760A pdb=" N PHE H 239 " --> pdb=" O HIS H 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN H 250 " --> pdb=" O GLN H 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN H 257 " --> pdb=" O GLY H 253 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 3240 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: 4.94 Time building geometry restraints manager: 7.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2847 1.32 - 1.45: 4847 1.45 - 1.57: 10082 1.57 - 1.70: 0 1.70 - 1.82: 296 Bond restraints: 18072 Sorted by residual: bond pdb=" CB MET G 98 " pdb=" CG MET G 98 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.48e+00 bond pdb=" CB MET A 98 " pdb=" CG MET A 98 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.48e+00 bond pdb=" CB MET E 98 " pdb=" CG MET E 98 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.43e+00 bond pdb=" CB MET C 98 " pdb=" CG MET C 98 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.43e+00 bond pdb=" CB MET B 98 " pdb=" CG MET B 98 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.31e+00 ... (remaining 18067 not shown) Histogram of bond angle deviations from ideal: 96.57 - 104.06: 375 104.06 - 111.56: 7464 111.56 - 119.05: 7277 119.05 - 126.54: 9196 126.54 - 134.04: 256 Bond angle restraints: 24568 Sorted by residual: angle pdb=" C GLN F 208 " pdb=" N ALA F 209 " pdb=" CA ALA F 209 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C GLN B 208 " pdb=" N ALA B 209 " pdb=" CA ALA B 209 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C GLN H 208 " pdb=" N ALA H 209 " pdb=" CA ALA H 209 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C GLN D 208 " pdb=" N ALA D 209 " pdb=" CA ALA D 209 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C GLN G 208 " pdb=" N ALA G 209 " pdb=" CA ALA G 209 " ideal model delta sigma weight residual 121.54 132.06 -10.52 1.91e+00 2.74e-01 3.03e+01 ... (remaining 24563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 9872 16.32 - 32.64: 440 32.64 - 48.95: 120 48.95 - 65.27: 48 65.27 - 81.59: 8 Dihedral angle restraints: 10488 sinusoidal: 4504 harmonic: 5984 Sorted by residual: dihedral pdb=" CA ALA E 209 " pdb=" C ALA E 209 " pdb=" N ALA E 210 " pdb=" CA ALA E 210 " ideal model delta harmonic sigma weight residual 180.00 155.65 24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ALA C 209 " pdb=" C ALA C 209 " pdb=" N ALA C 210 " pdb=" CA ALA C 210 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ALA G 209 " pdb=" C ALA G 209 " pdb=" N ALA G 210 " pdb=" CA ALA G 210 " ideal model delta harmonic sigma weight residual 180.00 155.69 24.31 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 10485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1758 0.056 - 0.112: 779 0.112 - 0.168: 167 0.168 - 0.224: 8 0.224 - 0.280: 16 Chirality restraints: 2728 Sorted by residual: chirality pdb=" CBE Y01 C 402 " pdb=" CAP Y01 C 402 " pdb=" CBB Y01 C 402 " pdb=" CBI Y01 C 402 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CBE Y01 E 402 " pdb=" CAP Y01 E 402 " pdb=" CBB Y01 E 402 " pdb=" CBI Y01 E 402 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CBE Y01 G 402 " pdb=" CAP Y01 G 402 " pdb=" CBB Y01 G 402 " pdb=" CBI Y01 G 402 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2725 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 137 " 0.027 2.00e-02 2.50e+03 2.38e-02 9.95e+00 pdb=" CG PHE C 137 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE C 137 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 137 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 137 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 137 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 137 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 137 " -0.027 2.00e-02 2.50e+03 2.38e-02 9.92e+00 pdb=" CG PHE G 137 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE G 137 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE G 137 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE G 137 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 137 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE G 137 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 137 " -0.027 2.00e-02 2.50e+03 2.38e-02 9.92e+00 pdb=" CG PHE A 137 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 137 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 137 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 137 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 137 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 137 " -0.005 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 6375 2.91 - 3.41: 16871 3.41 - 3.90: 29134 3.90 - 4.40: 34492 4.40 - 4.90: 56234 Nonbonded interactions: 143106 Sorted by model distance: nonbonded pdb=" O ASN F 72 " pdb=" NH2 ARG F 225 " model vdw 2.409 2.520 nonbonded pdb=" O ASN H 72 " pdb=" NH2 ARG H 225 " model vdw 2.409 2.520 nonbonded pdb=" O ASN D 72 " pdb=" NH2 ARG D 225 " model vdw 2.409 2.520 nonbonded pdb=" O ASN B 72 " pdb=" NH2 ARG B 225 " model vdw 2.409 2.520 nonbonded pdb=" O ASN E 72 " pdb=" NH2 ARG E 225 " model vdw 2.409 2.520 ... (remaining 143101 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' and (resid 7 through 260 or resid 401 through 403)) selection = (chain 'B' and (resid 7 through 260 or resid 401 through 403)) selection = (chain 'C' and (resid 7 through 260 or resid 401 through 403)) selection = (chain 'D' and (resid 7 through 260 or resid 401 through 403)) selection = (chain 'E' and (resid 7 through 260 or resid 401 through 403)) selection = (chain 'F' and (resid 7 through 260 or resid 401 through 403)) selection = (chain 'G' and (resid 7 through 260 or resid 401 through 403)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 192 5.16 5 C 11688 2.51 5 N 2696 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.550 Check model and map are aligned: 0.300 Convert atoms to be neutral: 0.170 Process input model: 46.530 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 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 : 0.012 0.125 18072 Z= 0.770 Angle : 1.138 15.192 24568 Z= 0.577 Chirality : 0.063 0.280 2728 Planarity : 0.008 0.057 2904 Dihedral : 11.630 81.587 6552 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.12), residues: 2016 helix: -2.86 (0.08), residues: 1464 sheet: None (None), residues: 0 loop : -2.61 (0.20), residues: 552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 413 average time/residue: 1.7022 time to fit residues: 762.6107 Evaluate side-chains 326 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 324 time to evaluate : 2.154 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.3014 time to fit residues: 3.6058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 80 optimal weight: 0.0980 chunk 156 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 181 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS B 73 ASN B 235 HIS C 235 HIS D 73 ASN D 235 HIS E 235 HIS F 73 ASN F 235 HIS G 235 HIS H 73 ASN H 235 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 18072 Z= 0.212 Angle : 0.706 13.679 24568 Z= 0.340 Chirality : 0.040 0.244 2728 Planarity : 0.005 0.048 2904 Dihedral : 9.714 58.193 2608 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 2.23 % 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: -0.20 (0.17), residues: 2016 helix: 0.21 (0.12), residues: 1512 sheet: None (None), residues: 0 loop : -0.85 (0.29), residues: 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 314 time to evaluate : 1.985 Fit side-chains outliers start: 40 outliers final: 18 residues processed: 329 average time/residue: 1.4930 time to fit residues: 539.3404 Evaluate side-chains 294 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 276 time to evaluate : 2.124 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 8 average time/residue: 0.2876 time to fit residues: 5.9574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 181 optimal weight: 0.6980 chunk 196 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 GLN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 GLN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 18072 Z= 0.340 Angle : 0.705 6.599 24568 Z= 0.336 Chirality : 0.044 0.188 2728 Planarity : 0.005 0.047 2904 Dihedral : 9.556 56.675 2608 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 3.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.18), residues: 2016 helix: 1.05 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.49 (0.30), residues: 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 296 time to evaluate : 1.977 Fit side-chains outliers start: 71 outliers final: 32 residues processed: 314 average time/residue: 1.4820 time to fit residues: 511.9467 Evaluate side-chains 314 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 282 time to evaluate : 1.999 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 20 residues processed: 20 average time/residue: 0.7516 time to fit residues: 20.3740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 182 optimal weight: 0.0010 chunk 193 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS B 71 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 HIS F 14 ASN F 71 ASN ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 HIS H 71 ASN ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 18072 Z= 0.213 Angle : 0.632 8.345 24568 Z= 0.302 Chirality : 0.039 0.252 2728 Planarity : 0.004 0.047 2904 Dihedral : 8.884 56.026 2608 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 2016 helix: 1.67 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.11 (0.31), residues: 504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 284 time to evaluate : 1.873 Fit side-chains outliers start: 53 outliers final: 28 residues processed: 309 average time/residue: 1.4707 time to fit residues: 500.9835 Evaluate side-chains 290 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 262 time to evaluate : 2.061 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 12 average time/residue: 0.5830 time to fit residues: 11.4444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS C 15 GLN ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 HIS D 15 GLN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 HIS ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 HIS ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 18072 Z= 0.248 Angle : 0.650 7.468 24568 Z= 0.308 Chirality : 0.040 0.203 2728 Planarity : 0.005 0.047 2904 Dihedral : 8.839 56.662 2608 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.19), residues: 2016 helix: 1.66 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : 0.03 (0.31), residues: 504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 276 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 22 residues processed: 306 average time/residue: 1.4701 time to fit residues: 496.6601 Evaluate side-chains 305 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 283 time to evaluate : 2.098 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 7 average time/residue: 0.2474 time to fit residues: 5.4482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.7980 chunk 174 optimal weight: 9.9990 chunk 38 optimal weight: 0.0070 chunk 113 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 160 optimal weight: 0.0970 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 HIS ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 HIS ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 18072 Z= 0.182 Angle : 0.612 8.002 24568 Z= 0.292 Chirality : 0.037 0.168 2728 Planarity : 0.004 0.047 2904 Dihedral : 8.323 56.028 2608 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 3.18 % 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: 2.19 (0.19), residues: 2016 helix: 1.88 (0.14), residues: 1512 sheet: None (None), residues: 0 loop : 0.27 (0.30), residues: 504 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 272 time to evaluate : 2.029 Fit side-chains outliers start: 57 outliers final: 20 residues processed: 295 average time/residue: 1.4391 time to fit residues: 468.2312 Evaluate side-chains 290 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 270 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 5 average time/residue: 0.2829 time to fit residues: 4.5398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 192 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 88 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN B 32 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN D 32 GLN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 18072 Z= 0.182 Angle : 0.611 6.771 24568 Z= 0.292 Chirality : 0.037 0.145 2728 Planarity : 0.004 0.047 2904 Dihedral : 8.185 56.279 2608 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 3.01 % 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: 2.32 (0.19), residues: 2016 helix: 1.97 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : 0.33 (0.30), residues: 504 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 270 time to evaluate : 2.090 Fit side-chains outliers start: 54 outliers final: 24 residues processed: 288 average time/residue: 1.5316 time to fit residues: 484.6766 Evaluate side-chains 287 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 263 time to evaluate : 2.157 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 9 average time/residue: 0.2811 time to fit residues: 6.7482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 18072 Z= 0.298 Angle : 0.687 6.852 24568 Z= 0.324 Chirality : 0.042 0.175 2728 Planarity : 0.004 0.048 2904 Dihedral : 8.928 55.776 2608 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.19), residues: 2016 helix: 1.68 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : 0.28 (0.29), residues: 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 282 time to evaluate : 2.040 Fit side-chains outliers start: 45 outliers final: 25 residues processed: 293 average time/residue: 1.4623 time to fit residues: 472.9880 Evaluate side-chains 294 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 269 time to evaluate : 1.991 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 15 residues processed: 14 average time/residue: 0.3704 time to fit residues: 9.8382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 179 optimal weight: 0.0970 chunk 108 optimal weight: 6.9990 chunk 78 optimal weight: 0.0070 chunk 141 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 18072 Z= 0.191 Angle : 0.634 9.794 24568 Z= 0.299 Chirality : 0.039 0.198 2728 Planarity : 0.004 0.047 2904 Dihedral : 8.533 55.911 2608 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 1.90 % 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: 2.29 (0.19), residues: 2016 helix: 1.96 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : 0.26 (0.29), residues: 504 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 263 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 282 average time/residue: 1.4275 time to fit residues: 444.7800 Evaluate side-chains 272 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 253 time to evaluate : 1.886 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 8 average time/residue: 0.7264 time to fit residues: 9.4186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 132 optimal weight: 7.9990 chunk 199 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 126 optimal weight: 0.2980 chunk 169 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN F 32 GLN ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 18072 Z= 0.192 Angle : 0.624 9.706 24568 Z= 0.294 Chirality : 0.039 0.220 2728 Planarity : 0.004 0.047 2904 Dihedral : 8.454 56.130 2608 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 1.62 % 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: 2.35 (0.19), residues: 2016 helix: 2.02 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : 0.25 (0.28), residues: 504 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 263 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 274 average time/residue: 1.4118 time to fit residues: 428.5539 Evaluate side-chains 273 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 253 time to evaluate : 2.107 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 9 average time/residue: 0.3195 time to fit residues: 6.9622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN B 32 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN D 32 GLN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN F 32 GLN ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 GLN H 32 GLN ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.191641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.118188 restraints weight = 17713.189| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.81 r_work: 0.3191 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 1.64 restraints_weight: 0.2500 r_work: 0.3139 rms_B_bonded: 1.77 restraints_weight: 0.1250 r_work: 0.3109 rms_B_bonded: 1.99 restraints_weight: 0.0625 r_work: 0.3073 rms_B_bonded: 2.31 restraints_weight: 0.0312 r_work: 0.3030 rms_B_bonded: 2.78 restraints_weight: 0.0156 r_work: 0.2978 rms_B_bonded: 3.42 restraints_weight: 0.0078 r_work: 0.2914 rms_B_bonded: 4.33 restraints_weight: 0.0039 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 18072 Z= 0.210 Angle : 0.631 8.831 24568 Z= 0.297 Chirality : 0.039 0.217 2728 Planarity : 0.004 0.047 2904 Dihedral : 8.636 59.359 2608 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 1.45 % 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: 2.29 (0.19), residues: 2016 helix: 1.97 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : 0.23 (0.28), residues: 504 =============================================================================== Job complete usr+sys time: 7126.41 seconds wall clock time: 126 minutes 42.00 seconds (7602.00 seconds total)