Starting phenix.real_space_refine (version: dev) on Tue Apr 5 16:32:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyg_30016/04_2022/6lyg_30016.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyg_30016/04_2022/6lyg_30016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyg_30016/04_2022/6lyg_30016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyg_30016/04_2022/6lyg_30016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyg_30016/04_2022/6lyg_30016.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyg_30016/04_2022/6lyg_30016.pdb" } resolution = 3.1 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 14688 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "F" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.48, per 1000 atoms: 0.58 Number of scatterers: 14688 At special positions: 0 Unit cell: (122.694, 122.694, 102.414, 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 120 16.00 O 2632 8.00 N 2384 7.00 C 9552 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=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 159 " distance=2.03 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 139 " " NAG B1001 " - " ASN B 139 " " NAG C1001 " - " ASN C 139 " " NAG D1001 " - " ASN D 139 " " NAG E1001 " - " ASN E 139 " " NAG F1001 " - " ASN F 139 " " NAG G1001 " - " ASN G 139 " " NAG H1001 " - " ASN H 139 " Time building additional restraints: 6.51 Conformation dependent library (CDL) restraints added in 2.2 seconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 78.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 47 through 70 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 204 Processing helix chain 'A' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE A 240 " --> pdb=" O HIS A 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 18 Processing helix chain 'B' and resid 25 through 36 Processing helix chain 'B' and resid 47 through 70 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 73 through 83 removed outlier: 3.629A pdb=" N LEU B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 107 Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 204 Processing helix chain 'B' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE B 240 " --> pdb=" O HIS B 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 18 Processing helix chain 'C' and resid 25 through 36 Processing helix chain 'C' and resid 47 through 70 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 129 Processing helix chain 'C' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 204 Processing helix chain 'C' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE C 240 " --> pdb=" O HIS C 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 18 Processing helix chain 'D' and resid 25 through 36 Processing helix chain 'D' and resid 47 through 70 Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG D 96 " --> pdb=" O PRO D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 204 Processing helix chain 'D' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE D 240 " --> pdb=" O HIS D 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 18 Processing helix chain 'E' and resid 25 through 36 Processing helix chain 'E' and resid 47 through 70 Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG E 96 " --> pdb=" O PRO E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 129 Processing helix chain 'E' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 204 Processing helix chain 'E' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE E 240 " --> pdb=" O HIS E 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 18 Processing helix chain 'F' and resid 25 through 36 Processing helix chain 'F' and resid 47 through 70 Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 73 through 83 removed outlier: 3.629A pdb=" N LEU F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG F 96 " --> pdb=" O PRO F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 129 Processing helix chain 'F' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE F 153 " --> pdb=" O GLU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 204 Processing helix chain 'F' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE F 240 " --> pdb=" O HIS F 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 18 Processing helix chain 'G' and resid 25 through 36 Processing helix chain 'G' and resid 47 through 70 Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 129 Processing helix chain 'G' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE G 153 " --> pdb=" O GLU G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 204 Processing helix chain 'G' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU G 213 " --> pdb=" O GLN G 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER G 239 " --> pdb=" O GLU G 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE G 240 " --> pdb=" O HIS G 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 18 Processing helix chain 'H' and resid 25 through 36 Processing helix chain 'H' and resid 47 through 70 Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU H 77 " --> pdb=" O ASN H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG H 96 " --> pdb=" O PRO H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA H 111 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 129 Processing helix chain 'H' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS H 152 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE H 153 " --> pdb=" O GLU H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 204 Processing helix chain 'H' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU H 213 " --> pdb=" O GLN H 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER H 239 " --> pdb=" O GLU H 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE H 240 " --> pdb=" O HIS H 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) 1049 hydrogen bonds defined for protein. 3147 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: 4.28 Time building geometry restraints manager: 7.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4495 1.34 - 1.46: 3261 1.46 - 1.58: 7092 1.58 - 1.69: 0 1.69 - 1.81: 176 Bond restraints: 15024 Sorted by residual: bond pdb=" N ALA G 93 " pdb=" CA ALA G 93 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.81e+00 bond pdb=" N ALA B 93 " pdb=" CA ALA B 93 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.27e-02 6.20e+03 4.65e+00 bond pdb=" N ALA E 93 " pdb=" CA ALA E 93 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.23e-02 6.61e+03 4.62e+00 bond pdb=" N ALA C 93 " pdb=" CA ALA C 93 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.23e-02 6.61e+03 4.62e+00 bond pdb=" N ALA H 93 " pdb=" CA ALA H 93 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.60e+00 ... (remaining 15019 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 450 107.13 - 113.85: 8460 113.85 - 120.57: 6378 120.57 - 127.29: 4896 127.29 - 134.01: 168 Bond angle restraints: 20352 Sorted by residual: angle pdb=" N ALA H 93 " pdb=" CA ALA H 93 " pdb=" C ALA H 93 " ideal model delta sigma weight residual 111.36 118.96 -7.60 1.09e+00 8.42e-01 4.86e+01 angle pdb=" N ALA D 93 " pdb=" CA ALA D 93 " pdb=" C ALA D 93 " ideal model delta sigma weight residual 111.36 118.96 -7.60 1.09e+00 8.42e-01 4.86e+01 angle pdb=" N ALA E 93 " pdb=" CA ALA E 93 " pdb=" C ALA E 93 " ideal model delta sigma weight residual 111.36 118.95 -7.59 1.09e+00 8.42e-01 4.85e+01 angle pdb=" N ALA C 93 " pdb=" CA ALA C 93 " pdb=" C ALA C 93 " ideal model delta sigma weight residual 111.36 118.95 -7.59 1.09e+00 8.42e-01 4.85e+01 angle pdb=" N ALA F 93 " pdb=" CA ALA F 93 " pdb=" C ALA F 93 " ideal model delta sigma weight residual 111.36 118.95 -7.59 1.09e+00 8.42e-01 4.85e+01 ... (remaining 20347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 8143 17.00 - 34.00: 629 34.00 - 51.00: 140 51.00 - 67.99: 48 67.99 - 84.99: 24 Dihedral angle restraints: 8984 sinusoidal: 3480 harmonic: 5504 Sorted by residual: dihedral pdb=" CB CYS B 43 " pdb=" SG CYS B 43 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.90 -26.90 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" CB CYS F 43 " pdb=" SG CYS F 43 " pdb=" SG CYS F 159 " pdb=" CB CYS F 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.90 -26.90 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 159 " pdb=" CB CYS C 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.89 -26.89 1 1.00e+01 1.00e-02 1.04e+01 ... (remaining 8981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2076 0.059 - 0.118: 242 0.118 - 0.178: 3 0.178 - 0.237: 9 0.237 - 0.296: 6 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA ALA F 93 " pdb=" N ALA F 93 " pdb=" C ALA F 93 " pdb=" CB ALA F 93 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ALA D 93 " pdb=" N ALA D 93 " pdb=" C ALA D 93 " pdb=" CB ALA D 93 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ALA G 93 " pdb=" N ALA G 93 " pdb=" C ALA G 93 " pdb=" CB ALA G 93 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 2333 not shown) Planarity restraints: 2512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 59 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO D 60 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 60 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 60 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 59 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO B 60 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 60 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 60 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 59 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.32e+00 pdb=" N PRO A 60 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " 0.026 5.00e-02 4.00e+02 ... (remaining 2509 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4363 2.82 - 3.34: 14844 3.34 - 3.86: 23737 3.86 - 4.38: 24593 4.38 - 4.90: 45157 Nonbonded interactions: 112694 Sorted by model distance: nonbonded pdb=" OH TYR H 68 " pdb=" OG1 THR H 103 " model vdw 2.299 2.440 nonbonded pdb=" OH TYR F 68 " pdb=" OG1 THR F 103 " model vdw 2.299 2.440 nonbonded pdb=" OH TYR B 68 " pdb=" OG1 THR B 103 " model vdw 2.299 2.440 nonbonded pdb=" OH TYR A 68 " pdb=" OG1 THR A 103 " model vdw 2.300 2.440 nonbonded pdb=" OH TYR G 68 " pdb=" OG1 THR G 103 " model vdw 2.300 2.440 ... (remaining 112689 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' selection = chain 'F' selection = chain 'G' 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 120 5.16 5 C 9552 2.51 5 N 2384 2.21 5 O 2632 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.910 Check model and map are aligned: 0.220 Convert atoms to be neutral: 0.140 Process input model: 39.710 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.100 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.003 0.039 15024 Z= 0.222 Angle : 0.568 7.601 20352 Z= 0.357 Chirality : 0.041 0.296 2336 Planarity : 0.004 0.046 2504 Dihedral : 14.347 84.992 5336 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -0.02 (0.19), residues: 1792 helix: 0.79 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -3.07 (0.27), residues: 376 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 509 time to evaluate : 1.826 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 0.3300 time to fit residues: 228.8370 Evaluate side-chains 347 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 1.926 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 15024 Z= 0.233 Angle : 0.545 6.459 20352 Z= 0.284 Chirality : 0.038 0.125 2336 Planarity : 0.005 0.045 2504 Dihedral : 3.723 15.478 2024 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer Outliers : 1.97 % 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: 1.93 (0.20), residues: 1792 helix: 2.15 (0.14), residues: 1408 sheet: None (None), residues: 0 loop : -2.19 (0.31), residues: 384 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 373 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 383 average time/residue: 0.2818 time to fit residues: 153.7213 Evaluate side-chains 331 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 315 time to evaluate : 1.846 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1242 time to fit residues: 6.1624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 70.0000 chunk 51 optimal weight: 0.6980 chunk 139 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 70.0000 chunk 167 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 57 optimal weight: 0.0570 chunk 134 optimal weight: 3.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 71 ASN C 71 ASN D 71 ASN E 71 ASN F 71 ASN G 71 ASN H 71 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 15024 Z= 0.238 Angle : 0.540 6.503 20352 Z= 0.281 Chirality : 0.037 0.124 2336 Planarity : 0.004 0.045 2504 Dihedral : 3.682 15.788 2024 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 0.79 % 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: 2.51 (0.21), residues: 1792 helix: 2.53 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : -1.97 (0.33), residues: 376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 374 time to evaluate : 1.715 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 374 average time/residue: 0.2738 time to fit residues: 147.7968 Evaluate side-chains 344 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 340 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1259 time to fit residues: 3.4058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.6980 chunk 125 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 112 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.7605 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.101 15024 Z= 0.268 Angle : 0.563 7.710 20352 Z= 0.292 Chirality : 0.037 0.125 2336 Planarity : 0.004 0.045 2504 Dihedral : 3.651 16.056 2024 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 1.25 % 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: 2.78 (0.20), residues: 1792 helix: 2.70 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.80 (0.33), residues: 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 347 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 4 residues processed: 355 average time/residue: 0.2782 time to fit residues: 141.0375 Evaluate side-chains 332 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 328 time to evaluate : 1.836 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1301 time to fit residues: 3.4739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 90 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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: 0.7599 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.113 15024 Z= 0.270 Angle : 0.579 9.394 20352 Z= 0.302 Chirality : 0.037 0.125 2336 Planarity : 0.004 0.045 2504 Dihedral : 3.655 16.199 2024 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 0.86 % 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: 3.01 (0.20), residues: 1792 helix: 2.84 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.58 (0.34), residues: 376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 339 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 343 average time/residue: 0.2804 time to fit residues: 137.7989 Evaluate side-chains 338 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 333 time to evaluate : 1.856 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1363 time to fit residues: 3.7673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.0670 chunk 160 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- 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: 0.7611 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.127 15024 Z= 0.285 Angle : 0.571 10.145 20352 Z= 0.296 Chirality : 0.038 0.140 2336 Planarity : 0.005 0.053 2504 Dihedral : 3.630 16.256 2024 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 1.97 % 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: 3.12 (0.20), residues: 1792 helix: 2.90 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.47 (0.34), residues: 376 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 332 time to evaluate : 1.801 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 11 residues processed: 342 average time/residue: 0.2804 time to fit residues: 137.6071 Evaluate side-chains 341 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 330 time to evaluate : 1.731 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1332 time to fit residues: 5.3235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7585 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 15024 Z= 0.224 Angle : 0.559 11.516 20352 Z= 0.291 Chirality : 0.037 0.163 2336 Planarity : 0.005 0.057 2504 Dihedral : 3.623 16.591 2024 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer Outliers : 0.46 % 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: 3.31 (0.20), residues: 1792 helix: 3.04 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.42 (0.34), residues: 376 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 335 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 338 average time/residue: 0.2742 time to fit residues: 132.7905 Evaluate side-chains 326 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 322 time to evaluate : 1.851 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1285 time to fit residues: 3.5375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 120 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS B 236 HIS D 236 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.133 15024 Z= 0.280 Angle : 0.576 12.354 20352 Z= 0.309 Chirality : 0.038 0.174 2336 Planarity : 0.005 0.076 2504 Dihedral : 3.572 16.412 2024 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 0.46 % 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: 3.35 (0.20), residues: 1792 helix: 3.06 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.37 (0.34), residues: 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 324 time to evaluate : 1.739 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 327 average time/residue: 0.2684 time to fit residues: 126.4874 Evaluate side-chains 316 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 1.796 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 HIS C 236 HIS D 236 HIS F 236 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.196 15024 Z= 0.274 Angle : 0.582 14.832 20352 Z= 0.311 Chirality : 0.038 0.224 2336 Planarity : 0.005 0.072 2504 Dihedral : 3.590 16.530 2024 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer Outliers : 0.07 % 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: 3.32 (0.20), residues: 1792 helix: 3.03 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -1.70 (0.33), residues: 352 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 310 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 310 average time/residue: 0.2782 time to fit residues: 123.8338 Evaluate side-chains 307 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 306 time to evaluate : 1.780 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1245 time to fit residues: 2.6591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 145 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 HIS D 236 HIS F 236 HIS H 236 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.347 15024 Z= 0.384 Angle : 0.634 24.046 20352 Z= 0.344 Chirality : 0.039 0.244 2336 Planarity : 0.006 0.094 2504 Dihedral : 3.642 19.780 2024 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: 3.19 (0.20), residues: 1792 helix: 2.99 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.72 (0.32), residues: 368 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.2880 time to fit residues: 126.7000 Evaluate side-chains 304 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.759 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 HIS D 236 HIS E 236 HIS F 236 HIS G 236 HIS H 236 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.160669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.103089 restraints weight = 18041.391| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.34 r_work: 0.3093 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work: 0.3059 rms_B_bonded: 2.13 restraints_weight: 0.1250 r_work: 0.3041 rms_B_bonded: 2.23 restraints_weight: 0.0625 r_work: 0.3022 rms_B_bonded: 2.38 restraints_weight: 0.0312 r_work: 0.3001 rms_B_bonded: 2.58 restraints_weight: 0.0156 r_work: 0.2979 rms_B_bonded: 2.82 restraints_weight: 0.0078 r_work: 0.2955 rms_B_bonded: 3.11 restraints_weight: 0.0039 r_work: 0.2929 rms_B_bonded: 3.47 restraints_weight: 0.0020 r_work: 0.2900 rms_B_bonded: 3.88 restraints_weight: 0.0010 r_work: 0.2870 rms_B_bonded: 4.37 restraints_weight: 0.0005 r_work: 0.2836 rms_B_bonded: 4.94 restraints_weight: 0.0002 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.206 15024 Z= 0.314 Angle : 0.590 16.354 20352 Z= 0.316 Chirality : 0.039 0.226 2336 Planarity : 0.005 0.084 2504 Dihedral : 3.648 19.280 2024 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: 3.20 (0.20), residues: 1792 helix: 2.99 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.69 (0.32), residues: 368 =============================================================================== Job complete usr+sys time: 3137.58 seconds wall clock time: 57 minutes 35.12 seconds (3455.12 seconds total)