Starting phenix.real_space_refine (version: dev) on Fri Feb 24 12:44:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svv_25454/02_2023/7svv_25454_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svv_25454/02_2023/7svv_25454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svv_25454/02_2023/7svv_25454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svv_25454/02_2023/7svv_25454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svv_25454/02_2023/7svv_25454_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svv_25454/02_2023/7svv_25454_updated.pdb" } resolution = 3.54 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= 0.004 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 Process input model Symmetric amino acids flipped Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 574": "OD1" <-> "OD2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 574": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 574": "OD1" <-> "OD2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 574": "OD1" <-> "OD2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 574": "OD1" <-> "OD2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 574": "OD1" <-> "OD2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 574": "OD1" <-> "OD2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 574": "OD1" <-> "OD2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 574": "OD1" <-> "OD2" Residue "J PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 574": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23046 Number of models: 1 Model: "" Number of chains: 32 Chain: "1" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 380 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "2" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain breaks: 2 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "a" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "b" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "c" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "d" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "e" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "f" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "g" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "h" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 126 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "i" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "J" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "j" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.90, per 1000 atoms: 0.52 Number of scatterers: 23046 At special positions: 0 Unit cell: (142.31, 136.99, 135.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 68 15.00 Mg 10 11.99 O 4368 8.00 N 4153 7.00 C 14367 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.52 Conformation dependent library (CDL) restraints added in 3.1 seconds 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 140 helices and 10 sheets defined 54.6% alpha, 7.4% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 6.03 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.757A pdb=" N ARG A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 removed outlier: 4.162A pdb=" N PHE A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 107 " --> pdb=" O LYS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.665A pdb=" N ALA A 155 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP A 159 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 160 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.144A pdb=" N ARG A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.849A pdb=" N ILE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 257 removed outlier: 3.546A pdb=" N GLU A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 removed outlier: 3.908A pdb=" N GLU A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'a' and resid 575 through 580 Processing helix chain 'B' and resid 20 through 28 removed outlier: 3.757A pdb=" N ARG B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.656A pdb=" N ARG B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 removed outlier: 4.163A pdb=" N PHE B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.665A pdb=" N ALA B 155 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 158 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 160 " --> pdb=" O VAL B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 removed outlier: 4.143A pdb=" N ARG B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 201 through 214 Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.849A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 257 removed outlier: 3.546A pdb=" N GLU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 274 removed outlier: 3.908A pdb=" N GLU B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'b' and resid 575 through 580 Processing helix chain 'C' and resid 20 through 28 removed outlier: 3.757A pdb=" N ARG C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS C 51 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 removed outlier: 4.162A pdb=" N PHE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 107 " --> pdb=" O LYS C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.664A pdb=" N ALA C 155 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 160 " --> pdb=" O VAL C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 182 removed outlier: 4.143A pdb=" N ARG C 182 " --> pdb=" O ALA C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 189 Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.849A pdb=" N ILE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 257 removed outlier: 3.546A pdb=" N GLU C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 274 removed outlier: 3.909A pdb=" N GLU C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'c' and resid 575 through 580 Processing helix chain 'D' and resid 20 through 28 removed outlier: 3.756A pdb=" N ARG D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS D 51 " --> pdb=" O ASP D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 112 removed outlier: 4.163A pdb=" N PHE D 106 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 107 " --> pdb=" O LYS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 151 through 163 removed outlier: 3.664A pdb=" N ALA D 155 " --> pdb=" O GLU D 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG D 158 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 160 " --> pdb=" O VAL D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 removed outlier: 4.143A pdb=" N ARG D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 Processing helix chain 'D' and resid 201 through 214 Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.849A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 257 removed outlier: 3.547A pdb=" N GLU D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 274 removed outlier: 3.908A pdb=" N GLU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'd' and resid 575 through 580 Processing helix chain 'E' and resid 20 through 28 removed outlier: 3.757A pdb=" N ARG E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 52 removed outlier: 3.567A pdb=" N LYS E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 removed outlier: 4.162A pdb=" N PHE E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 151 through 163 removed outlier: 3.664A pdb=" N ALA E 155 " --> pdb=" O GLU E 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG E 158 " --> pdb=" O ALA E 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE E 160 " --> pdb=" O VAL E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 4.144A pdb=" N ARG E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'E' and resid 201 through 214 Processing helix chain 'E' and resid 227 through 237 removed outlier: 3.850A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 257 removed outlier: 3.546A pdb=" N GLU E 246 " --> pdb=" O GLY E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 274 removed outlier: 3.909A pdb=" N GLU E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) Processing helix chain 'e' and resid 575 through 580 Processing helix chain 'F' and resid 20 through 28 removed outlier: 3.756A pdb=" N ARG F 27 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 4.162A pdb=" N PHE F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS F 107 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 146 through 148 No H-bonds generated for 'chain 'F' and resid 146 through 148' Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.665A pdb=" N ALA F 155 " --> pdb=" O GLU F 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG F 158 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 160 " --> pdb=" O VAL F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 182 removed outlier: 4.143A pdb=" N ARG F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 Processing helix chain 'F' and resid 201 through 214 Processing helix chain 'F' and resid 227 through 237 removed outlier: 3.850A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 257 removed outlier: 3.547A pdb=" N GLU F 246 " --> pdb=" O GLY F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 274 removed outlier: 3.908A pdb=" N GLU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'f' and resid 575 through 580 Processing helix chain 'G' and resid 20 through 28 removed outlier: 3.757A pdb=" N ARG G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS G 51 " --> pdb=" O ASP G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 removed outlier: 4.162A pdb=" N PHE G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 146 through 148 No H-bonds generated for 'chain 'G' and resid 146 through 148' Processing helix chain 'G' and resid 151 through 163 removed outlier: 3.665A pdb=" N ALA G 155 " --> pdb=" O GLU G 152 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE G 160 " --> pdb=" O VAL G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 182 removed outlier: 4.143A pdb=" N ARG G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 Processing helix chain 'G' and resid 201 through 214 Processing helix chain 'G' and resid 227 through 237 removed outlier: 3.850A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 257 removed outlier: 3.547A pdb=" N GLU G 246 " --> pdb=" O GLY G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 274 removed outlier: 3.908A pdb=" N GLU G 274 " --> pdb=" O GLU G 270 " (cutoff:3.500A) Processing helix chain 'g' and resid 575 through 580 Processing helix chain 'H' and resid 20 through 28 removed outlier: 3.757A pdb=" N ARG H 27 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS H 51 " --> pdb=" O ASP H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 112 removed outlier: 4.162A pdb=" N PHE H 106 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS H 107 " --> pdb=" O LYS H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 151 through 163 removed outlier: 3.665A pdb=" N ALA H 155 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG H 158 " --> pdb=" O ALA H 155 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE H 160 " --> pdb=" O VAL H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 182 removed outlier: 4.144A pdb=" N ARG H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 189 Processing helix chain 'H' and resid 201 through 214 Processing helix chain 'H' and resid 227 through 237 removed outlier: 3.850A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 257 removed outlier: 3.546A pdb=" N GLU H 246 " --> pdb=" O GLY H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 274 removed outlier: 3.908A pdb=" N GLU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'h' and resid 575 through 580 Processing helix chain 'I' and resid 20 through 28 removed outlier: 3.756A pdb=" N ARG I 27 " --> pdb=" O ALA I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS I 51 " --> pdb=" O ASP I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 112 removed outlier: 4.163A pdb=" N PHE I 106 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS I 107 " --> pdb=" O LYS I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 133 Processing helix chain 'I' and resid 146 through 148 No H-bonds generated for 'chain 'I' and resid 146 through 148' Processing helix chain 'I' and resid 151 through 163 removed outlier: 3.665A pdb=" N ALA I 155 " --> pdb=" O GLU I 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG I 158 " --> pdb=" O ALA I 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP I 159 " --> pdb=" O ASP I 156 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE I 160 " --> pdb=" O VAL I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 182 removed outlier: 4.144A pdb=" N ARG I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'I' and resid 201 through 214 Processing helix chain 'I' and resid 227 through 237 removed outlier: 3.849A pdb=" N ILE I 232 " --> pdb=" O GLU I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 257 removed outlier: 3.546A pdb=" N GLU I 246 " --> pdb=" O GLY I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 274 removed outlier: 3.909A pdb=" N GLU I 274 " --> pdb=" O GLU I 270 " (cutoff:3.500A) Processing helix chain 'i' and resid 575 through 580 Processing helix chain 'J' and resid 20 through 28 removed outlier: 3.756A pdb=" N ARG J 27 " --> pdb=" O ALA J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS J 51 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 112 removed outlier: 4.162A pdb=" N PHE J 106 " --> pdb=" O PRO J 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS J 107 " --> pdb=" O LYS J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 133 Processing helix chain 'J' and resid 146 through 148 No H-bonds generated for 'chain 'J' and resid 146 through 148' Processing helix chain 'J' and resid 151 through 163 removed outlier: 3.665A pdb=" N ALA J 155 " --> pdb=" O GLU J 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG J 158 " --> pdb=" O ALA J 155 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP J 159 " --> pdb=" O ASP J 156 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE J 160 " --> pdb=" O VAL J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 182 removed outlier: 4.143A pdb=" N ARG J 182 " --> pdb=" O ALA J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 Processing helix chain 'J' and resid 201 through 214 Processing helix chain 'J' and resid 227 through 237 removed outlier: 3.849A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 257 removed outlier: 3.546A pdb=" N GLU J 246 " --> pdb=" O GLY J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 274 removed outlier: 3.909A pdb=" N GLU J 274 " --> pdb=" O GLU J 270 " (cutoff:3.500A) Processing helix chain 'j' and resid 575 through 580 Processing sheet with id= A, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.667A pdb=" N ARG A 57 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE A 196 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 59 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 193 through 196 removed outlier: 6.667A pdb=" N ARG B 57 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE B 196 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 59 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 193 through 196 removed outlier: 6.668A pdb=" N ARG C 57 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE C 196 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C 59 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 193 through 196 removed outlier: 6.668A pdb=" N ARG D 57 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE D 196 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL D 59 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 193 through 196 removed outlier: 6.667A pdb=" N ARG E 57 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE E 196 " --> pdb=" O ARG E 57 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL E 59 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 193 through 196 removed outlier: 6.667A pdb=" N ARG F 57 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE F 196 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL F 59 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 193 through 196 removed outlier: 6.667A pdb=" N ARG G 57 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE G 196 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL G 59 " --> pdb=" O PHE G 196 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 193 through 196 removed outlier: 6.668A pdb=" N ARG H 57 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE H 196 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL H 59 " --> pdb=" O PHE H 196 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 193 through 196 removed outlier: 6.667A pdb=" N ARG I 57 " --> pdb=" O LEU I 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE I 196 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL I 59 " --> pdb=" O PHE I 196 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 193 through 196 removed outlier: 6.667A pdb=" N ARG J 57 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE J 196 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL J 59 " --> pdb=" O PHE J 196 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2610 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 6.30 Time building geometry restraints manager: 9.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3736 1.28 - 1.41: 5774 1.41 - 1.55: 13745 1.55 - 1.68: 92 1.68 - 1.81: 140 Bond restraints: 23487 Sorted by residual: bond pdb=" O3A ANP F 300 " pdb=" PB ANP F 300 " ideal model delta sigma weight residual 1.700 1.506 0.194 2.00e-02 2.50e+03 9.43e+01 bond pdb=" O3A ANP E 300 " pdb=" PB ANP E 300 " ideal model delta sigma weight residual 1.700 1.506 0.194 2.00e-02 2.50e+03 9.41e+01 bond pdb=" O3A ANP G 300 " pdb=" PB ANP G 300 " ideal model delta sigma weight residual 1.700 1.538 0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" O3A ANP H 300 " pdb=" PB ANP H 300 " ideal model delta sigma weight residual 1.700 1.538 0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" O3A ANP J 300 " pdb=" PB ANP J 300 " ideal model delta sigma weight residual 1.700 1.540 0.160 2.00e-02 2.50e+03 6.43e+01 ... (remaining 23482 not shown) Histogram of bond angle deviations from ideal: 86.12 - 96.36: 5 96.36 - 106.60: 1057 106.60 - 116.83: 15364 116.83 - 127.07: 15043 127.07 - 137.31: 330 Bond angle restraints: 31799 Sorted by residual: angle pdb=" N LYS I 265 " pdb=" CA LYS I 265 " pdb=" C LYS I 265 " ideal model delta sigma weight residual 111.07 120.80 -9.73 1.07e+00 8.73e-01 8.27e+01 angle pdb=" N LYS A 265 " pdb=" CA LYS A 265 " pdb=" C LYS A 265 " ideal model delta sigma weight residual 111.07 120.79 -9.72 1.07e+00 8.73e-01 8.25e+01 angle pdb=" N LYS E 265 " pdb=" CA LYS E 265 " pdb=" C LYS E 265 " ideal model delta sigma weight residual 111.07 120.79 -9.72 1.07e+00 8.73e-01 8.25e+01 angle pdb=" N LYS C 265 " pdb=" CA LYS C 265 " pdb=" C LYS C 265 " ideal model delta sigma weight residual 111.07 120.78 -9.71 1.07e+00 8.73e-01 8.23e+01 angle pdb=" N LYS G 265 " pdb=" CA LYS G 265 " pdb=" C LYS G 265 " ideal model delta sigma weight residual 111.07 120.78 -9.71 1.07e+00 8.73e-01 8.23e+01 ... (remaining 31794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 13859 34.93 - 69.85: 344 69.85 - 104.78: 20 104.78 - 139.71: 3 139.71 - 174.63: 10 Dihedral angle restraints: 14236 sinusoidal: 6376 harmonic: 7860 Sorted by residual: dihedral pdb=" C TYR h 582 " pdb=" N TYR h 582 " pdb=" CA TYR h 582 " pdb=" CB TYR h 582 " ideal model delta harmonic sigma weight residual -122.60 -137.09 14.49 0 2.50e+00 1.60e-01 3.36e+01 dihedral pdb=" C TYR a 582 " pdb=" N TYR a 582 " pdb=" CA TYR a 582 " pdb=" CB TYR a 582 " ideal model delta harmonic sigma weight residual -122.60 -137.09 14.49 0 2.50e+00 1.60e-01 3.36e+01 dihedral pdb=" C TYR e 582 " pdb=" N TYR e 582 " pdb=" CA TYR e 582 " pdb=" CB TYR e 582 " ideal model delta harmonic sigma weight residual -122.60 -137.08 14.48 0 2.50e+00 1.60e-01 3.36e+01 ... (remaining 14233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 3065 0.131 - 0.262: 409 0.262 - 0.394: 45 0.394 - 0.525: 2 0.525 - 0.656: 10 Chirality restraints: 3531 Sorted by residual: chirality pdb=" CA TYR a 582 " pdb=" N TYR a 582 " pdb=" C TYR a 582 " pdb=" CB TYR a 582 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA TYR h 582 " pdb=" N TYR h 582 " pdb=" C TYR h 582 " pdb=" CB TYR h 582 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA TYR d 582 " pdb=" N TYR d 582 " pdb=" C TYR d 582 " pdb=" CB TYR d 582 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.07e+01 ... (remaining 3528 not shown) Planarity restraints: 3858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 255 " -0.030 2.00e-02 2.50e+03 5.94e-02 3.53e+01 pdb=" C SER J 255 " 0.103 2.00e-02 2.50e+03 pdb=" O SER J 255 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU J 256 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 255 " 0.030 2.00e-02 2.50e+03 5.94e-02 3.53e+01 pdb=" C SER A 255 " -0.103 2.00e-02 2.50e+03 pdb=" O SER A 255 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU A 256 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 255 " -0.030 2.00e-02 2.50e+03 5.94e-02 3.52e+01 pdb=" C SER B 255 " 0.103 2.00e-02 2.50e+03 pdb=" O SER B 255 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU B 256 " -0.036 2.00e-02 2.50e+03 ... (remaining 3855 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 15 2.04 - 2.75: 3822 2.75 - 3.47: 30987 3.47 - 4.18: 53369 4.18 - 4.90: 92165 Nonbonded interactions: 180358 Sorted by model distance: nonbonded pdb=" O1G ANP C 300 " pdb="MG MG C 301 " model vdw 1.320 2.170 nonbonded pdb=" O1G ANP G 300 " pdb="MG MG G 301 " model vdw 1.413 2.170 nonbonded pdb=" O1G ANP D 300 " pdb="MG MG D 301 " model vdw 1.557 2.170 nonbonded pdb=" O1G ANP A 300 " pdb="MG MG A 301 " model vdw 1.564 2.170 nonbonded pdb=" O1G ANP J 300 " pdb="MG MG J 301 " model vdw 1.567 2.170 ... (remaining 180353 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' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'a' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'b' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'c' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'd' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'e' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'f' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'g' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = chain 'h' selection = (chain 'i' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'j' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) } 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: 6 Type Number sf(0) Gaussians P 68 5.49 5 Mg 10 5.21 5 S 80 5.16 5 C 14367 2.51 5 N 4153 2.21 5 O 4368 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 5.750 Check model and map are aligned: 0.300 Process input model: 56.740 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 0.020 0.194 23487 Z= 1.324 Angle : 1.877 26.945 31799 Z= 1.297 Chirality : 0.100 0.656 3531 Planarity : 0.010 0.059 3858 Dihedral : 14.272 174.635 9156 Min Nonbonded Distance : 1.320 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.39 % 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: -0.21 (0.15), residues: 2670 helix: -0.55 (0.11), residues: 1560 sheet: 2.55 (0.30), residues: 230 loop : 0.25 (0.20), residues: 880 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 718 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 718 average time/residue: 0.4923 time to fit residues: 485.9892 Evaluate side-chains 373 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 2.585 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 237 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN I 37 GLN I 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 23487 Z= 0.205 Angle : 0.559 5.989 31799 Z= 0.298 Chirality : 0.041 0.143 3531 Planarity : 0.005 0.031 3858 Dihedral : 15.163 176.285 3438 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 1.98 % 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: 1.16 (0.16), residues: 2670 helix: 1.03 (0.13), residues: 1580 sheet: 2.34 (0.31), residues: 230 loop : 0.01 (0.20), residues: 860 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 383 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 27 residues processed: 412 average time/residue: 0.4278 time to fit residues: 254.5984 Evaluate side-chains 337 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 310 time to evaluate : 2.905 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2445 time to fit residues: 15.7523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN E 269 GLN F 206 ASN g 577 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 23487 Z= 0.417 Angle : 0.682 7.588 31799 Z= 0.351 Chirality : 0.046 0.182 3531 Planarity : 0.005 0.040 3858 Dihedral : 15.317 179.867 3438 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.94 % 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: 0.54 (0.16), residues: 2670 helix: 0.68 (0.13), residues: 1580 sheet: 1.75 (0.26), residues: 280 loop : -0.61 (0.21), residues: 810 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 342 time to evaluate : 2.761 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 23 residues processed: 371 average time/residue: 0.4570 time to fit residues: 247.2956 Evaluate side-chains 307 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 284 time to evaluate : 2.678 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2722 time to fit residues: 14.3654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 253 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 98 GLN g 577 GLN H 213 GLN H 223 ASN I 206 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 23487 Z= 0.160 Angle : 0.490 6.824 31799 Z= 0.257 Chirality : 0.039 0.157 3531 Planarity : 0.004 0.031 3858 Dihedral : 15.189 179.981 3438 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.72 % 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: 1.01 (0.16), residues: 2670 helix: 1.09 (0.13), residues: 1590 sheet: 1.66 (0.26), residues: 280 loop : -0.41 (0.21), residues: 800 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 326 time to evaluate : 2.757 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 338 average time/residue: 0.4217 time to fit residues: 209.0059 Evaluate side-chains 283 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 274 time to evaluate : 2.764 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1980 time to fit residues: 7.1847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 188 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 227 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN G 269 GLN g 577 GLN H 223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 23487 Z= 0.219 Angle : 0.522 6.656 31799 Z= 0.272 Chirality : 0.040 0.167 3531 Planarity : 0.004 0.032 3858 Dihedral : 15.137 179.872 3438 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.27 % 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 (0.16), residues: 2670 helix: 1.07 (0.13), residues: 1590 sheet: 1.53 (0.26), residues: 280 loop : -0.49 (0.21), residues: 800 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 292 time to evaluate : 2.988 Fit side-chains outliers start: 30 outliers final: 20 residues processed: 310 average time/residue: 0.4160 time to fit residues: 189.8017 Evaluate side-chains 296 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 276 time to evaluate : 2.675 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2433 time to fit residues: 11.9843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 253 optimal weight: 1.9990 chunk 210 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 133 optimal weight: 0.0270 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 269 GLN g 577 GLN H 213 GLN I 206 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 23487 Z= 0.142 Angle : 0.469 7.959 31799 Z= 0.248 Chirality : 0.039 0.168 3531 Planarity : 0.003 0.030 3858 Dihedral : 15.049 179.704 3438 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.16), residues: 2670 helix: 1.22 (0.13), residues: 1600 sheet: 1.53 (0.26), residues: 280 loop : -0.32 (0.22), residues: 790 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 299 time to evaluate : 3.511 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 303 average time/residue: 0.4133 time to fit residues: 186.7030 Evaluate side-chains 285 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 275 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2259 time to fit residues: 8.4052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 185 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 213 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 252 optimal weight: 2.9990 chunk 158 optimal weight: 0.0570 chunk 153 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN G 269 GLN g 577 GLN H 213 GLN I 206 ASN J 223 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 23487 Z= 0.133 Angle : 0.459 7.432 31799 Z= 0.241 Chirality : 0.038 0.175 3531 Planarity : 0.003 0.030 3858 Dihedral : 14.975 178.989 3438 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.38 % 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: 1.35 (0.16), residues: 2670 helix: 1.41 (0.13), residues: 1590 sheet: 1.55 (0.25), residues: 280 loop : -0.27 (0.22), residues: 800 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 302 time to evaluate : 2.744 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 307 average time/residue: 0.3890 time to fit residues: 179.1850 Evaluate side-chains 285 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 281 time to evaluate : 2.686 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2024 time to fit residues: 5.2354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 3.9990 chunk 100 optimal weight: 0.0670 chunk 150 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 172 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 198 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 269 GLN g 577 GLN I 206 ASN J 223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 23487 Z= 0.127 Angle : 0.451 7.708 31799 Z= 0.238 Chirality : 0.038 0.184 3531 Planarity : 0.003 0.030 3858 Dihedral : 14.923 178.217 3438 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.16), residues: 2670 helix: 1.47 (0.13), residues: 1600 sheet: 1.55 (0.25), residues: 280 loop : -0.30 (0.22), residues: 790 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 308 time to evaluate : 3.429 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 309 average time/residue: 0.4322 time to fit residues: 198.8254 Evaluate side-chains 297 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 291 time to evaluate : 2.851 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2194 time to fit residues: 6.2845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 0.8980 chunk 241 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 184 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 269 GLN g 577 GLN J 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 23487 Z= 0.158 Angle : 0.479 7.602 31799 Z= 0.250 Chirality : 0.039 0.195 3531 Planarity : 0.003 0.030 3858 Dihedral : 14.925 177.922 3438 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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: 1.35 (0.16), residues: 2670 helix: 1.47 (0.13), residues: 1590 sheet: 1.47 (0.26), residues: 280 loop : -0.40 (0.22), residues: 800 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 290 time to evaluate : 3.049 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 294 average time/residue: 0.4304 time to fit residues: 189.3583 Evaluate side-chains 289 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 282 time to evaluate : 2.947 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2372 time to fit residues: 7.1764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 0.9990 chunk 248 optimal weight: 0.4980 chunk 151 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 172 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 240 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 21 optimal weight: 0.1980 chunk 160 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 269 GLN G 269 GLN g 577 GLN J 223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 23487 Z= 0.136 Angle : 0.469 9.311 31799 Z= 0.245 Chirality : 0.039 0.189 3531 Planarity : 0.003 0.028 3858 Dihedral : 14.910 177.425 3438 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.04 % 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: 1.46 (0.16), residues: 2670 helix: 1.56 (0.13), residues: 1590 sheet: 1.48 (0.25), residues: 280 loop : -0.36 (0.22), residues: 800 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 291 time to evaluate : 3.076 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 291 average time/residue: 0.3933 time to fit residues: 171.5886 Evaluate side-chains 288 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 287 time to evaluate : 2.729 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2120 time to fit residues: 4.0454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 0.8980 chunk 221 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 208 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 577 GLN H 213 GLN J 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.141068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.108134 restraints weight = 29815.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.109504 restraints weight = 32959.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.110098 restraints weight = 26919.915| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 23487 Z= 0.147 Angle : 0.476 9.819 31799 Z= 0.249 Chirality : 0.039 0.191 3531 Planarity : 0.003 0.060 3858 Dihedral : 14.918 179.034 3438 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.25 % 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: 1.44 (0.16), residues: 2670 helix: 1.55 (0.13), residues: 1590 sheet: 1.45 (0.26), residues: 280 loop : -0.35 (0.22), residues: 800 =============================================================================== Job complete usr+sys time: 4430.31 seconds wall clock time: 81 minutes 13.24 seconds (4873.24 seconds total)