Starting phenix.real_space_refine (version: dev) on Mon Feb 20 22:55:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5n_20650/02_2023/6u5n_20650.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5n_20650/02_2023/6u5n_20650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5n_20650/02_2023/6u5n_20650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5n_20650/02_2023/6u5n_20650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5n_20650/02_2023/6u5n_20650.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5n_20650/02_2023/6u5n_20650.pdb" } resolution = 3.2 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= 0.006 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 ARG 116": "NH1" <-> "NH2" Residue "A ASP 169": "OD1" <-> "OD2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E ASP 169": "OD1" <-> "OD2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "E ASP 226": "OD1" <-> "OD2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 244": "OD1" <-> "OD2" Residue "E ASP 254": "OD1" <-> "OD2" Residue "E ARG 262": "NH1" <-> "NH2" Residue "E ASP 282": "OD1" <-> "OD2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "F ARG 116": "NH1" <-> "NH2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F ASP 226": "OD1" <-> "OD2" Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 244": "OD1" <-> "OD2" Residue "F ASP 245": "OD1" <-> "OD2" Residue "F ARG 262": "NH1" <-> "NH2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ASP 169": "OD1" <-> "OD2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 116": "NH1" <-> "NH2" Residue "G PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 145": "OD1" <-> "OD2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "G ASP 226": "OD1" <-> "OD2" Residue "G PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G ASP 254": "OD1" <-> "OD2" Residue "G ARG 262": "NH1" <-> "NH2" Residue "G ASP 282": "OD1" <-> "OD2" Residue "G GLU 325": "OE1" <-> "OE2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "H ARG 116": "NH1" <-> "NH2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "H ASP 226": "OD1" <-> "OD2" Residue "H PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 244": "OD1" <-> "OD2" Residue "H ASP 245": "OD1" <-> "OD2" Residue "H ARG 262": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13262 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1662 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Conformer: "B" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 bond proxies already assigned to first conformer: 1660 Chain: "E" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1654 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1652 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1647 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 1662 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Conformer: "B" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 bond proxies already assigned to first conformer: 1660 Chain: "G" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1654 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1652 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "H" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1647 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 241 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 241 " occ=0.50 residue: pdb=" N AARG C 241 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 241 " occ=0.50 Time building chain proxies: 9.47, per 1000 atoms: 0.71 Number of scatterers: 13262 At special positions: 0 Unit cell: (141.384, 137, 69.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 24 19.99 S 56 16.00 O 2506 8.00 N 2374 7.00 C 8302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.69 Conformation dependent library (CDL) restraints added in 2.4 seconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3268 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 16 sheets defined 45.9% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 155 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.623A pdb=" N ALA A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.530A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'E' and resid 124 through 133 Processing helix chain 'E' and resid 148 through 155 removed outlier: 3.521A pdb=" N SER E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.566A pdb=" N ALA E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.659A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.617A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.586A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.799A pdb=" N LEU E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 289 removed outlier: 3.594A pdb=" N VAL E 288 " --> pdb=" O ASP E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 334 Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 148 through 155 Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.512A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.582A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.555A pdb=" N VAL B 288 " --> pdb=" O ASP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 148 through 155 removed outlier: 3.857A pdb=" N SER F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.637A pdb=" N ALA F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.627A pdb=" N ILE F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.559A pdb=" N GLY F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 241 Processing helix chain 'F' and resid 246 through 256 removed outlier: 3.596A pdb=" N MET F 250 " --> pdb=" O GLY F 246 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU F 256 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.689A pdb=" N ASP F 284 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.565A pdb=" N VAL F 288 " --> pdb=" O ASP F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 334 Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.623A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.530A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 242 Processing helix chain 'C' and resid 246 through 256 Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 323 through 334 Processing helix chain 'G' and resid 124 through 133 Processing helix chain 'G' and resid 148 through 155 removed outlier: 3.521A pdb=" N SER G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 173 removed outlier: 3.566A pdb=" N ALA G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.659A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.616A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 241 removed outlier: 3.586A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 256 removed outlier: 3.799A pdb=" N LEU G 256 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 289 removed outlier: 3.594A pdb=" N VAL G 288 " --> pdb=" O ASP G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 334 Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 148 through 155 Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.512A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.582A pdb=" N ILE D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 256 Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.555A pdb=" N VAL D 288 " --> pdb=" O ASP D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 148 through 155 removed outlier: 3.857A pdb=" N SER H 155 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 173 removed outlier: 3.637A pdb=" N ALA H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 removed outlier: 3.628A pdb=" N ILE H 201 " --> pdb=" O GLY H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 224 removed outlier: 3.558A pdb=" N GLY H 224 " --> pdb=" O LEU H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 241 Processing helix chain 'H' and resid 246 through 256 removed outlier: 3.596A pdb=" N MET H 250 " --> pdb=" O GLY H 246 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU H 256 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.689A pdb=" N ASP H 284 " --> pdb=" O VAL H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.566A pdb=" N VAL H 288 " --> pdb=" O ASP H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.501A pdb=" N VAL A 139 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL A 160 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL A 141 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 207 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE A 229 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA A 209 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 7.220A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.552A pdb=" N ALA E 143 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL E 118 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU E 142 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE E 120 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL E 181 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLU E 210 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL E 183 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE E 207 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE E 229 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA E 209 " --> pdb=" O ILE E 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 263 through 268 removed outlier: 7.515A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU E 301 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.402A pdb=" N VAL B 139 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS B 117 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA B 180 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE B 208 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 181 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N GLU B 210 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL B 183 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 263 through 268 removed outlier: 7.185A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.482A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL F 118 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU F 142 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE F 120 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N HIS F 117 " --> pdb=" O ALA F 178 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA F 180 " --> pdb=" O HIS F 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 263 through 268 removed outlier: 7.258A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.500A pdb=" N VAL C 139 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL C 160 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL C 141 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE C 207 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE C 229 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA C 209 " --> pdb=" O ILE C 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 263 through 268 removed outlier: 7.220A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 158 through 161 removed outlier: 3.551A pdb=" N ALA G 143 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL G 118 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU G 142 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE G 120 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL G 181 " --> pdb=" O ILE G 208 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU G 210 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL G 183 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE G 207 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE G 229 " --> pdb=" O ILE G 207 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA G 209 " --> pdb=" O ILE G 229 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 263 through 268 removed outlier: 7.515A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU G 301 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.401A pdb=" N VAL D 139 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS D 117 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA D 180 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE D 208 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL D 181 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLU D 210 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL D 183 " --> pdb=" O GLU D 210 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 263 through 268 removed outlier: 7.185A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.482A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL H 118 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU H 142 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE H 120 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N HIS H 117 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA H 180 " --> pdb=" O HIS H 117 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 7.258A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4523 1.34 - 1.45: 1252 1.45 - 1.57: 7537 1.57 - 1.69: 0 1.69 - 1.80: 88 Bond restraints: 13400 Sorted by residual: bond pdb=" N PRO C 324 " pdb=" CD PRO C 324 " ideal model delta sigma weight residual 1.473 1.408 0.065 1.40e-02 5.10e+03 2.15e+01 bond pdb=" N PRO A 324 " pdb=" CD PRO A 324 " ideal model delta sigma weight residual 1.473 1.408 0.065 1.40e-02 5.10e+03 2.15e+01 bond pdb=" CA GLU B 212 " pdb=" C GLU B 212 " ideal model delta sigma weight residual 1.524 1.556 -0.033 1.26e-02 6.30e+03 6.69e+00 bond pdb=" CA GLU D 212 " pdb=" C GLU D 212 " ideal model delta sigma weight residual 1.524 1.556 -0.032 1.26e-02 6.30e+03 6.63e+00 bond pdb=" CG1 ILE C 195 " pdb=" CD1 ILE C 195 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.03e+00 ... (remaining 13395 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.29: 256 106.29 - 113.22: 7629 113.22 - 120.15: 4709 120.15 - 127.09: 5466 127.09 - 134.02: 92 Bond angle restraints: 18152 Sorted by residual: angle pdb=" N ARG D 298 " pdb=" CA ARG D 298 " pdb=" C ARG D 298 " ideal model delta sigma weight residual 109.07 118.60 -9.53 1.61e+00 3.86e-01 3.50e+01 angle pdb=" N ARG B 298 " pdb=" CA ARG B 298 " pdb=" C ARG B 298 " ideal model delta sigma weight residual 109.07 118.56 -9.49 1.61e+00 3.86e-01 3.47e+01 angle pdb=" N PRO A 324 " pdb=" CA PRO A 324 " pdb=" C PRO A 324 " ideal model delta sigma weight residual 113.65 119.91 -6.26 1.35e+00 5.49e-01 2.15e+01 angle pdb=" N PRO C 324 " pdb=" CA PRO C 324 " pdb=" C PRO C 324 " ideal model delta sigma weight residual 113.65 119.91 -6.26 1.35e+00 5.49e-01 2.15e+01 angle pdb=" N GLU D 212 " pdb=" CA GLU D 212 " pdb=" C GLU D 212 " ideal model delta sigma weight residual 111.14 115.20 -4.06 1.08e+00 8.57e-01 1.42e+01 ... (remaining 18147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 7345 17.29 - 34.58: 679 34.58 - 51.87: 106 51.87 - 69.16: 36 69.16 - 86.45: 14 Dihedral angle restraints: 8180 sinusoidal: 3108 harmonic: 5072 Sorted by residual: dihedral pdb=" CA ASP G 284 " pdb=" C ASP G 284 " pdb=" N ILE G 285 " pdb=" CA ILE G 285 " ideal model delta harmonic sigma weight residual -180.00 -162.03 -17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP E 284 " pdb=" C ASP E 284 " pdb=" N ILE E 285 " pdb=" CA ILE E 285 " ideal model delta harmonic sigma weight residual -180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP G 245 " pdb=" C ASP G 245 " pdb=" N GLY G 246 " pdb=" CA GLY G 246 " ideal model delta harmonic sigma weight residual -180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 8177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1456 0.047 - 0.095: 470 0.095 - 0.142: 223 0.142 - 0.189: 19 0.189 - 0.237: 6 Chirality restraints: 2174 Sorted by residual: chirality pdb=" CA PRO C 324 " pdb=" N PRO C 324 " pdb=" C PRO C 324 " pdb=" CB PRO C 324 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO A 324 " pdb=" N PRO A 324 " pdb=" C PRO A 324 " pdb=" CB PRO A 324 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB VAL B 278 " pdb=" CA VAL B 278 " pdb=" CG1 VAL B 278 " pdb=" CG2 VAL B 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2171 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 323 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO D 324 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 324 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 324 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 323 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO B 324 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 324 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 324 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 267 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO D 268 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 268 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 268 " -0.027 5.00e-02 4.00e+02 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 83 2.51 - 3.10: 8642 3.10 - 3.70: 19374 3.70 - 4.30: 28296 4.30 - 4.90: 49370 Nonbonded interactions: 105765 Sorted by model distance: nonbonded pdb=" O ASP C 244 " pdb=" OD1 ASP C 245 " model vdw 1.907 3.040 nonbonded pdb=" O ASP A 244 " pdb=" OD1 ASP A 245 " model vdw 1.907 3.040 nonbonded pdb=" O GLY E 290 " pdb="CA CA E 402 " model vdw 2.034 2.510 nonbonded pdb=" O GLY G 290 " pdb="CA CA G 402 " model vdw 2.034 2.510 nonbonded pdb=" O GLY C 290 " pdb="CA CA C 403 " model vdw 2.058 2.510 ... (remaining 105760 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 or (resid 135 and (name N or name CA o \ r name C or name O or name CB )) or resid 136 through 137 or (resid 138 and (nam \ e N or name CA or name C or name O or name CB )) or resid 139 through 143 or (re \ sid 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 170 or (resid 171 and (name N or name CA or name C or name \ O or name CB )) or resid 172 through 240 or resid 242 through 244 or (resid 245 \ and (name N or name CA or name C or name O or name CB )) or resid 246 through 2 \ 53 or (resid 254 and (name N or name CA or name C or name O or name CB )) or res \ id 255 through 262 or (resid 263 and (name N or name CA or name C or name O or n \ ame CB )) or resid 264 through 273 or (resid 274 and (name N or name CA or name \ C or name O or name CB )) or resid 275 through 283 or (resid 284 and (name N or \ name CA or name C or name O or name CB )) or resid 285 through 286 or (resid 287 \ and (name N or name CA or name C or name O or name CB )) or resid 288 through 2 \ 97 or (resid 298 and (name N or name CA or name C or name O or name CB )) or res \ id 299 through 312 or (resid 313 through 314 and (name N or name CA or name C or \ name O or name CB )) or resid 315 through 324 or (resid 325 and (name N or name \ CA or name C or name O or name CB )) or resid 326 through 327 or (resid 328 and \ (name N or name CA or name C or name O or name CB )) or resid 329 through 336 o \ r resid 401 through 402)) selection = (chain 'B' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 137 or (resid 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 throug \ h 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) or \ resid 148 or (resid 149 through 150 and (name N or name CA or name C or name O o \ r name CB )) or resid 151 through 153 or (resid 154 and (name N or name CA or na \ me C or name O or name CB )) or resid 155 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 240 or resid 2 \ 42 through 253 or (resid 254 and (name N or name CA or name C or name O or name \ CB )) or resid 255 through 270 or (resid 271 and (name N or name CA or name C or \ name O or name CB )) or resid 272 through 273 or (resid 274 and (name N or name \ CA or name C or name O or name CB )) or resid 275 or (resid 276 and (name N or \ name CA or name C or name O or name CB )) or resid 277 through 280 or (resid 281 \ through 284 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 85 through 297 or (resid 298 and (name N or name CA or name C or name O or name \ CB )) or resid 299 through 312 or (resid 313 through 314 and (name N or name CA \ or name C or name O or name CB )) or resid 315 through 336 or resid 401 through \ 402)) selection = (chain 'C' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 or (resid 135 and (name N or name CA o \ r name C or name O or name CB )) or resid 136 through 137 or (resid 138 and (nam \ e N or name CA or name C or name O or name CB )) or resid 139 through 143 or (re \ sid 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 170 or (resid 171 and (name N or name CA or name C or name \ O or name CB )) or resid 172 through 240 or resid 242 through 244 or (resid 245 \ and (name N or name CA or name C or name O or name CB )) or resid 246 through 2 \ 53 or (resid 254 and (name N or name CA or name C or name O or name CB )) or res \ id 255 through 262 or (resid 263 and (name N or name CA or name C or name O or n \ ame CB )) or resid 264 through 273 or (resid 274 and (name N or name CA or name \ C or name O or name CB )) or resid 275 through 283 or (resid 284 and (name N or \ name CA or name C or name O or name CB )) or resid 285 through 286 or (resid 287 \ and (name N or name CA or name C or name O or name CB )) or resid 288 through 2 \ 97 or (resid 298 and (name N or name CA or name C or name O or name CB )) or res \ id 299 through 312 or (resid 313 through 314 and (name N or name CA or name C or \ name O or name CB )) or resid 315 through 324 or (resid 325 and (name N or name \ CA or name C or name O or name CB )) or resid 326 through 327 or (resid 328 and \ (name N or name CA or name C or name O or name CB )) or resid 329 through 336 o \ r resid 401 through 402)) selection = (chain 'D' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 137 or (resid 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 throug \ h 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) or \ resid 148 or (resid 149 through 150 and (name N or name CA or name C or name O o \ r name CB )) or resid 151 through 153 or (resid 154 and (name N or name CA or na \ me C or name O or name CB )) or resid 155 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 240 or resid 2 \ 42 through 253 or (resid 254 and (name N or name CA or name C or name O or name \ CB )) or resid 255 through 270 or (resid 271 and (name N or name CA or name C or \ name O or name CB )) or resid 272 through 273 or (resid 274 and (name N or name \ CA or name C or name O or name CB )) or resid 275 or (resid 276 and (name N or \ name CA or name C or name O or name CB )) or resid 277 through 280 or (resid 281 \ through 284 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 85 through 297 or (resid 298 and (name N or name CA or name C or name O or name \ CB )) or resid 299 through 312 or (resid 313 through 314 and (name N or name CA \ or name C or name O or name CB )) or resid 315 through 336 or resid 401 through \ 402)) selection = (chain 'E' and (resid 115 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 148 or (resid 149 through 150 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 15 \ 3 or (resid 154 and (name N or name CA or name C or name O or name CB )) or resi \ d 155 through 170 or (resid 171 and (name N or name CA or name C or name O or na \ me CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C \ or name O or name CB )) or resid 204 through 217 or (resid 218 and (name N or n \ ame CA or name C or name O or name CB )) or resid 219 through 240 or resid 242 t \ hrough 243 or (resid 244 through 245 and (name N or name CA or name C or name O \ or name CB )) or resid 246 through 253 or (resid 254 and (name N or name CA or n \ ame C or name O or name CB )) or resid 255 through 262 or (resid 263 and (name N \ or name CA or name C or name O or name CB )) or resid 264 through 281 or (resid \ 282 through 284 and (name N or name CA or name C or name O or name CB )) or res \ id 285 through 300 or (resid 301 and (name N or name CA or name C or name O or n \ ame CB )) or resid 302 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 312 or (resid 313 through 314 and \ (name N or name CA or name C or name O or name CB )) or resid 315 through 324 o \ r (resid 325 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 26 through 336 or resid 401 through 402)) selection = (chain 'F' and (resid 115 through 143 or (resid 144 and (name N or name CA or na \ me C or name O or name CB )) or resid 145 or (resid 146 through 147 and (name N \ or name CA or name C or name O or name CB )) or resid 148 or (resid 149 through \ 150 and (name N or name CA or name C or name O or name CB )) or resid 151 throug \ h 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) or \ resid 155 through 217 or (resid 218 and (name N or name CA or name C or name O o \ r name CB )) or resid 219 through 240 or resid 242 through 243 or (resid 244 thr \ ough 245 and (name N or name CA or name C or name O or name CB )) or resid 246 t \ hrough 280 or (resid 281 through 284 and (name N or name CA or name C or name O \ or name CB )) or resid 285 through 286 or (resid 287 and (name N or name CA or n \ ame C or name O or name CB )) or resid 288 through 297 or (resid 298 and (name N \ or name CA or name C or name O or name CB )) or resid 299 or (resid 300 through \ 301 and (name N or name CA or name C or name O or name CB )) or resid 302 throu \ gh 307 or (resid 308 through 309 and (name N or name CA or name C or name O or n \ ame CB )) or resid 310 through 324 or (resid 325 and (name N or name CA or name \ C or name O or name CB )) or resid 326 through 327 or (resid 328 and (name N or \ name CA or name C or name O or name CB )) or resid 329 through 336 or resid 401 \ through 402)) selection = (chain 'G' and (resid 115 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 148 or (resid 149 through 150 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 15 \ 3 or (resid 154 and (name N or name CA or name C or name O or name CB )) or resi \ d 155 through 170 or (resid 171 and (name N or name CA or name C or name O or na \ me CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C \ or name O or name CB )) or resid 204 through 217 or (resid 218 and (name N or n \ ame CA or name C or name O or name CB )) or resid 219 through 240 or resid 242 t \ hrough 243 or (resid 244 through 245 and (name N or name CA or name C or name O \ or name CB )) or resid 246 through 253 or (resid 254 and (name N or name CA or n \ ame C or name O or name CB )) or resid 255 through 262 or (resid 263 and (name N \ or name CA or name C or name O or name CB )) or resid 264 through 281 or (resid \ 282 through 284 and (name N or name CA or name C or name O or name CB )) or res \ id 285 through 300 or (resid 301 and (name N or name CA or name C or name O or n \ ame CB )) or resid 302 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 312 or (resid 313 through 314 and \ (name N or name CA or name C or name O or name CB )) or resid 315 through 324 o \ r (resid 325 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 26 through 336 or resid 401 through 402)) selection = (chain 'H' and (resid 115 through 143 or (resid 144 and (name N or name CA or na \ me C or name O or name CB )) or resid 145 or (resid 146 through 147 and (name N \ or name CA or name C or name O or name CB )) or resid 148 or (resid 149 through \ 150 and (name N or name CA or name C or name O or name CB )) or resid 151 throug \ h 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) or \ resid 155 through 217 or (resid 218 and (name N or name CA or name C or name O o \ r name CB )) or resid 219 through 240 or resid 242 through 243 or (resid 244 thr \ ough 245 and (name N or name CA or name C or name O or name CB )) or resid 246 t \ hrough 280 or (resid 281 through 284 and (name N or name CA or name C or name O \ or name CB )) or resid 285 through 286 or (resid 287 and (name N or name CA or n \ ame C or name O or name CB )) or resid 288 through 297 or (resid 298 and (name N \ or name CA or name C or name O or name CB )) or resid 299 or (resid 300 through \ 301 and (name N or name CA or name C or name O or name CB )) or resid 302 throu \ gh 307 or (resid 308 through 309 and (name N or name CA or name C or name O or n \ ame CB )) or resid 310 through 324 or (resid 325 and (name N or name CA or name \ C or name O or name CB )) or resid 326 through 327 or (resid 328 and (name N or \ name CA or name C or name O or name CB )) or resid 329 through 336 or resid 401 \ through 402)) } 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: 5 Type Number sf(0) Gaussians Ca 24 9.91 5 S 56 5.16 5 C 8302 2.51 5 N 2374 2.21 5 O 2506 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=0.50 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: 0.660 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: 4.050 Check model and map are aligned: 0.210 Process input model: 37.120 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 13400 Z= 0.394 Angle : 0.759 9.527 18152 Z= 0.466 Chirality : 0.055 0.237 2174 Planarity : 0.005 0.055 2360 Dihedral : 14.130 86.454 4912 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 0.15 % 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: -3.09 (0.16), residues: 1766 helix: -2.90 (0.12), residues: 838 sheet: 1.11 (0.27), residues: 304 loop : -2.23 (0.18), residues: 624 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.3868 time to fit residues: 158.9541 Evaluate side-chains 246 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.519 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 159 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8445 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 13400 Z= 0.159 Angle : 0.428 4.106 18152 Z= 0.234 Chirality : 0.046 0.138 2174 Planarity : 0.004 0.036 2360 Dihedral : 3.607 13.729 1942 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 1.09 % 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 (0.18), residues: 1766 helix: -1.06 (0.17), residues: 846 sheet: 1.15 (0.27), residues: 304 loop : -1.54 (0.20), residues: 616 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 257 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 264 average time/residue: 0.3444 time to fit residues: 120.8362 Evaluate side-chains 228 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 221 time to evaluate : 1.506 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1254 time to fit residues: 3.8295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 158 optimal weight: 0.0070 chunk 54 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN C 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13400 Z= 0.199 Angle : 0.416 3.604 18152 Z= 0.224 Chirality : 0.046 0.143 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.405 14.363 1942 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 1.16 % 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: -0.60 (0.19), residues: 1766 helix: -0.36 (0.18), residues: 846 sheet: 1.13 (0.27), residues: 304 loop : -1.06 (0.21), residues: 616 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 236 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 246 average time/residue: 0.3176 time to fit residues: 106.3113 Evaluate side-chains 230 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 221 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1210 time to fit residues: 4.3485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN C 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 13400 Z= 0.282 Angle : 0.447 3.881 18152 Z= 0.238 Chirality : 0.048 0.143 2174 Planarity : 0.004 0.035 2360 Dihedral : 3.490 16.150 1942 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.87 % 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: -0.30 (0.19), residues: 1766 helix: -0.15 (0.18), residues: 846 sheet: 1.14 (0.27), residues: 304 loop : -0.78 (0.23), residues: 616 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 224 time to evaluate : 1.683 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 230 average time/residue: 0.3442 time to fit residues: 106.1842 Evaluate side-chains 216 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 209 time to evaluate : 1.571 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1169 time to fit residues: 3.7585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 70 optimal weight: 0.3980 chunk 145 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 13400 Z= 0.197 Angle : 0.418 4.402 18152 Z= 0.224 Chirality : 0.046 0.138 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.398 14.675 1942 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.80 % 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: 0.03 (0.19), residues: 1766 helix: 0.14 (0.18), residues: 846 sheet: 1.23 (0.28), residues: 304 loop : -0.60 (0.23), residues: 616 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 221 time to evaluate : 1.518 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 227 average time/residue: 0.3439 time to fit residues: 103.7885 Evaluate side-chains 207 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 202 time to evaluate : 1.599 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1251 time to fit residues: 3.3654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 1.9990 chunk 33 optimal weight: 0.0020 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 170 optimal weight: 0.1980 chunk 141 optimal weight: 0.0670 chunk 78 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 overall best weight: 0.3926 ------------------------------------------------------------------------------- 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: 0.8436 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 13400 Z= 0.119 Angle : 0.383 4.393 18152 Z= 0.206 Chirality : 0.045 0.143 2174 Planarity : 0.003 0.033 2360 Dihedral : 3.181 12.713 1942 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1766 helix: 0.57 (0.19), residues: 846 sheet: 1.29 (0.28), residues: 304 loop : -0.47 (0.23), residues: 616 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 222 time to evaluate : 1.632 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 226 average time/residue: 0.3571 time to fit residues: 107.3650 Evaluate side-chains 213 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 209 time to evaluate : 1.717 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1246 time to fit residues: 3.2598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 78 optimal weight: 0.3980 chunk 104 optimal weight: 0.0040 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 13400 Z= 0.200 Angle : 0.406 3.852 18152 Z= 0.218 Chirality : 0.046 0.142 2174 Planarity : 0.003 0.033 2360 Dihedral : 3.229 13.605 1942 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.80 % 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: 0.52 (0.20), residues: 1766 helix: 0.60 (0.19), residues: 846 sheet: 1.31 (0.29), residues: 304 loop : -0.36 (0.24), residues: 616 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 216 time to evaluate : 1.767 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 221 average time/residue: 0.3591 time to fit residues: 106.2711 Evaluate side-chains 212 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 207 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1324 time to fit residues: 3.4544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8453 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 13400 Z= 0.172 Angle : 0.409 7.652 18152 Z= 0.216 Chirality : 0.046 0.139 2174 Planarity : 0.003 0.033 2360 Dihedral : 3.219 13.072 1942 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1766 helix: 0.70 (0.19), residues: 846 sheet: 1.37 (0.28), residues: 304 loop : -0.31 (0.24), residues: 616 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 216 time to evaluate : 1.763 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 216 average time/residue: 0.3528 time to fit residues: 102.5949 Evaluate side-chains 213 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 211 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1514 time to fit residues: 2.7593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.9980 chunk 148 optimal weight: 0.5980 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 chunk 124 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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: 0.8451 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 13400 Z= 0.164 Angle : 0.405 6.919 18152 Z= 0.215 Chirality : 0.046 0.137 2174 Planarity : 0.003 0.033 2360 Dihedral : 3.197 12.880 1942 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1766 helix: 0.78 (0.19), residues: 846 sheet: 1.38 (0.28), residues: 304 loop : -0.27 (0.24), residues: 616 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 212 time to evaluate : 1.659 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 213 average time/residue: 0.3410 time to fit residues: 98.1622 Evaluate side-chains 205 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.627 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 116 optimal weight: 1.9990 chunk 175 optimal weight: 0.0970 chunk 161 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 110 optimal weight: 0.9980 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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: 0.8439 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 13400 Z= 0.136 Angle : 0.397 7.055 18152 Z= 0.211 Chirality : 0.045 0.136 2174 Planarity : 0.003 0.032 2360 Dihedral : 3.136 13.114 1942 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.22 % 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: 0.85 (0.20), residues: 1766 helix: 0.90 (0.19), residues: 846 sheet: 1.41 (0.28), residues: 304 loop : -0.21 (0.24), residues: 616 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.660 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 214 average time/residue: 0.3434 time to fit residues: 99.3538 Evaluate side-chains 206 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 1.694 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1322 time to fit residues: 2.6114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.0000 chunk 42 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 0.0040 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.149331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.113739 restraints weight = 25747.072| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 4.06 r_work: 0.2833 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 13400 Z= 0.127 Angle : 0.390 7.059 18152 Z= 0.208 Chirality : 0.045 0.137 2174 Planarity : 0.003 0.032 2360 Dihedral : 3.066 13.308 1942 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 1766 helix: 1.01 (0.19), residues: 846 sheet: 1.46 (0.29), residues: 304 loop : -0.16 (0.24), residues: 616 =============================================================================== Job complete usr+sys time: 3076.24 seconds wall clock time: 55 minutes 52.27 seconds (3352.27 seconds total)