Starting phenix.real_space_refine (version: dev) on Mon Feb 20 22:41:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ux4_20929/02_2023/6ux4_20929.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ux4_20929/02_2023/6ux4_20929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ux4_20929/02_2023/6ux4_20929.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ux4_20929/02_2023/6ux4_20929.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ux4_20929/02_2023/6ux4_20929.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ux4_20929/02_2023/6ux4_20929.pdb" } resolution = 3.5 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 163": "OD1" <-> "OD2" Residue "A ASP 169": "OD1" <-> "OD2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 245": "OD1" <-> "OD2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ASP 169": "OD1" <-> "OD2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E ASP 202": "OD1" <-> "OD2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 248": "OE1" <-> "OE2" Residue "E ASP 254": "OD1" <-> "OD2" Residue "E ARG 262": "NH1" <-> "NH2" Residue "E ASP 282": "OD1" <-> "OD2" Residue "E ASP 316": "OD1" <-> "OD2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B ASP 184": "OD1" <-> "OD2" 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 ASP 169": "OD1" <-> "OD2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F ASP 202": "OD1" <-> "OD2" Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 244": "OD1" <-> "OD2" Residue "F ARG 262": "NH1" <-> "NH2" Residue "F ASP 287": "OD1" <-> "OD2" Residue "F ASP 300": "OD1" <-> "OD2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ASP 169": "OD1" <-> "OD2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C ASP 226": "OD1" <-> "OD2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 245": "OD1" <-> "OD2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "G ARG 116": "NH1" <-> "NH2" Residue "G ASP 145": "OD1" <-> "OD2" Residue "G ASP 184": "OD1" <-> "OD2" Residue "G PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 245": "OD1" <-> "OD2" Residue "G ASP 254": "OD1" <-> "OD2" Residue "G ARG 262": "NH1" <-> "NH2" Residue "G ASP 282": "OD1" <-> "OD2" Residue "G ASP 316": "OD1" <-> "OD2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D ASP 163": "OD1" <-> "OD2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D ASP 184": "OD1" <-> "OD2" 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 ASP 169": "OD1" <-> "OD2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "H ASP 202": "OD1" <-> "OD2" Residue "H PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 244": "OD1" <-> "OD2" Residue "H ARG 262": "NH1" <-> "NH2" Residue "H ASP 287": "OD1" <-> "OD2" Residue "H ASP 300": "OD1" <-> "OD2" Residue "H GLU 325": "OE1" <-> "OE2" 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: 13257 Number of models: 1 Model: "" Number of chains: 19 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" 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: "A" 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} 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: 9.06, per 1000 atoms: 0.68 Number of scatterers: 13257 At special positions: 0 Unit cell: (138.03, 133.75, 66.34, 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 2501 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: 5.24 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: 87 helices and 16 sheets defined 43.5% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.711A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.798A pdb=" N ALA A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 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: 3.572A 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 247 through 256 removed outlier: 3.969A pdb=" N LEU A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) 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 removed outlier: 3.882A pdb=" N GLU E 133 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 147 No H-bonds generated for 'chain 'E' and resid 145 through 147' Processing helix chain 'E' and resid 148 through 155 Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.947A pdb=" N ALA E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.624A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.668A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.693A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.629A pdb=" N MET E 250 " --> pdb=" O GLY E 246 " (cutoff:3.500A) removed outlier: 3.906A 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: 3.596A 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 removed outlier: 3.632A pdb=" N GLU B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 155 removed outlier: 3.616A pdb=" N ARG B 154 " --> pdb=" O LYS B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 187 through 202 removed outlier: 3.745A pdb=" N ILE B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 230 through 241 removed outlier: 3.580A pdb=" N SER B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.807A pdb=" N LEU B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 323 through 332 removed outlier: 3.526A pdb=" N ASN B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 133 removed outlier: 3.790A pdb=" N GLU F 133 " --> pdb=" O GLU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 155 Processing helix chain 'F' and resid 166 through 171 Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.562A pdb=" N THR F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 223 Processing helix chain 'F' and resid 230 through 240 removed outlier: 3.727A pdb=" N SER F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 removed outlier: 3.756A pdb=" N ASP F 254 " --> pdb=" O MET F 250 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU F 256 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 284 Processing helix chain 'F' and resid 284 through 289 Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.539A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 132 removed outlier: 3.620A pdb=" N GLU C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 156 removed outlier: 3.583A pdb=" N SER C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.564A pdb=" N GLU C 171 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.573A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) 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: 3.610A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 240 Processing helix chain 'C' and resid 247 through 256 removed outlier: 3.738A pdb=" N VAL C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) 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 332 removed outlier: 3.515A pdb=" N GLU C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 133 removed outlier: 3.528A pdb=" N GLU G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU G 133 " --> pdb=" O GLU G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 147 No H-bonds generated for 'chain 'G' and resid 145 through 147' Processing helix chain 'G' and resid 148 through 155 removed outlier: 3.580A pdb=" N SER G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 171 Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.530A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.761A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 240 removed outlier: 3.573A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 256 removed outlier: 3.657A pdb=" N GLN G 253 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 3.878A 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: 3.610A pdb=" N VAL G 288 " --> pdb=" O ASP G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 334 removed outlier: 3.543A pdb=" N ASN G 332 " --> pdb=" O GLU G 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 134 removed outlier: 3.623A pdb=" N GLU D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 155 removed outlier: 3.617A pdb=" N ARG D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 187 through 202 removed outlier: 3.743A pdb=" N ILE D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 230 through 241 removed outlier: 3.581A pdb=" N SER D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.809A pdb=" N LEU D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 323 through 332 removed outlier: 3.526A pdb=" N ASN D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 133 removed outlier: 3.794A pdb=" N GLU H 133 " --> pdb=" O GLU H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 155 Processing helix chain 'H' and resid 166 through 171 Processing helix chain 'H' and resid 187 through 202 removed outlier: 3.557A pdb=" N THR H 191 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS H 200 " --> pdb=" O LEU H 196 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE H 201 " --> pdb=" O GLY H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 223 Processing helix chain 'H' and resid 230 through 240 removed outlier: 3.511A pdb=" N ILE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 256 removed outlier: 3.756A pdb=" N ASP H 254 " --> pdb=" O MET H 250 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU H 256 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 284 Processing helix chain 'H' and resid 284 through 289 Processing helix chain 'H' and resid 323 through 334 removed outlier: 3.556A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN H 332 " --> pdb=" O GLU H 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.398A pdb=" N VAL A 139 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL A 160 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL A 141 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 118 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE A 120 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 207 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE A 229 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.259A 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: 3.512A pdb=" N GLY A 295 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.422A 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: 3.519A pdb=" N ALA E 143 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL E 118 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU E 142 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE E 120 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL E 119 " --> pdb=" O ILE E 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 263 through 268 removed outlier: 3.664A pdb=" N GLY E 322 " --> pdb=" O ARG E 263 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY E 295 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.654A pdb=" N ALA B 143 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 119 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE B 207 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE B 229 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 209 " --> pdb=" O ILE B 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.577A pdb=" N GLY B 322 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 317 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL B 296 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU B 319 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 296 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.245A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL F 118 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU F 142 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE F 120 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL F 119 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL F 181 " --> pdb=" O ILE F 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 263 through 268 removed outlier: 3.695A pdb=" N GLY F 322 " --> pdb=" O ARG F 263 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE F 317 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL F 296 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU F 319 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.402A pdb=" N VAL C 139 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL C 160 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL C 141 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 118 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU C 142 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE C 120 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE C 207 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE C 229 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 6.384A 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: 3.516A pdb=" N GLY C 295 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 157 through 161 removed outlier: 3.520A pdb=" N ALA G 143 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL G 118 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU G 142 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE G 120 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL G 119 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 263 through 268 removed outlier: 3.695A pdb=" N GLY G 322 " --> pdb=" O ARG G 263 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY G 295 " --> pdb=" O LEU G 319 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.650A pdb=" N ALA D 143 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL D 119 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE D 207 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE D 229 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA D 209 " --> pdb=" O ILE D 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.580A pdb=" N GLY D 322 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE D 317 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL D 296 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU D 319 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 296 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.245A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL H 118 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU H 142 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE H 120 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL H 119 " --> pdb=" O ILE H 182 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL H 181 " --> pdb=" O ILE H 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 3.731A pdb=" N GLY H 322 " --> pdb=" O ARG H 263 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE H 317 " --> pdb=" O VAL H 296 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL H 296 " --> pdb=" O ILE H 317 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU H 319 " --> pdb=" O ILE H 294 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1417 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: 3.85 Time building geometry restraints manager: 5.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3364 1.33 - 1.45: 2169 1.45 - 1.57: 7779 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 13400 Sorted by residual: bond pdb=" CG GLN A 227 " pdb=" CD GLN A 227 " ideal model delta sigma weight residual 1.516 1.467 0.049 2.50e-02 1.60e+03 3.91e+00 bond pdb=" CG LEU E 220 " pdb=" CD2 LEU E 220 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.74e+00 bond pdb=" CG LEU D 220 " pdb=" CD2 LEU D 220 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.73e+00 bond pdb=" CG GLN C 227 " pdb=" CD GLN C 227 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.66e+00 bond pdb=" CG LEU B 220 " pdb=" CD2 LEU B 220 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.61e+00 ... (remaining 13395 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.26: 250 106.26 - 113.19: 7645 113.19 - 120.13: 4850 120.13 - 127.06: 5307 127.06 - 133.99: 100 Bond angle restraints: 18152 Sorted by residual: angle pdb=" C GLU B 266 " pdb=" N VAL B 267 " pdb=" CA VAL B 267 " ideal model delta sigma weight residual 123.33 119.66 3.67 8.70e-01 1.32e+00 1.77e+01 angle pdb=" N GLU D 259 " pdb=" CA GLU D 259 " pdb=" C GLU D 259 " ideal model delta sigma weight residual 114.56 109.45 5.11 1.27e+00 6.20e-01 1.62e+01 angle pdb=" N GLU B 259 " pdb=" CA GLU B 259 " pdb=" C GLU B 259 " ideal model delta sigma weight residual 114.56 109.46 5.10 1.27e+00 6.20e-01 1.61e+01 angle pdb=" C GLU D 266 " pdb=" N VAL D 267 " pdb=" CA VAL D 267 " ideal model delta sigma weight residual 123.33 119.84 3.49 8.70e-01 1.32e+00 1.61e+01 angle pdb=" C VAL B 267 " pdb=" CA VAL B 267 " pdb=" CB VAL B 267 " ideal model delta sigma weight residual 110.13 113.16 -3.03 9.70e-01 1.06e+00 9.74e+00 ... (remaining 18147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 7441 17.54 - 35.09: 624 35.09 - 52.63: 83 52.63 - 70.18: 19 70.18 - 87.72: 13 Dihedral angle restraints: 8180 sinusoidal: 3108 harmonic: 5072 Sorted by residual: dihedral pdb=" CA ASN B 147 " pdb=" C ASN B 147 " pdb=" N VAL B 148 " pdb=" CA VAL B 148 " ideal model delta harmonic sigma weight residual 180.00 162.18 17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASN D 147 " pdb=" C ASN D 147 " pdb=" N VAL D 148 " pdb=" CA VAL D 148 " ideal model delta harmonic sigma weight residual 180.00 162.22 17.78 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CB GLU A 171 " pdb=" CG GLU A 171 " pdb=" CD GLU A 171 " pdb=" OE1 GLU A 171 " ideal model delta sinusoidal sigma weight residual 0.00 87.72 -87.72 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 8177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1791 0.077 - 0.155: 360 0.155 - 0.232: 19 0.232 - 0.310: 2 0.310 - 0.387: 2 Chirality restraints: 2174 Sorted by residual: chirality pdb=" CB ILE C 293 " pdb=" CA ILE C 293 " pdb=" CG1 ILE C 293 " pdb=" CG2 ILE C 293 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CB ILE A 293 " pdb=" CA ILE A 293 " pdb=" CG1 ILE A 293 " pdb=" CG2 ILE A 293 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CB VAL B 205 " pdb=" CA VAL B 205 " pdb=" CG1 VAL B 205 " pdb=" CG2 VAL B 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 2171 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 267 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C VAL A 267 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A 267 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO A 268 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 267 " -0.012 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C VAL C 267 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL C 267 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO C 268 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 267 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO C 268 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 268 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 268 " -0.031 5.00e-02 4.00e+02 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3224 2.78 - 3.31: 10984 3.31 - 3.84: 21168 3.84 - 4.37: 24208 4.37 - 4.90: 44003 Nonbonded interactions: 103587 Sorted by model distance: nonbonded pdb=" OD1 ASP A 184 " pdb=" O HOH A 501 " model vdw 2.254 2.440 nonbonded pdb=" O ILE D 285 " pdb=" OG1 THR D 289 " model vdw 2.262 2.440 nonbonded pdb=" O LEU A 185 " pdb=" O HOH A 501 " model vdw 2.263 2.440 nonbonded pdb=" OG SER E 124 " pdb=" OD2 ASP E 184 " model vdw 2.266 2.440 nonbonded pdb=" OG SER A 124 " pdb=" OD2 ASP A 184 " model vdw 2.268 2.440 ... (remaining 103582 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)) 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)) 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)) 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)) 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)) 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) \ ) 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)) 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) \ ) } 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 2501 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 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: 0.810 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: 4.030 Check model and map are aligned: 0.160 Process input model: 37.690 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.130 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: 46.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 : 0.011 0.071 13400 Z= 0.709 Angle : 0.832 8.155 18152 Z= 0.481 Chirality : 0.060 0.387 2174 Planarity : 0.005 0.056 2360 Dihedral : 13.470 87.723 4912 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % 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: -4.46 (0.15), residues: 1766 helix: -4.39 (0.08), residues: 790 sheet: 0.19 (0.23), residues: 384 loop : -2.71 (0.20), residues: 592 *********************** 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 267 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 265 time to evaluate : 1.565 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 265 average time/residue: 0.3489 time to fit residues: 122.7053 Evaluate side-chains 196 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 194 time to evaluate : 1.578 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1159 time to fit residues: 2.6385 ------------------------------------------------------------------------------- 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: 0.2980 chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 137 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN F 286 HIS F 332 ASN C 219 GLN C 332 ASN H 286 HIS H 332 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 13400 Z= 0.135 Angle : 0.427 5.011 18152 Z= 0.232 Chirality : 0.045 0.136 2174 Planarity : 0.004 0.042 2360 Dihedral : 3.769 12.764 1942 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 1.38 % 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: -2.64 (0.17), residues: 1766 helix: -2.59 (0.14), residues: 798 sheet: 0.94 (0.26), residues: 336 loop : -1.90 (0.21), residues: 632 *********************** 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 249 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 232 time to evaluate : 1.663 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 238 average time/residue: 0.3096 time to fit residues: 101.5213 Evaluate side-chains 211 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 199 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1980 time to fit residues: 5.7777 ------------------------------------------------------------------------------- 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: 4.9990 chunk 49 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 142 optimal weight: 0.2980 chunk 158 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 128 optimal weight: 0.6980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN E 332 ASN B 253 GLN F 286 HIS C 332 ASN G 253 GLN D 253 GLN H 286 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 13400 Z= 0.274 Angle : 0.463 4.819 18152 Z= 0.243 Chirality : 0.047 0.148 2174 Planarity : 0.004 0.034 2360 Dihedral : 3.572 12.489 1942 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.73 % 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: -1.60 (0.19), residues: 1766 helix: -1.44 (0.17), residues: 798 sheet: 0.97 (0.27), residues: 336 loop : -1.50 (0.22), residues: 632 *********************** 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 219 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 211 time to evaluate : 1.653 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 214 average time/residue: 0.2977 time to fit residues: 88.5105 Evaluate side-chains 199 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 195 time to evaluate : 1.513 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1173 time to fit residues: 3.0953 ------------------------------------------------------------------------------- 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: 6.9990 chunk 120 optimal weight: 1.9990 chunk 83 optimal weight: 0.0020 chunk 17 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 107 optimal weight: 0.0050 chunk 160 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN B 253 GLN C 253 GLN D 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 13400 Z= 0.138 Angle : 0.395 4.497 18152 Z= 0.210 Chirality : 0.045 0.140 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.204 11.214 1942 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: -0.80 (0.20), residues: 1766 helix: -0.65 (0.18), residues: 798 sheet: 1.19 (0.27), residues: 336 loop : -1.18 (0.23), residues: 632 *********************** 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 218 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 208 time to evaluate : 1.738 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 213 average time/residue: 0.2910 time to fit residues: 87.5410 Evaluate side-chains 207 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 201 time to evaluate : 1.694 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1316 time to fit residues: 3.7024 ------------------------------------------------------------------------------- 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: 0.5980 chunk 2 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN B 253 GLN D 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 13400 Z= 0.283 Angle : 0.455 4.401 18152 Z= 0.238 Chirality : 0.047 0.147 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.371 13.597 1942 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.94 % 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: -0.55 (0.20), residues: 1766 helix: -0.41 (0.19), residues: 798 sheet: 1.16 (0.27), residues: 336 loop : -0.99 (0.24), residues: 632 *********************** 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 209 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 198 time to evaluate : 1.561 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 205 average time/residue: 0.2975 time to fit residues: 84.9405 Evaluate side-chains 194 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 185 time to evaluate : 1.487 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1553 time to fit residues: 4.6758 ------------------------------------------------------------------------------- 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: 4.9990 chunk 33 optimal weight: 0.4980 chunk 99 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN D 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 13400 Z= 0.174 Angle : 0.405 4.373 18152 Z= 0.215 Chirality : 0.046 0.140 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.163 12.783 1942 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.73 % 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: -0.19 (0.20), residues: 1766 helix: -0.05 (0.19), residues: 798 sheet: 1.26 (0.27), residues: 336 loop : -0.86 (0.24), residues: 632 *********************** 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 213 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 205 time to evaluate : 1.622 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 210 average time/residue: 0.2978 time to fit residues: 87.9151 Evaluate side-chains 194 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 1.565 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1813 time to fit residues: 3.9638 ------------------------------------------------------------------------------- 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: 0.5980 chunk 97 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN B 253 GLN D 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 13400 Z= 0.178 Angle : 0.410 4.285 18152 Z= 0.217 Chirality : 0.046 0.146 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.100 12.874 1942 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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 (0.20), residues: 1766 helix: 0.15 (0.19), residues: 798 sheet: 1.32 (0.27), residues: 336 loop : -0.75 (0.25), residues: 632 *********************** 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 207 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 198 time to evaluate : 1.629 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 203 average time/residue: 0.3013 time to fit residues: 85.2761 Evaluate side-chains 197 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 2.048 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1339 time to fit residues: 4.3246 ------------------------------------------------------------------------------- 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: 0.5980 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN B 253 GLN D 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13400 Z= 0.203 Angle : 0.424 4.874 18152 Z= 0.224 Chirality : 0.046 0.137 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.112 13.006 1942 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 0.73 % 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: 0.10 (0.20), residues: 1766 helix: 0.22 (0.19), residues: 798 sheet: 1.30 (0.28), residues: 336 loop : -0.69 (0.25), residues: 632 *********************** 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 205 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 197 time to evaluate : 1.844 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 200 average time/residue: 0.3058 time to fit residues: 85.1120 Evaluate side-chains 196 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1218 time to fit residues: 2.9831 ------------------------------------------------------------------------------- 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: 1.9990 chunk 148 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN D 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 13400 Z= 0.390 Angle : 0.513 4.800 18152 Z= 0.268 Chirality : 0.049 0.174 2174 Planarity : 0.004 0.034 2360 Dihedral : 3.489 13.966 1942 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.58 % 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: -0.18 (0.20), residues: 1766 helix: -0.08 (0.19), residues: 798 sheet: 1.16 (0.28), residues: 336 loop : -0.73 (0.25), residues: 632 *********************** 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 200 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 1.628 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 197 average time/residue: 0.3210 time to fit residues: 87.1132 Evaluate side-chains 191 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1724 time to fit residues: 4.0917 ------------------------------------------------------------------------------- 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: 0.5980 chunk 102 optimal weight: 0.0060 chunk 79 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 14 optimal weight: 0.0060 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN B 253 GLN C 253 GLN D 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 13400 Z= 0.123 Angle : 0.410 5.741 18152 Z= 0.217 Chirality : 0.046 0.268 2174 Planarity : 0.003 0.033 2360 Dihedral : 3.059 12.101 1942 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: 0.27 (0.21), residues: 1766 helix: 0.40 (0.20), residues: 798 sheet: 1.30 (0.28), residues: 336 loop : -0.60 (0.25), residues: 632 ********************** 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 197 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.622 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 197 average time/residue: 0.3188 time to fit residues: 86.5939 Evaluate side-chains 186 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.694 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1280 time to fit residues: 2.5664 ------------------------------------------------------------------------------- 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: 4.9990 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN B 253 GLN C 332 ASN D 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.140481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.109651 restraints weight = 24621.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.110765 restraints weight = 14297.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.112251 restraints weight = 12071.389| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 13400 Z= 0.302 Angle : 0.472 5.004 18152 Z= 0.246 Chirality : 0.048 0.264 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.296 14.725 1942 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.65 % 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: 0.10 (0.20), residues: 1766 helix: 0.18 (0.19), residues: 798 sheet: 1.27 (0.28), residues: 336 loop : -0.60 (0.25), residues: 632 =============================================================================== Job complete usr+sys time: 2522.94 seconds wall clock time: 46 minutes 6.07 seconds (2766.07 seconds total)