Starting phenix.real_space_refine on Sat Jan 20 02:08:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5p_20652/01_2024/6u5p_20652.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5p_20652/01_2024/6u5p_20652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5p_20652/01_2024/6u5p_20652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5p_20652/01_2024/6u5p_20652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5p_20652/01_2024/6u5p_20652.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5p_20652/01_2024/6u5p_20652.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.005 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 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 8322 2.51 5 N 2378 2.21 5 O 2528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 245": "OD1" <-> "OD2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "E ASP 202": "OD1" <-> "OD2" Residue "E GLU 215": "OE1" <-> "OE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 262": "NH1" <-> "NH2" Residue "E ASP 309": "OD1" <-> "OD2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B ASP 309": "OD1" <-> "OD2" Residue "F ARG 116": "NH1" <-> "NH2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F GLU 215": "OE1" <-> "OE2" Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 259": "OE1" <-> "OE2" Residue "F ARG 262": "NH1" <-> "NH2" Residue "F ASP 282": "OD1" <-> "OD2" Residue "F ASP 309": "OD1" <-> "OD2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 245": "OD1" <-> "OD2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C GLU 301": "OE1" <-> "OE2" Residue "G ARG 116": "NH1" <-> "NH2" Residue "G GLU 171": "OE1" <-> "OE2" Residue "G ASP 184": "OD1" <-> "OD2" Residue "G ASP 202": "OD1" <-> "OD2" Residue "G GLU 215": "OE1" <-> "OE2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 262": "NH1" <-> "NH2" Residue "G ASP 309": "OD1" <-> "OD2" Residue "G GLU 325": "OE1" <-> "OE2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D ASP 145": "OD1" <-> "OD2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D ASP 287": "OD1" <-> "OD2" Residue "D ASP 309": "OD1" <-> "OD2" Residue "H ARG 116": "NH1" <-> "NH2" Residue "H GLU 129": "OE1" <-> "OE2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "H GLU 215": "OE1" <-> "OE2" Residue "H PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 259": "OE1" <-> "OE2" Residue "H ARG 262": "NH1" <-> "NH2" Residue "H ASP 282": "OD1" <-> "OD2" Residue "H ASP 309": "OD1" <-> "OD2" Residue "H GLU 328": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13308 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1650 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "E" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1678 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1658 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "F" 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: 88 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1650 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "G" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1678 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1658 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "H" 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: 88 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 62 Chain: "A" 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: "E" 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: "B" 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: "F" 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: "C" 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: "G" 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: "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: "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} Time building chain proxies: 7.29, per 1000 atoms: 0.55 Number of scatterers: 13308 At special positions: 0 Unit cell: (139.192, 139.192, 64.664, 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 2528 8.00 N 2378 7.00 C 8322 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: 4.72 Conformation dependent library (CDL) restraints added in 2.2 seconds 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3264 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 16 sheets defined 45.3% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 148 through 156 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.807A pdb=" N ALA A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.535A pdb=" N THR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 230 through 241 Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.502A pdb=" N MET A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.831A pdb=" N VAL A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) 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: 3.813A pdb=" N SER E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.704A pdb=" N ALA E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.649A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.585A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 240 removed outlier: 3.592A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.548A pdb=" N MET E 250 " --> pdb=" O GLY E 246 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 removed outlier: 3.563A pdb=" N ASP E 284 " --> pdb=" O VAL E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 289 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 156 Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.791A pdb=" N ALA B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.693A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.531A 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 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 154 Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.940A pdb=" N ALA F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.709A pdb=" N ILE F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.582A pdb=" N GLY F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 241 removed outlier: 3.565A pdb=" N ILE F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 256 removed outlier: 3.790A pdb=" N LEU F 256 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.600A pdb=" N ASP F 284 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.583A 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 148 through 156 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.807A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.535A pdb=" N THR C 191 " --> pdb=" O SER C 187 " (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 Processing helix chain 'C' and resid 230 through 241 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.503A pdb=" N MET C 250 " --> pdb=" O GLY C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 290 removed outlier: 3.831A pdb=" N VAL C 288 " --> pdb=" O ASP C 284 " (cutoff:3.500A) 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: 3.812A pdb=" N SER G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 173 removed outlier: 3.705A pdb=" N ALA G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.648A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.588A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 240 removed outlier: 3.590A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 256 removed outlier: 3.548A pdb=" N MET G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU G 256 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 removed outlier: 3.562A pdb=" N ASP G 284 " --> pdb=" O VAL G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 289 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 156 Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.790A pdb=" N ALA D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.694A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.532A 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 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 154 Processing helix chain 'H' and resid 166 through 173 removed outlier: 3.941A pdb=" N ALA H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 removed outlier: 3.709A pdb=" N ILE H 201 " --> pdb=" O GLY H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 224 removed outlier: 3.583A pdb=" N GLY H 224 " --> pdb=" O LEU H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 241 removed outlier: 3.564A pdb=" N ILE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 256 removed outlier: 3.788A pdb=" N LEU H 256 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.598A pdb=" N ASP H 284 " --> pdb=" O VAL H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.583A 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: 6.408A pdb=" N VAL A 139 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 160 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL A 141 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 118 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 120 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 7.389A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.685A 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: 6.500A pdb=" N VAL E 139 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL E 160 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL E 141 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL E 181 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLU E 210 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL E 183 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE E 207 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE E 229 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 6.494A 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: 7.219A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.599A 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: 6.549A pdb=" N VAL B 139 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N HIS B 117 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA B 180 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE B 208 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 181 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLU B 210 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL B 183 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 207 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE B 229 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.654A 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: 7.240A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.671A 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: 6.391A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 263 through 268 removed outlier: 7.230A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.544A 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: 6.408A pdb=" N VAL C 139 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL C 160 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL C 141 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL C 118 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU C 142 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE C 120 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.719A pdb=" N ILE C 317 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL C 296 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU C 319 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 158 through 161 removed outlier: 6.499A pdb=" N VAL G 139 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL G 160 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL G 141 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL G 181 " --> pdb=" O ILE G 208 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLU G 210 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL G 183 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE G 207 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE G 229 " --> pdb=" O ILE G 207 " (cutoff:3.500A) removed outlier: 6.494A 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: 7.220A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.598A 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: 6.549A pdb=" N VAL D 139 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N HIS D 117 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA D 180 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE D 208 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL D 181 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLU D 210 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL D 183 " --> pdb=" O GLU D 210 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE D 207 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE D 229 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 6.656A 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: 7.239A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.670A 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: 6.391A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 7.230A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1707 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: 3.94 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 - 1.33: 4011 1.33 - 1.45: 1578 1.45 - 1.57: 7767 1.57 - 1.69: 0 1.69 - 1.80: 88 Bond restraints: 13444 Sorted by residual: bond pdb=" CG GLN B 227 " pdb=" CD GLN B 227 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.80e+00 bond pdb=" CG1 ILE C 195 " pdb=" CD1 ILE C 195 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.73e+00 bond pdb=" CG GLN D 227 " pdb=" CD GLN D 227 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.68e+00 bond pdb=" CG1 ILE A 195 " pdb=" CD1 ILE A 195 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" CG LEU D 220 " pdb=" CD2 LEU D 220 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.66e+00 ... (remaining 13439 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.80: 282 106.80 - 113.61: 7756 113.61 - 120.41: 5131 120.41 - 127.22: 4946 127.22 - 134.03: 93 Bond angle restraints: 18208 Sorted by residual: angle pdb=" N GLU B 171 " pdb=" CA GLU B 171 " pdb=" C GLU B 171 " ideal model delta sigma weight residual 111.28 114.64 -3.36 1.09e+00 8.42e-01 9.51e+00 angle pdb=" N GLU D 171 " pdb=" CA GLU D 171 " pdb=" C GLU D 171 " ideal model delta sigma weight residual 111.28 114.63 -3.35 1.09e+00 8.42e-01 9.43e+00 angle pdb=" N GLY D 162 " pdb=" CA GLY D 162 " pdb=" C GLY D 162 " ideal model delta sigma weight residual 110.88 115.28 -4.40 1.48e+00 4.57e-01 8.82e+00 angle pdb=" N GLY B 162 " pdb=" CA GLY B 162 " pdb=" C GLY B 162 " ideal model delta sigma weight residual 110.88 115.26 -4.38 1.48e+00 4.57e-01 8.76e+00 angle pdb=" C LEU B 170 " pdb=" N GLU B 171 " pdb=" CA GLU B 171 " ideal model delta sigma weight residual 120.28 124.05 -3.77 1.34e+00 5.57e-01 7.93e+00 ... (remaining 18203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 7248 16.60 - 33.21: 783 33.21 - 49.81: 131 49.81 - 66.41: 28 66.41 - 83.02: 18 Dihedral angle restraints: 8208 sinusoidal: 3144 harmonic: 5064 Sorted by residual: dihedral pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " pdb=" CG ASP A 287 " pdb=" OD1 ASP A 287 " ideal model delta sinusoidal sigma weight residual -30.00 -82.92 52.92 1 2.00e+01 2.50e-03 9.53e+00 dihedral pdb=" CA ASP C 287 " pdb=" CB ASP C 287 " pdb=" CG ASP C 287 " pdb=" OD1 ASP C 287 " ideal model delta sinusoidal sigma weight residual -30.00 -82.89 52.89 1 2.00e+01 2.50e-03 9.52e+00 dihedral pdb=" N LYS G 200 " pdb=" CA LYS G 200 " pdb=" CB LYS G 200 " pdb=" CG LYS G 200 " ideal model delta sinusoidal sigma weight residual -60.00 -116.90 56.90 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 8205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1467 0.046 - 0.092: 465 0.092 - 0.137: 218 0.137 - 0.183: 22 0.183 - 0.229: 4 Chirality restraints: 2176 Sorted by residual: chirality pdb=" CB ILE B 303 " pdb=" CA ILE B 303 " pdb=" CG1 ILE B 303 " pdb=" CG2 ILE B 303 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE D 303 " pdb=" CA ILE D 303 " pdb=" CG1 ILE D 303 " pdb=" CG2 ILE D 303 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+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 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2173 not shown) Planarity restraints: 2372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 169 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.48e+00 pdb=" C ASP D 169 " -0.050 2.00e-02 2.50e+03 pdb=" O ASP D 169 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU D 170 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 169 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C ASP B 169 " -0.050 2.00e-02 2.50e+03 pdb=" O ASP B 169 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU B 170 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 267 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C VAL B 267 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL B 267 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO B 268 " 0.012 2.00e-02 2.50e+03 ... (remaining 2369 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2404 2.77 - 3.30: 11435 3.30 - 3.83: 21451 3.83 - 4.37: 24497 4.37 - 4.90: 45416 Nonbonded interactions: 105203 Sorted by model distance: nonbonded pdb=" OG SER C 124 " pdb=" OD2 ASP C 184 " model vdw 2.236 2.440 nonbonded pdb=" OG SER A 124 " pdb=" OD2 ASP A 184 " model vdw 2.236 2.440 nonbonded pdb=" O ILE A 285 " pdb=" OG1 THR A 289 " model vdw 2.278 2.440 nonbonded pdb=" O ILE C 285 " pdb=" OG1 THR C 289 " model vdw 2.280 2.440 nonbonded pdb=" OG SER E 124 " pdb=" OD2 ASP E 184 " model vdw 2.282 2.440 ... (remaining 105198 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 146 or (resid 147 and (nam \ e N or name CA or name C or name O or name CB )) or resid 148 through 202 or (re \ sid 203 and (name N or name CA or name C or name O or name CB )) or resid 204 th \ rough 262 or (resid 263 and (name N or name CA or name C or name O or name 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 o \ r name C or name O or name CB )) or resid 285 through 286 or (resid 287 and (nam \ e N or name CA or name C or name O or name CB )) or resid 288 through 300 or (re \ sid 301 and (name N or name CA or name C or name O or name CB )) or resid 302 th \ rough 312 or (resid 313 through 314 and (name N or name CA or name C or name O o \ r name CB )) or resid 315 through 324 or (resid 325 and (name N or name CA or na \ me C or name O or name CB )) or resid 326 through 327 or (resid 328 through 329 \ and (name N or name CA or name C or name O or name CB )) or resid 330 through 33 \ 6 or 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 or (resid 135 and (name N or name CA o \ r name C or name O or name CB )) or resid 136 through 143 or (resid 144 and (nam \ e N or name CA or name C or name O or name CB )) or resid 145 through 146 or (re \ sid 147 and (name N or name CA or name C or name O or name CB )) or resid 148 th \ rough 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) \ or resid 155 through 170 or (resid 171 and (name N or name CA or name C or name \ O or name CB )) or resid 172 through 202 or (resid 203 and (name N or name CA o \ r name C or name O or name CB )) or resid 204 through 217 or (resid 218 and (nam \ e N or name CA or name C or name O or name CB )) or resid 219 through 253 or (re \ sid 254 and (name N or name CA or name C or name O or name CB )) or resid 255 th \ rough 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 286 or (resid 287 and (name N or name \ CA or name C or name O or name CB )) or resid 288 through 307 or (resid 308 and \ (name N or name CA or name C or name O or name CB )) or resid 309 through 328 or \ (resid 329 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 0 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 146 or (resid 147 and (nam \ e N or name CA or name C or name O or name CB )) or resid 148 through 202 or (re \ sid 203 and (name N or name CA or name C or name O or name CB )) or resid 204 th \ rough 262 or (resid 263 and (name N or name CA or name C or name O or name 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 o \ r name C or name O or name CB )) or resid 285 through 286 or (resid 287 and (nam \ e N or name CA or name C or name O or name CB )) or resid 288 through 300 or (re \ sid 301 and (name N or name CA or name C or name O or name CB )) or resid 302 th \ rough 312 or (resid 313 through 314 and (name N or name CA or name C or name O o \ r name CB )) or resid 315 through 324 or (resid 325 and (name N or name CA or na \ me C or name O or name CB )) or resid 326 through 327 or (resid 328 through 329 \ and (name N or name CA or name C or name O or name CB )) or resid 330 through 33 \ 6 or 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 or (resid 135 and (name N or name CA o \ r name C or name O or name CB )) or resid 136 through 143 or (resid 144 and (nam \ e N or name CA or name C or name O or name CB )) or resid 145 through 146 or (re \ sid 147 and (name N or name CA or name C or name O or name CB )) or resid 148 th \ rough 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) \ or resid 155 through 170 or (resid 171 and (name N or name CA or name C or name \ O or name CB )) or resid 172 through 202 or (resid 203 and (name N or name CA o \ r name C or name O or name CB )) or resid 204 through 217 or (resid 218 and (nam \ e N or name CA or name C or name O or name CB )) or resid 219 through 253 or (re \ sid 254 and (name N or name CA or name C or name O or name CB )) or resid 255 th \ rough 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 286 or (resid 287 and (name N or name \ CA or name C or name O or name CB )) or resid 288 through 307 or (resid 308 and \ (name N or name CA or name C or name O or name CB )) or resid 309 through 328 or \ (resid 329 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 0 through 336 or resid 401 through 402)) selection = (chain 'E' 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 145 or (resid \ 146 through 147 and (name N or name CA or name C or name O or name CB )) or resi \ d 148 through 153 or (resid 154 and (name N or name CA or name C or name O or na \ me CB )) or resid 155 through 170 or (resid 171 and (name N or name CA or name C \ or name O or name CB )) or resid 172 through 202 or (resid 203 and (name N or n \ ame CA or name C or name O or name CB )) or resid 204 through 217 or (resid 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 through 24 \ 3 or (resid 244 and (name N or name CA or name C or name O or name CB )) or resi \ d 245 through 253 or (resid 254 and (name N or name CA or name C or name O or na \ me CB )) or resid 255 through 258 or (resid 259 and (name N or name CA or name C \ or name O or name CB )) or resid 260 through 262 or (resid 263 and (name N or n \ ame CA or name C or name O or name CB )) or resid 264 through 275 or (resid 276 \ and (name N or name CA or name C or name O or name CB )) or resid 277 through 28 \ 6 or (resid 287 and (name N or name CA or name C or name O or name CB )) or resi \ d 288 through 297 or (resid 298 and (name N or name CA or name C or name O or na \ me CB )) or resid 299 through 307 or (resid 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 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 32 \ 6 through 327 or (resid 328 through 329 and (name N or name CA or name C or name \ O or name CB )) or resid 330 through 336 or resid 401 through 402)) selection = (chain 'F' and (resid 115 through 134 or (resid 135 and (name N or name CA or na \ me C or name O or name CB )) or resid 136 through 170 or (resid 171 and (name N \ or name CA or name C or name O or name CB )) or resid 172 through 217 or (resid \ 218 and (name N or name CA or name C or name O or name CB )) or resid 219 throug \ h 243 or (resid 244 and (name N or name CA or name C or name O or name CB )) or \ resid 245 through 253 or (resid 254 and (name N or name CA or name C or name O o \ r name CB )) or resid 255 through 258 or (resid 259 and (name N or name CA or na \ me C or name O or name CB )) or resid 260 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 resi \ d 285 through 297 or (resid 298 and (name N or name CA or name C or name O or na \ me CB )) or (resid 299 through 301 and (name N or name CA or name C or name O or \ name CB )) or resid 302 through 307 or (resid 308 and (name N or name CA or nam \ e C or name O or name CB )) or resid 309 through 312 or (resid 313 through 314 a \ nd (name N or name CA or name C or name O or name CB )) or resid 315 through 327 \ or (resid 328 through 329 and (name N or name CA or name C or name O or name CB \ )) or resid 330 through 336 or resid 401 through 402)) selection = (chain 'G' 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 145 or (resid \ 146 through 147 and (name N or name CA or name C or name O or name CB )) or resi \ d 148 through 153 or (resid 154 and (name N or name CA or name C or name O or na \ me CB )) or resid 155 through 170 or (resid 171 and (name N or name CA or name C \ or name O or name CB )) or resid 172 through 202 or (resid 203 and (name N or n \ ame CA or name C or name O or name CB )) or resid 204 through 217 or (resid 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 through 24 \ 3 or (resid 244 and (name N or name CA or name C or name O or name CB )) or resi \ d 245 through 253 or (resid 254 and (name N or name CA or name C or name O or na \ me CB )) or resid 255 through 258 or (resid 259 and (name N or name CA or name C \ or name O or name CB )) or resid 260 through 262 or (resid 263 and (name N or n \ ame CA or name C or name O or name CB )) or resid 264 through 275 or (resid 276 \ and (name N or name CA or name C or name O or name CB )) or resid 277 through 28 \ 6 or (resid 287 and (name N or name CA or name C or name O or name CB )) or resi \ d 288 through 297 or (resid 298 and (name N or name CA or name C or name O or na \ me CB )) or resid 299 through 307 or (resid 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 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 32 \ 6 through 327 or (resid 328 through 329 and (name N or name CA or name C or name \ O or name CB )) or resid 330 through 336 or resid 401 through 402)) selection = (chain 'H' and (resid 115 through 134 or (resid 135 and (name N or name CA or na \ me C or name O or name CB )) or resid 136 through 170 or (resid 171 and (name N \ or name CA or name C or name O or name CB )) or resid 172 through 217 or (resid \ 218 and (name N or name CA or name C or name O or name CB )) or resid 219 throug \ h 243 or (resid 244 and (name N or name CA or name C or name O or name CB )) or \ resid 245 through 253 or (resid 254 and (name N or name CA or name C or name O o \ r name CB )) or resid 255 through 258 or (resid 259 and (name N or name CA or na \ me C or name O or name CB )) or resid 260 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 resi \ d 285 through 297 or (resid 298 and (name N or name CA or name C or name O or na \ me CB )) or (resid 299 through 301 and (name N or name CA or name C or name O or \ name CB )) or resid 302 through 307 or (resid 308 and (name N or name CA or nam \ e C or name O or name CB )) or resid 309 through 312 or (resid 313 through 314 a \ nd (name N or name CA or name C or name O or name CB )) or resid 315 through 327 \ or (resid 328 through 329 and (name N or name CA or name C or name O or name CB \ )) or resid 330 through 336 or resid 401 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 3.530 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 36.270 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 0.051 13444 Z= 0.391 Angle : 0.750 6.134 18208 Z= 0.456 Chirality : 0.053 0.229 2176 Planarity : 0.005 0.048 2372 Dihedral : 14.368 83.017 4944 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.43 % Allowed : 7.33 % Favored : 92.24 % 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: -3.37 (0.15), residues: 1760 helix: -3.01 (0.12), residues: 832 sheet: 0.58 (0.24), residues: 352 loop : -2.58 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 123 HIS 0.014 0.002 HIS E 193 PHE 0.009 0.001 PHE E 251 TYR 0.011 0.002 TYR G 247 ARG 0.003 0.001 ARG G 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 328 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7459 (mtt180) cc_final: 0.7198 (mtm-85) REVERT: A 247 TYR cc_start: 0.8720 (m-80) cc_final: 0.7775 (m-80) REVERT: A 333 TYR cc_start: 0.7628 (t80) cc_final: 0.7259 (t80) REVERT: E 154 ARG cc_start: 0.7827 (ttp-110) cc_final: 0.7545 (mtm-85) REVERT: E 190 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7096 (mt-10) REVERT: E 266 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8442 (mt-10) REVERT: E 303 ILE cc_start: 0.8591 (mt) cc_final: 0.8080 (mm) REVERT: E 310 TYR cc_start: 0.7930 (t80) cc_final: 0.7450 (t80) REVERT: B 239 MET cc_start: 0.8673 (mtm) cc_final: 0.8368 (mtm) REVERT: F 266 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7959 (mt-10) REVERT: F 303 ILE cc_start: 0.8476 (mt) cc_final: 0.8204 (mm) REVERT: C 132 ARG cc_start: 0.7462 (mtt180) cc_final: 0.7193 (mtm-85) REVERT: C 247 TYR cc_start: 0.8718 (m-80) cc_final: 0.7774 (m-80) REVERT: C 333 TYR cc_start: 0.7603 (t80) cc_final: 0.7251 (t80) REVERT: G 154 ARG cc_start: 0.7789 (ttp-110) cc_final: 0.7504 (mtm-85) REVERT: G 190 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7107 (mt-10) REVERT: G 266 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8445 (mt-10) REVERT: G 303 ILE cc_start: 0.8600 (mt) cc_final: 0.8096 (mm) REVERT: G 310 TYR cc_start: 0.7898 (t80) cc_final: 0.7410 (t80) REVERT: D 239 MET cc_start: 0.8673 (mtm) cc_final: 0.8365 (mtm) REVERT: H 266 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7971 (mt-10) REVERT: H 303 ILE cc_start: 0.8481 (mt) cc_final: 0.8211 (mm) outliers start: 6 outliers final: 6 residues processed: 330 average time/residue: 0.3635 time to fit residues: 156.7662 Evaluate side-chains 243 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 237 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain H residue 245 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 G 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13444 Z= 0.195 Angle : 0.451 4.632 18208 Z= 0.243 Chirality : 0.047 0.167 2176 Planarity : 0.003 0.027 2372 Dihedral : 4.114 28.928 1954 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.58 % Allowed : 12.79 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 1760 helix: -1.28 (0.17), residues: 832 sheet: 0.58 (0.26), residues: 304 loop : -1.85 (0.19), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 123 HIS 0.005 0.001 HIS G 193 PHE 0.005 0.001 PHE G 251 TYR 0.006 0.001 TYR B 247 ARG 0.002 0.000 ARG G 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 245 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7498 (mtt180) cc_final: 0.7209 (mtm-85) REVERT: A 245 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7168 (p0) REVERT: A 333 TYR cc_start: 0.7598 (t80) cc_final: 0.7182 (t80) REVERT: E 154 ARG cc_start: 0.8031 (ttp-110) cc_final: 0.7725 (mtm-85) REVERT: E 190 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7195 (mt-10) REVERT: E 266 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8342 (mt-10) REVERT: E 303 ILE cc_start: 0.8620 (mt) cc_final: 0.8152 (mm) REVERT: E 310 TYR cc_start: 0.7860 (t80) cc_final: 0.7324 (t80) REVERT: B 212 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7194 (mp0) REVERT: B 239 MET cc_start: 0.8685 (mtm) cc_final: 0.8392 (mtm) REVERT: F 285 ILE cc_start: 0.8188 (mm) cc_final: 0.7934 (mm) REVERT: C 132 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7206 (mtm-85) REVERT: C 245 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7174 (p0) REVERT: C 333 TYR cc_start: 0.7585 (t80) cc_final: 0.7177 (t80) REVERT: G 154 ARG cc_start: 0.8031 (ttp-110) cc_final: 0.7728 (mtm-85) REVERT: G 190 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7194 (mt-10) REVERT: G 266 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8322 (mt-10) REVERT: G 303 ILE cc_start: 0.8626 (mt) cc_final: 0.8163 (mm) REVERT: G 310 TYR cc_start: 0.7829 (t80) cc_final: 0.7287 (t80) REVERT: D 212 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7196 (mp0) REVERT: D 239 MET cc_start: 0.8684 (mtm) cc_final: 0.8390 (mtm) REVERT: H 285 ILE cc_start: 0.8190 (mm) cc_final: 0.7935 (mm) outliers start: 22 outliers final: 15 residues processed: 258 average time/residue: 0.3233 time to fit residues: 113.1139 Evaluate side-chains 256 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 239 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP 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: 0.0270 chunk 133 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13444 Z= 0.214 Angle : 0.433 4.425 18208 Z= 0.231 Chirality : 0.047 0.152 2176 Planarity : 0.003 0.025 2372 Dihedral : 3.799 27.522 1954 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.08 % Allowed : 15.73 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 1760 helix: -0.46 (0.18), residues: 832 sheet: 0.52 (0.26), residues: 304 loop : -1.46 (0.20), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 123 HIS 0.007 0.001 HIS E 193 PHE 0.004 0.001 PHE D 312 TYR 0.006 0.001 TYR B 247 ARG 0.001 0.000 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 243 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7445 (p0) cc_final: 0.7183 (p0) REVERT: A 247 TYR cc_start: 0.8763 (m-80) cc_final: 0.7952 (m-80) REVERT: A 333 TYR cc_start: 0.7626 (t80) cc_final: 0.7318 (t80) REVERT: E 154 ARG cc_start: 0.8151 (ttp-110) cc_final: 0.7915 (mtm-85) REVERT: E 184 ASP cc_start: 0.8131 (t0) cc_final: 0.7903 (t0) REVERT: E 190 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7174 (mt-10) REVERT: E 303 ILE cc_start: 0.8476 (mt) cc_final: 0.8025 (mm) REVERT: B 212 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7383 (mp0) REVERT: B 239 MET cc_start: 0.8720 (mtm) cc_final: 0.8434 (mtm) REVERT: F 285 ILE cc_start: 0.8207 (mm) cc_final: 0.7917 (mm) REVERT: F 301 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.6876 (pm20) REVERT: C 245 ASP cc_start: 0.7446 (p0) cc_final: 0.7179 (p0) REVERT: C 247 TYR cc_start: 0.8761 (m-80) cc_final: 0.7950 (m-80) REVERT: C 333 TYR cc_start: 0.7609 (t80) cc_final: 0.7312 (t80) REVERT: G 154 ARG cc_start: 0.8152 (ttp-110) cc_final: 0.7914 (mtm-85) REVERT: G 184 ASP cc_start: 0.8132 (t0) cc_final: 0.7905 (t0) REVERT: G 190 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7169 (mt-10) REVERT: G 303 ILE cc_start: 0.8487 (mt) cc_final: 0.8042 (mm) REVERT: D 184 ASP cc_start: 0.8488 (t0) cc_final: 0.8287 (t0) REVERT: D 212 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7408 (mp0) REVERT: D 239 MET cc_start: 0.8721 (mtm) cc_final: 0.8435 (mtm) REVERT: H 285 ILE cc_start: 0.8207 (mm) cc_final: 0.7924 (mm) REVERT: H 301 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.6898 (pm20) outliers start: 29 outliers final: 23 residues processed: 262 average time/residue: 0.2986 time to fit residues: 107.6654 Evaluate side-chains 260 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 235 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 301 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 301 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 17 optimal weight: 0.3980 chunk 76 optimal weight: 0.9980 chunk 107 optimal weight: 0.0020 chunk 160 optimal weight: 2.9990 chunk 170 optimal weight: 0.0770 chunk 152 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 overall best weight: 0.4546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13444 Z= 0.125 Angle : 0.398 6.637 18208 Z= 0.211 Chirality : 0.045 0.146 2176 Planarity : 0.003 0.027 2372 Dihedral : 3.389 27.145 1946 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.44 % Allowed : 16.38 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.19), residues: 1760 helix: 0.02 (0.19), residues: 832 sheet: 0.53 (0.26), residues: 304 loop : -1.19 (0.21), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 123 HIS 0.003 0.000 HIS G 193 PHE 0.003 0.001 PHE C 312 TYR 0.007 0.001 TYR C 333 ARG 0.002 0.000 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 231 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 TYR cc_start: 0.8682 (m-80) cc_final: 0.8039 (m-80) REVERT: A 333 TYR cc_start: 0.7646 (t80) cc_final: 0.7326 (t80) REVERT: E 303 ILE cc_start: 0.8543 (mt) cc_final: 0.8113 (mm) REVERT: B 212 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7412 (mp0) REVERT: F 285 ILE cc_start: 0.8181 (mm) cc_final: 0.7887 (mm) REVERT: F 301 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7153 (pm20) REVERT: C 333 TYR cc_start: 0.7623 (t80) cc_final: 0.7335 (t80) REVERT: G 303 ILE cc_start: 0.8528 (mt) cc_final: 0.8081 (mm) REVERT: D 212 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7414 (mp0) REVERT: H 285 ILE cc_start: 0.8181 (mm) cc_final: 0.7887 (mm) REVERT: H 301 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7203 (pm20) outliers start: 34 outliers final: 26 residues processed: 249 average time/residue: 0.3215 time to fit residues: 109.1015 Evaluate side-chains 240 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 212 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 301 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 301 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13444 Z= 0.290 Angle : 0.457 6.307 18208 Z= 0.239 Chirality : 0.048 0.142 2176 Planarity : 0.003 0.028 2372 Dihedral : 3.538 24.795 1946 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.59 % Allowed : 17.74 % Favored : 79.67 % 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: -0.50 (0.19), residues: 1760 helix: 0.00 (0.19), residues: 832 sheet: 0.53 (0.26), residues: 304 loop : -1.08 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 123 HIS 0.008 0.001 HIS G 193 PHE 0.006 0.001 PHE G 251 TYR 0.010 0.001 TYR G 310 ARG 0.003 0.000 ARG C 241 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 226 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 TYR cc_start: 0.7617 (t80) cc_final: 0.7266 (t80) REVERT: E 190 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7160 (mt-10) REVERT: E 266 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8536 (mt-10) REVERT: E 303 ILE cc_start: 0.8577 (mt) cc_final: 0.8054 (mm) REVERT: B 212 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7501 (mp0) REVERT: F 285 ILE cc_start: 0.8262 (mm) cc_final: 0.7959 (mm) REVERT: C 245 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7291 (p0) REVERT: C 333 TYR cc_start: 0.7631 (t80) cc_final: 0.7289 (t80) REVERT: G 190 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7161 (mt-10) REVERT: G 266 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8543 (mt-10) REVERT: G 303 ILE cc_start: 0.8602 (mt) cc_final: 0.8092 (mm) REVERT: D 212 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7499 (mp0) REVERT: H 285 ILE cc_start: 0.8256 (mm) cc_final: 0.7966 (mm) outliers start: 36 outliers final: 26 residues processed: 248 average time/residue: 0.2966 time to fit residues: 102.0816 Evaluate side-chains 245 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 216 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP 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: 2.9990 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 164 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13444 Z= 0.161 Angle : 0.416 7.536 18208 Z= 0.217 Chirality : 0.046 0.143 2176 Planarity : 0.003 0.043 2372 Dihedral : 3.285 12.860 1942 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.59 % Allowed : 18.32 % Favored : 79.09 % 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: -0.23 (0.19), residues: 1760 helix: 0.24 (0.19), residues: 832 sheet: 0.57 (0.26), residues: 304 loop : -0.91 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 123 HIS 0.004 0.001 HIS G 193 PHE 0.004 0.001 PHE G 251 TYR 0.008 0.001 TYR E 310 ARG 0.003 0.000 ARG C 241 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 214 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 TYR cc_start: 0.7670 (t80) cc_final: 0.7400 (t80) REVERT: E 190 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7128 (mt-10) REVERT: E 245 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7719 (p0) REVERT: E 266 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8592 (mt-10) REVERT: E 303 ILE cc_start: 0.8554 (mt) cc_final: 0.8040 (mm) REVERT: F 285 ILE cc_start: 0.8295 (mm) cc_final: 0.7988 (mm) REVERT: C 262 ARG cc_start: 0.7871 (mmt-90) cc_final: 0.7554 (mpt180) REVERT: C 333 TYR cc_start: 0.7651 (t80) cc_final: 0.7390 (t80) REVERT: G 190 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7129 (mt-10) REVERT: G 245 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7721 (p0) REVERT: G 266 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8504 (mt-10) REVERT: G 303 ILE cc_start: 0.8553 (mt) cc_final: 0.8050 (mm) REVERT: H 285 ILE cc_start: 0.8298 (mm) cc_final: 0.7993 (mm) outliers start: 36 outliers final: 28 residues processed: 235 average time/residue: 0.3147 time to fit residues: 101.0266 Evaluate side-chains 236 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 204 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain H residue 245 ASP 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: 2.9990 chunk 124 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13444 Z= 0.251 Angle : 0.444 5.517 18208 Z= 0.233 Chirality : 0.047 0.142 2176 Planarity : 0.003 0.040 2372 Dihedral : 3.402 13.334 1942 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.73 % Allowed : 18.10 % Favored : 79.17 % 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: -0.22 (0.19), residues: 1760 helix: 0.22 (0.19), residues: 832 sheet: 0.55 (0.26), residues: 304 loop : -0.85 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 123 HIS 0.007 0.001 HIS G 193 PHE 0.005 0.001 PHE C 232 TYR 0.008 0.001 TYR E 310 ARG 0.002 0.000 ARG C 241 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 209 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.6710 (p0) REVERT: A 333 TYR cc_start: 0.7616 (t80) cc_final: 0.7322 (t80) REVERT: E 190 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7156 (mt-10) REVERT: E 245 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7679 (p0) REVERT: E 266 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8609 (mt-10) REVERT: E 303 ILE cc_start: 0.8565 (mt) cc_final: 0.8040 (mm) REVERT: F 285 ILE cc_start: 0.8347 (mm) cc_final: 0.8022 (mm) REVERT: C 210 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7029 (mt-10) REVERT: C 245 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6658 (p0) REVERT: C 333 TYR cc_start: 0.7633 (t80) cc_final: 0.7347 (t80) REVERT: G 190 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7151 (mt-10) REVERT: G 245 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7678 (p0) REVERT: G 266 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8564 (mt-10) REVERT: G 303 ILE cc_start: 0.8559 (mt) cc_final: 0.8025 (mm) REVERT: H 285 ILE cc_start: 0.8334 (mm) cc_final: 0.8042 (mm) outliers start: 38 outliers final: 31 residues processed: 233 average time/residue: 0.3191 time to fit residues: 102.1430 Evaluate side-chains 236 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 198 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain H residue 245 ASP 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: 1.9990 chunk 51 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13444 Z= 0.145 Angle : 0.407 7.449 18208 Z= 0.212 Chirality : 0.046 0.146 2176 Planarity : 0.003 0.036 2372 Dihedral : 3.203 13.338 1942 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.87 % Allowed : 18.46 % Favored : 78.66 % 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: 0.07 (0.20), residues: 1760 helix: 0.49 (0.19), residues: 832 sheet: 0.64 (0.27), residues: 304 loop : -0.73 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 123 HIS 0.003 0.000 HIS G 193 PHE 0.005 0.001 PHE G 251 TYR 0.008 0.001 TYR A 333 ARG 0.003 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 225 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6726 (p0) REVERT: A 333 TYR cc_start: 0.7684 (t80) cc_final: 0.7465 (t80) REVERT: E 190 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7108 (mt-10) REVERT: E 245 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7666 (p0) REVERT: E 266 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8520 (mt-10) REVERT: E 303 ILE cc_start: 0.8544 (mt) cc_final: 0.8025 (mm) REVERT: F 285 ILE cc_start: 0.8333 (mm) cc_final: 0.8049 (mm) REVERT: C 210 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6959 (mt-10) REVERT: C 245 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.6838 (p0) REVERT: C 333 TYR cc_start: 0.7611 (t80) cc_final: 0.7341 (t80) REVERT: G 190 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7102 (mt-10) REVERT: G 245 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7670 (p0) REVERT: G 266 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8506 (mt-10) REVERT: G 303 ILE cc_start: 0.8550 (mt) cc_final: 0.8037 (mm) REVERT: D 221 ARG cc_start: 0.7722 (mtt90) cc_final: 0.7504 (mtt180) REVERT: H 285 ILE cc_start: 0.8330 (mm) cc_final: 0.7997 (mm) outliers start: 40 outliers final: 30 residues processed: 249 average time/residue: 0.3495 time to fit residues: 119.9263 Evaluate side-chains 252 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 215 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain H residue 245 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 95 optimal weight: 0.0070 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13444 Z= 0.149 Angle : 0.427 10.526 18208 Z= 0.218 Chirality : 0.046 0.157 2176 Planarity : 0.003 0.039 2372 Dihedral : 3.147 13.257 1942 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.80 % Allowed : 19.04 % Favored : 78.16 % 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: 0.20 (0.20), residues: 1760 helix: 0.59 (0.19), residues: 832 sheet: 0.70 (0.27), residues: 304 loop : -0.64 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 123 HIS 0.003 0.000 HIS E 193 PHE 0.005 0.001 PHE G 251 TYR 0.007 0.001 TYR A 333 ARG 0.002 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 227 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.6785 (p0) REVERT: A 333 TYR cc_start: 0.7653 (t80) cc_final: 0.7404 (t80) REVERT: E 190 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7125 (mt-10) REVERT: E 245 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7632 (p0) REVERT: E 266 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8526 (mt-10) REVERT: E 303 ILE cc_start: 0.8520 (mt) cc_final: 0.8003 (mm) REVERT: F 285 ILE cc_start: 0.8362 (mm) cc_final: 0.8020 (mm) REVERT: C 245 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6773 (p0) REVERT: C 262 ARG cc_start: 0.7753 (mpt180) cc_final: 0.7379 (mpt180) REVERT: C 333 TYR cc_start: 0.7601 (t80) cc_final: 0.7372 (t80) REVERT: G 190 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7127 (mt-10) REVERT: G 245 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7639 (p0) REVERT: G 266 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8490 (mt-10) REVERT: G 303 ILE cc_start: 0.8532 (mt) cc_final: 0.8017 (mm) REVERT: H 285 ILE cc_start: 0.8283 (mm) cc_final: 0.8026 (mm) outliers start: 39 outliers final: 31 residues processed: 250 average time/residue: 0.3311 time to fit residues: 112.3309 Evaluate side-chains 257 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 220 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 266 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 0.0000 chunk 110 optimal weight: 0.6980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13444 Z= 0.186 Angle : 0.435 9.446 18208 Z= 0.223 Chirality : 0.046 0.162 2176 Planarity : 0.003 0.037 2372 Dihedral : 3.207 13.604 1942 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.87 % Allowed : 18.89 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1760 helix: 0.57 (0.19), residues: 832 sheet: 0.72 (0.27), residues: 304 loop : -0.64 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 123 HIS 0.004 0.001 HIS E 193 PHE 0.006 0.001 PHE G 251 TYR 0.007 0.001 TYR A 333 ARG 0.002 0.000 ARG C 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 216 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.6781 (p0) REVERT: A 333 TYR cc_start: 0.7628 (t80) cc_final: 0.7392 (t80) REVERT: E 190 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7139 (mt-10) REVERT: E 245 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7636 (p0) REVERT: E 266 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8514 (mt-10) REVERT: E 303 ILE cc_start: 0.8555 (mt) cc_final: 0.8039 (mm) REVERT: C 210 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6991 (mt-10) REVERT: C 245 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6804 (p0) REVERT: C 262 ARG cc_start: 0.7741 (mpt180) cc_final: 0.7308 (mpt180) REVERT: C 333 TYR cc_start: 0.7609 (t80) cc_final: 0.7375 (t80) REVERT: G 190 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7142 (mt-10) REVERT: G 245 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7637 (p0) REVERT: G 266 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8515 (mt-10) REVERT: G 303 ILE cc_start: 0.8565 (mt) cc_final: 0.8050 (mm) REVERT: H 285 ILE cc_start: 0.8302 (mm) cc_final: 0.8045 (mm) outliers start: 40 outliers final: 32 residues processed: 241 average time/residue: 0.3254 time to fit residues: 105.5703 Evaluate side-chains 256 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 217 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 266 GLU 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: 6.9990 chunk 128 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.150742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.113831 restraints weight = 14445.219| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.04 r_work: 0.2922 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13444 Z= 0.318 Angle : 0.493 8.572 18208 Z= 0.254 Chirality : 0.049 0.172 2176 Planarity : 0.003 0.035 2372 Dihedral : 3.487 13.995 1942 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.80 % Allowed : 19.25 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1760 helix: 0.36 (0.19), residues: 832 sheet: 0.62 (0.27), residues: 304 loop : -0.69 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 123 HIS 0.008 0.001 HIS E 193 PHE 0.008 0.001 PHE G 251 TYR 0.010 0.001 TYR D 247 ARG 0.002 0.000 ARG A 241 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: