Starting phenix.real_space_refine on Thu Feb 15 20:05:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwn_20925/02_2024/6uwn_20925.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwn_20925/02_2024/6uwn_20925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwn_20925/02_2024/6uwn_20925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwn_20925/02_2024/6uwn_20925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwn_20925/02_2024/6uwn_20925.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwn_20925/02_2024/6uwn_20925.pdb" } resolution = 3.5 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 8302 2.51 5 N 2374 2.21 5 O 2502 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 GLU 129": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E ASP 163": "OD1" <-> "OD2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 244": "OD1" <-> "OD2" Residue "E ASP 245": "OD1" <-> "OD2" Residue "E ARG 262": "NH1" <-> "NH2" Residue "E ASP 284": "OD1" <-> "OD2" Residue "E GLU 301": "OE1" <-> "OE2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B ASP 282": "OD1" <-> "OD2" Residue "F ARG 116": "NH1" <-> "NH2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F ASP 145": "OD1" <-> "OD2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 245": "OD1" <-> "OD2" Residue "F ARG 262": "NH1" <-> "NH2" Residue "F ASP 287": "OD1" <-> "OD2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 116": "NH1" <-> "NH2" Residue "G GLU 138": "OE1" <-> "OE2" Residue "G ASP 163": "OD1" <-> "OD2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G GLU 171": "OE1" <-> "OE2" Residue "G ASP 188": "OD1" <-> "OD2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "G PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G ASP 254": "OD1" <-> "OD2" Residue "G ARG 262": "NH1" <-> "NH2" Residue "G ASP 284": "OD1" <-> "OD2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D ASP 145": "OD1" <-> "OD2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "H ARG 116": "NH1" <-> "NH2" Residue "H GLU 144": "OE1" <-> "OE2" Residue "H ASP 145": "OD1" <-> "OD2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "H PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 245": "OD1" <-> "OD2" Residue "H ARG 262": "NH1" <-> "NH2" Residue "H ASP 287": "OD1" <-> "OD2" Residue "H ASP 316": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13258 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1662 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Conformer: "B" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 bond proxies already assigned to first conformer: 1660 Chain: "E" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1654 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1652 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1647 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 1662 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Conformer: "B" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 bond proxies already assigned to first conformer: 1660 Chain: "G" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1654 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1652 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "H" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1647 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "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} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 241 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 241 " occ=0.50 residue: pdb=" N AARG C 241 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 241 " occ=0.50 Time building chain proxies: 8.56, per 1000 atoms: 0.65 Number of scatterers: 13258 At special positions: 0 Unit cell: (138.03, 135.89, 66.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 24 19.99 S 56 16.00 O 2502 8.00 N 2374 7.00 C 8302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.68 Conformation dependent library (CDL) restraints added in 2.9 seconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3268 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 16 sheets defined 43.7% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.581A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.666A 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 223 Processing helix chain 'A' and resid 230 through 241 Processing helix chain 'A' and resid 247 through 256 removed outlier: 3.655A pdb=" N LEU A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.531A 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 134 removed outlier: 3.565A pdb=" N GLU E 133 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 155 Processing helix chain 'E' and resid 166 through 172 Processing helix chain 'E' and resid 187 through 202 Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.664A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.571A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.608A pdb=" N MET E 250 " --> pdb=" O GLY E 246 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 323 through 334 Processing helix chain 'B' and resid 124 through 131 removed outlier: 3.528A pdb=" N GLU B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 148 through 155 Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 187 through 202 removed outlier: 3.643A pdb=" N ILE B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.532A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.533A pdb=" N SER B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.664A pdb=" N LEU B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.645A pdb=" N ASP B 284 " --> pdb=" O VAL B 280 " (cutoff:3.500A) 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 removed outlier: 3.655A pdb=" N GLU F 133 " --> pdb=" O GLU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 147 No H-bonds generated for 'chain 'F' and resid 145 through 147' Processing helix chain 'F' and resid 148 through 155 Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.755A pdb=" N ALA F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 Processing helix chain 'F' and resid 216 through 223 Processing helix chain 'F' and resid 230 through 240 removed outlier: 3.505A pdb=" N ILE F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 removed outlier: 3.689A pdb=" N ASP F 254 " --> pdb=" O MET F 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU F 256 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.803A pdb=" N ASP F 284 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 289 Processing helix chain 'F' and resid 323 through 332 removed outlier: 3.507A pdb=" N ASN F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.894A pdb=" N GLU C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.530A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.594A pdb=" N THR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 230 through 242 Processing helix chain 'C' and resid 247 through 256 removed outlier: 3.509A pdb=" N VAL C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP C 254 " --> pdb=" O MET C 250 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 289 removed outlier: 3.535A 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 removed outlier: 3.531A pdb=" N GLU G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 155 Processing helix chain 'G' and resid 166 through 172 removed outlier: 3.501A pdb=" N LYS G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.643A pdb=" N GLY G 197 " --> pdb=" O HIS G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.557A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 241 removed outlier: 3.888A pdb=" N SER G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 256 removed outlier: 3.529A pdb=" N MET G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU G 256 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 289 Processing helix chain 'G' and resid 323 through 334 removed outlier: 3.879A pdb=" N GLU G 328 " --> pdb=" O PRO G 324 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN G 332 " --> pdb=" O GLU G 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 131 removed outlier: 3.519A pdb=" N GLU D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 148 through 155 Processing helix chain 'D' and resid 166 through 172 Processing helix chain 'D' and resid 187 through 202 removed outlier: 3.650A pdb=" N ILE D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.684A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.528A pdb=" N SER D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.664A pdb=" N LEU D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 284 removed outlier: 3.641A pdb=" N ASP D 284 " --> pdb=" O VAL D 280 " (cutoff:3.500A) 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 removed outlier: 3.664A pdb=" N GLU H 133 " --> pdb=" O GLU H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing helix chain 'H' and resid 148 through 155 Processing helix chain 'H' and resid 166 through 173 removed outlier: 3.761A pdb=" N ALA H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 Processing helix chain 'H' and resid 216 through 223 Processing helix chain 'H' and resid 230 through 241 removed outlier: 3.503A pdb=" N ILE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 256 removed outlier: 3.687A pdb=" N ASP H 254 " --> pdb=" O MET H 250 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU H 256 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.801A pdb=" N ASP H 284 " --> pdb=" O VAL H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 Processing helix chain 'H' and resid 323 through 332 removed outlier: 3.539A pdb=" N ASN H 332 " --> pdb=" O GLU H 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.792A pdb=" N VAL A 139 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL A 160 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 141 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 119 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 3.501A pdb=" N GLY A 295 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.540A pdb=" N ALA E 143 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL E 181 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLU E 210 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL E 183 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE E 229 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 263 through 268 removed outlier: 7.485A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU E 301 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.567A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 207 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE B 229 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA B 209 " --> pdb=" O ILE B 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.670A pdb=" N GLY B 322 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE B 317 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL B 296 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU B 319 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.504A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 6.027A 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: 3.566A pdb=" N GLY F 322 " --> pdb=" O ARG F 263 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE F 317 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL F 296 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU F 319 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.781A pdb=" N VAL C 139 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL C 160 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL C 141 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C 119 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 263 through 268 removed outlier: 3.501A pdb=" N GLY C 295 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 158 through 161 removed outlier: 3.524A pdb=" N ALA G 143 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL G 181 " --> pdb=" O ILE G 208 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N GLU G 210 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL G 183 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE G 229 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 263 through 268 removed outlier: 7.467A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU G 301 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.559A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE D 207 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE D 229 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA D 209 " --> pdb=" O ILE D 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.667A pdb=" N GLY D 322 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE D 317 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL D 296 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU D 319 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.506A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 6.027A 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: 3.558A pdb=" N GLY H 322 " --> pdb=" O ARG H 263 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE H 317 " --> pdb=" O VAL H 296 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL H 296 " --> pdb=" O ILE H 317 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU H 319 " --> pdb=" O ILE H 294 " (cutoff:3.500A) 563 hydrogen bonds defined for protein. 1600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4531 1.34 - 1.45: 1220 1.45 - 1.57: 7561 1.57 - 1.69: 0 1.69 - 1.80: 88 Bond restraints: 13400 Sorted by residual: bond pdb=" CG LEU E 220 " pdb=" CD2 LEU E 220 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.72e+00 bond pdb=" CG1 ILE D 195 " pdb=" CD1 ILE D 195 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.33e+00 bond pdb=" CG1 ILE C 195 " pdb=" CD1 ILE C 195 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.21e+00 bond pdb=" CG LEU G 220 " pdb=" CD2 LEU G 220 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.18e+00 bond pdb=" CG LEU D 220 " pdb=" CD2 LEU D 220 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.16e+00 ... (remaining 13395 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.78: 283 106.78 - 113.58: 7825 113.58 - 120.38: 5178 120.38 - 127.18: 4768 127.18 - 133.98: 98 Bond angle restraints: 18152 Sorted by residual: angle pdb=" N ILE H 334 " pdb=" CA ILE H 334 " pdb=" C ILE H 334 " ideal model delta sigma weight residual 112.29 109.82 2.47 9.40e-01 1.13e+00 6.90e+00 angle pdb=" CA LEU E 275 " pdb=" CB LEU E 275 " pdb=" CG LEU E 275 " ideal model delta sigma weight residual 116.30 125.26 -8.96 3.50e+00 8.16e-02 6.56e+00 angle pdb=" N ILE F 334 " pdb=" CA ILE F 334 " pdb=" C ILE F 334 " ideal model delta sigma weight residual 112.29 109.88 2.41 9.40e-01 1.13e+00 6.55e+00 angle pdb=" CA LEU G 275 " pdb=" CB LEU G 275 " pdb=" CG LEU G 275 " ideal model delta sigma weight residual 116.30 125.23 -8.93 3.50e+00 8.16e-02 6.51e+00 angle pdb=" C ARG A 132 " pdb=" N GLU A 133 " pdb=" CA GLU A 133 " ideal model delta sigma weight residual 122.06 117.83 4.23 1.86e+00 2.89e-01 5.16e+00 ... (remaining 18147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 7465 18.04 - 36.07: 585 36.07 - 54.11: 98 54.11 - 72.15: 22 72.15 - 90.19: 10 Dihedral angle restraints: 8180 sinusoidal: 3108 harmonic: 5072 Sorted by residual: dihedral pdb=" CA GLU D 129 " pdb=" C GLU D 129 " pdb=" N CYS D 130 " pdb=" CA CYS D 130 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLU B 129 " pdb=" C GLU B 129 " pdb=" N CYS B 130 " pdb=" CA CYS B 130 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ASP C 169 " pdb=" CB ASP C 169 " pdb=" CG ASP C 169 " pdb=" OD1 ASP C 169 " ideal model delta sinusoidal sigma weight residual -30.00 -88.73 58.73 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 8177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1531 0.054 - 0.109: 520 0.109 - 0.163: 113 0.163 - 0.217: 8 0.217 - 0.272: 2 Chirality restraints: 2174 Sorted by residual: chirality pdb=" CB ILE D 293 " pdb=" CA ILE D 293 " pdb=" CG1 ILE D 293 " pdb=" CG2 ILE D 293 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE B 293 " pdb=" CA ILE B 293 " pdb=" CG1 ILE B 293 " pdb=" CG2 ILE B 293 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL D 205 " pdb=" CA VAL D 205 " pdb=" CG1 VAL D 205 " pdb=" CG2 VAL D 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2171 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 267 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO A 268 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 267 " -0.039 5.00e-02 4.00e+02 5.91e-02 5.58e+00 pdb=" N PRO C 268 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 268 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 268 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 267 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C VAL C 267 " 0.035 2.00e-02 2.50e+03 pdb=" O VAL C 267 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO C 268 " -0.012 2.00e-02 2.50e+03 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3815 2.81 - 3.33: 10954 3.33 - 3.85: 21131 3.85 - 4.38: 23886 4.38 - 4.90: 43557 Nonbonded interactions: 103343 Sorted by model distance: nonbonded pdb=" OE2 GLU G 212 " pdb=" O HOH G 501 " model vdw 2.285 2.440 nonbonded pdb=" OD1 ASP E 184 " pdb=" O HOH E 501 " model vdw 2.286 2.440 nonbonded pdb=" O ILE F 285 " pdb=" OG1 THR F 289 " model vdw 2.286 2.440 nonbonded pdb=" O ILE H 285 " pdb=" OG1 THR H 289 " model vdw 2.288 2.440 nonbonded pdb=" OD1 ASP G 184 " pdb=" O HOH G 501 " model vdw 2.289 2.440 ... (remaining 103338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 or (resid 135 and (name N or name CA o \ r name C or name O or name CB )) or resid 136 through 137 or (resid 138 and (nam \ e N or name CA or name C or name O or name CB )) or resid 139 through 143 or (re \ sid 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 170 or (resid 171 and (name N or name CA or name C or name \ O or name CB )) or resid 172 through 240 or resid 242 through 244 or (resid 245 \ and (name N or name CA or name C or name O or name CB )) or resid 246 through 2 \ 53 or (resid 254 and (name N or name CA or name C or name O or name CB )) or res \ id 255 through 262 or (resid 263 and (name N or name CA or name C or name O or n \ ame CB )) or resid 264 through 273 or (resid 274 and (name N or name CA or name \ C or name O or name CB )) or resid 275 through 283 or (resid 284 and (name N or \ name CA or name C or name O or name CB )) or resid 285 through 286 or (resid 287 \ and (name N or name CA or name C or name O or name CB )) or resid 288 through 2 \ 97 or (resid 298 and (name N or name CA or name C or name O or name CB )) or res \ id 299 through 312 or (resid 313 through 314 and (name N or name CA or name C or \ name O or name CB )) or resid 315 through 324 or (resid 325 and (name N or name \ CA or name C or name O or name CB )) or resid 326 through 327 or (resid 328 and \ (name N or name CA or name C or name O or name CB )) or resid 329 through 336 o \ r resid 401 through 402)) selection = (chain 'B' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 137 or (resid 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 throug \ h 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) or \ resid 148 or (resid 149 through 150 and (name N or name CA or name C or name O o \ r name CB )) or resid 151 through 153 or (resid 154 and (name N or name CA or na \ me C or name O or name CB )) or resid 155 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 240 or resid 2 \ 42 through 253 or (resid 254 and (name N or name CA or name C or name O or name \ CB )) or resid 255 through 270 or (resid 271 and (name N or name CA or name C or \ name O or name CB )) or resid 272 through 273 or (resid 274 and (name N or name \ CA or name C or name O or name CB )) or resid 275 or (resid 276 and (name N or \ name CA or name C or name O or name CB )) or resid 277 through 280 or (resid 281 \ through 284 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 85 through 297 or (resid 298 and (name N or name CA or name C or name O or name \ CB )) or resid 299 through 312 or (resid 313 through 314 and (name N or name CA \ or name C or name O or name CB )) or resid 315 through 336 or resid 401 through \ 402)) selection = (chain 'C' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 or (resid 135 and (name N or name CA o \ r name C or name O or name CB )) or resid 136 through 137 or (resid 138 and (nam \ e N or name CA or name C or name O or name CB )) or resid 139 through 143 or (re \ sid 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 170 or (resid 171 and (name N or name CA or name C or name \ O or name CB )) or resid 172 through 240 or resid 242 through 244 or (resid 245 \ and (name N or name CA or name C or name O or name CB )) or resid 246 through 2 \ 53 or (resid 254 and (name N or name CA or name C or name O or name CB )) or res \ id 255 through 262 or (resid 263 and (name N or name CA or name C or name O or n \ ame CB )) or resid 264 through 273 or (resid 274 and (name N or name CA or name \ C or name O or name CB )) or resid 275 through 283 or (resid 284 and (name N or \ name CA or name C or name O or name CB )) or resid 285 through 286 or (resid 287 \ and (name N or name CA or name C or name O or name CB )) or resid 288 through 2 \ 97 or (resid 298 and (name N or name CA or name C or name O or name CB )) or res \ id 299 through 312 or (resid 313 through 314 and (name N or name CA or name C or \ name O or name CB )) or resid 315 through 324 or (resid 325 and (name N or name \ CA or name C or name O or name CB )) or resid 326 through 327 or (resid 328 and \ (name N or name CA or name C or name O or name CB )) or resid 329 through 336 o \ r resid 401 through 402)) selection = (chain 'D' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 137 or (resid 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 throug \ h 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) or \ resid 148 or (resid 149 through 150 and (name N or name CA or name C or name O o \ r name CB )) or resid 151 through 153 or (resid 154 and (name N or name CA or na \ me C or name O or name CB )) or resid 155 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 240 or resid 2 \ 42 through 253 or (resid 254 and (name N or name CA or name C or name O or name \ CB )) or resid 255 through 270 or (resid 271 and (name N or name CA or name C or \ name O or name CB )) or resid 272 through 273 or (resid 274 and (name N or name \ CA or name C or name O or name CB )) or resid 275 or (resid 276 and (name N or \ name CA or name C or name O or name CB )) or resid 277 through 280 or (resid 281 \ through 284 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 85 through 297 or (resid 298 and (name N or name CA or name C or name O or name \ CB )) or resid 299 through 312 or (resid 313 through 314 and (name N or name CA \ or name C or name O or name CB )) or resid 315 through 336 or resid 401 through \ 402)) selection = (chain 'E' and (resid 115 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 148 or (resid 149 through 150 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 15 \ 3 or (resid 154 and (name N or name CA or name C or name O or name CB )) or resi \ d 155 through 170 or (resid 171 and (name N or name CA or name C or name O or na \ me CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C \ or name O or name CB )) or resid 204 through 217 or (resid 218 and (name N or n \ ame CA or name C or name O or name CB )) or resid 219 through 240 or resid 242 t \ hrough 243 or (resid 244 through 245 and (name N or name CA or name C or name O \ or name CB )) or resid 246 through 253 or (resid 254 and (name N or name CA or n \ ame C or name O or name CB )) or resid 255 through 262 or (resid 263 and (name N \ or name CA or name C or name O or name CB )) or resid 264 through 281 or (resid \ 282 through 284 and (name N or name CA or name C or name O or name CB )) or res \ id 285 through 300 or (resid 301 and (name N or name CA or name C or name O or n \ ame CB )) or resid 302 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 312 or (resid 313 through 314 and \ (name N or name CA or name C or name O or name CB )) or resid 315 through 324 o \ r (resid 325 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 26 through 336 or resid 401 through 402)) selection = (chain 'F' and (resid 115 through 143 or (resid 144 and (name N or name CA or na \ me C or name O or name CB )) or resid 145 or (resid 146 through 147 and (name N \ or name CA or name C or name O or name CB )) or resid 148 or (resid 149 through \ 150 and (name N or name CA or name C or name O or name CB )) or resid 151 throug \ h 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) or \ resid 155 through 217 or (resid 218 and (name N or name CA or name C or name O o \ r name CB )) or resid 219 through 240 or resid 242 through 243 or (resid 244 thr \ ough 245 and (name N or name CA or name C or name O or name CB )) or resid 246 t \ hrough 280 or (resid 281 through 284 and (name N or name CA or name C or name O \ or name CB )) or resid 285 through 286 or (resid 287 and (name N or name CA or n \ ame C or name O or name CB )) or resid 288 through 297 or (resid 298 and (name N \ or name CA or name C or name O or name CB )) or resid 299 or (resid 300 through \ 301 and (name N or name CA or name C or name O or name CB )) or resid 302 throu \ gh 307 or (resid 308 through 309 and (name N or name CA or name C or name O or n \ ame CB )) or resid 310 through 324 or (resid 325 and (name N or name CA or name \ C or name O or name CB )) or resid 326 through 327 or (resid 328 and (name N or \ name CA or name C or name O or name CB )) or resid 329 through 336 or resid 401 \ through 402)) selection = (chain 'G' and (resid 115 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 148 or (resid 149 through 150 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 15 \ 3 or (resid 154 and (name N or name CA or name C or name O or name CB )) or resi \ d 155 through 170 or (resid 171 and (name N or name CA or name C or name O or na \ me CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C \ or name O or name CB )) or resid 204 through 217 or (resid 218 and (name N or n \ ame CA or name C or name O or name CB )) or resid 219 through 240 or resid 242 t \ hrough 243 or (resid 244 through 245 and (name N or name CA or name C or name O \ or name CB )) or resid 246 through 253 or (resid 254 and (name N or name CA or n \ ame C or name O or name CB )) or resid 255 through 262 or (resid 263 and (name N \ or name CA or name C or name O or name CB )) or resid 264 through 281 or (resid \ 282 through 284 and (name N or name CA or name C or name O or name CB )) or res \ id 285 through 300 or (resid 301 and (name N or name CA or name C or name O or n \ ame CB )) or resid 302 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 312 or (resid 313 through 314 and \ (name N or name CA or name C or name O or name CB )) or resid 315 through 324 o \ r (resid 325 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 26 through 336 or resid 401 through 402)) selection = (chain 'H' and (resid 115 through 143 or (resid 144 and (name N or name CA or na \ me C or name O or name CB )) or resid 145 or (resid 146 through 147 and (name N \ or name CA or name C or name O or name CB )) or resid 148 or (resid 149 through \ 150 and (name N or name CA or name C or name O or name CB )) or resid 151 throug \ h 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) or \ resid 155 through 217 or (resid 218 and (name N or name CA or name C or name O o \ r name CB )) or resid 219 through 240 or resid 242 through 243 or (resid 244 thr \ ough 245 and (name N or name CA or name C or name O or name CB )) or resid 246 t \ hrough 280 or (resid 281 through 284 and (name N or name CA or name C or name O \ or name CB )) or resid 285 through 286 or (resid 287 and (name N or name CA or n \ ame C or name O or name CB )) or resid 288 through 297 or (resid 298 and (name N \ or name CA or name C or name O or name CB )) or resid 299 or (resid 300 through \ 301 and (name N or name CA or name C or name O or name CB )) or resid 302 throu \ gh 307 or (resid 308 through 309 and (name N or name CA or name C or name O or n \ ame CB )) or resid 310 through 324 or (resid 325 and (name N or name CA or name \ C or name O or name CB )) or resid 326 through 327 or (resid 328 and (name N or \ name CA or name C or name O or name CB )) or resid 329 through 336 or resid 401 \ through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 3.560 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 38.400 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.070 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.007 0.060 13400 Z= 0.484 Angle : 0.728 8.965 18152 Z= 0.425 Chirality : 0.055 0.272 2174 Planarity : 0.005 0.060 2360 Dihedral : 13.753 90.187 4912 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.15 % Allowed : 6.89 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.15), residues: 1766 helix: -4.24 (0.08), residues: 814 sheet: 0.25 (0.24), residues: 384 loop : -2.64 (0.19), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 123 HIS 0.009 0.001 HIS G 193 PHE 0.013 0.002 PHE A 232 TYR 0.020 0.002 TYR D 247 ARG 0.004 0.001 ARG H 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.578 Fit side-chains REVERT: A 151 LYS cc_start: 0.8082 (ptpt) cc_final: 0.7625 (ttpt) REVERT: E 129 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8652 (mm-30) REVERT: E 190 GLU cc_start: 0.8501 (mp0) cc_final: 0.8121 (mt-10) REVERT: E 332 ASN cc_start: 0.8165 (m-40) cc_final: 0.7750 (t0) REVERT: B 226 ASP cc_start: 0.8346 (m-30) cc_final: 0.7758 (m-30) REVERT: B 310 TYR cc_start: 0.8518 (t80) cc_final: 0.7845 (t80) REVERT: F 125 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8476 (mm-30) REVERT: F 184 ASP cc_start: 0.8313 (t70) cc_final: 0.8079 (t0) REVERT: F 210 GLU cc_start: 0.8351 (tt0) cc_final: 0.7970 (tt0) REVERT: F 300 ASP cc_start: 0.7731 (t70) cc_final: 0.7320 (t70) REVERT: F 323 LYS cc_start: 0.8155 (mttm) cc_final: 0.7920 (mtpt) REVERT: C 151 LYS cc_start: 0.8013 (ptpt) cc_final: 0.7587 (ttpt) REVERT: G 210 GLU cc_start: 0.8411 (tt0) cc_final: 0.8077 (tt0) REVERT: G 239 MET cc_start: 0.8667 (mtt) cc_final: 0.8451 (mtt) REVERT: G 325 GLU cc_start: 0.8441 (tt0) cc_final: 0.8210 (tp30) REVERT: D 226 ASP cc_start: 0.8258 (m-30) cc_final: 0.7777 (m-30) REVERT: D 310 TYR cc_start: 0.8532 (t80) cc_final: 0.7877 (t80) REVERT: H 125 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8404 (mm-30) REVERT: H 184 ASP cc_start: 0.8302 (t70) cc_final: 0.8100 (t0) REVERT: H 210 GLU cc_start: 0.8337 (tt0) cc_final: 0.7993 (tt0) REVERT: H 300 ASP cc_start: 0.7683 (t70) cc_final: 0.7290 (t70) REVERT: H 323 LYS cc_start: 0.8173 (mttm) cc_final: 0.7936 (mtpt) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.3355 time to fit residues: 161.3223 Evaluate side-chains 283 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN B 227 GLN F 286 HIS F 332 ASN C 219 GLN C 253 GLN D 227 GLN H 117 HIS H 286 HIS H 332 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13400 Z= 0.186 Angle : 0.461 4.651 18152 Z= 0.254 Chirality : 0.046 0.148 2174 Planarity : 0.004 0.039 2360 Dihedral : 3.875 18.321 1942 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.81 % Allowed : 12.19 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.17), residues: 1766 helix: -2.30 (0.15), residues: 830 sheet: 0.52 (0.26), residues: 336 loop : -1.87 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 123 HIS 0.005 0.001 HIS G 193 PHE 0.007 0.001 PHE G 251 TYR 0.015 0.001 TYR E 333 ARG 0.008 0.000 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 284 time to evaluate : 1.529 Fit side-chains REVERT: A 151 LYS cc_start: 0.8072 (ptpt) cc_final: 0.7615 (ttpt) REVERT: A 284 ASP cc_start: 0.8285 (t0) cc_final: 0.8019 (t0) REVERT: E 129 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8746 (mm-30) REVERT: E 190 GLU cc_start: 0.8370 (mp0) cc_final: 0.8088 (mt-10) REVERT: B 226 ASP cc_start: 0.8283 (m-30) cc_final: 0.7570 (m-30) REVERT: B 239 MET cc_start: 0.8860 (mtp) cc_final: 0.8394 (mtt) REVERT: B 303 ILE cc_start: 0.8614 (mp) cc_final: 0.8237 (tp) REVERT: F 184 ASP cc_start: 0.8348 (t70) cc_final: 0.8008 (t0) REVERT: F 210 GLU cc_start: 0.8384 (tt0) cc_final: 0.8027 (tt0) REVERT: F 300 ASP cc_start: 0.7683 (t70) cc_final: 0.7271 (t70) REVERT: C 151 LYS cc_start: 0.7897 (ptpt) cc_final: 0.7504 (ttpt) REVERT: C 284 ASP cc_start: 0.8292 (t0) cc_final: 0.8027 (t0) REVERT: D 226 ASP cc_start: 0.8189 (m-30) cc_final: 0.7613 (m-30) REVERT: D 239 MET cc_start: 0.8851 (mtp) cc_final: 0.8397 (mtt) REVERT: H 184 ASP cc_start: 0.8312 (t70) cc_final: 0.7980 (t0) REVERT: H 210 GLU cc_start: 0.8406 (tt0) cc_final: 0.8062 (tt0) REVERT: H 300 ASP cc_start: 0.7695 (t70) cc_final: 0.7287 (t70) outliers start: 23 outliers final: 14 residues processed: 294 average time/residue: 0.2655 time to fit residues: 109.9867 Evaluate side-chains 281 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 267 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 327 ILE 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: 0.7980 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 0.2980 chunk 172 optimal weight: 0.0570 chunk 142 optimal weight: 0.0020 chunk 158 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 overall best weight: 0.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 253 GLN F 117 HIS G 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 13400 Z= 0.120 Angle : 0.407 4.831 18152 Z= 0.220 Chirality : 0.045 0.137 2174 Planarity : 0.003 0.033 2360 Dihedral : 3.377 16.500 1942 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.10 % Allowed : 14.37 % Favored : 83.53 % 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: -1.27 (0.19), residues: 1766 helix: -0.94 (0.17), residues: 830 sheet: 0.70 (0.26), residues: 336 loop : -1.38 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 123 HIS 0.003 0.000 HIS G 193 PHE 0.006 0.001 PHE B 140 TYR 0.022 0.002 TYR A 333 ARG 0.007 0.000 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 300 time to evaluate : 1.314 Fit side-chains REVERT: A 151 LYS cc_start: 0.8086 (ptpt) cc_final: 0.7696 (ttpt) REVERT: A 284 ASP cc_start: 0.8281 (t0) cc_final: 0.8009 (t0) REVERT: A 294 ILE cc_start: 0.8795 (pt) cc_final: 0.8459 (mt) REVERT: E 129 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8729 (mm-30) REVERT: E 145 ASP cc_start: 0.8573 (t70) cc_final: 0.8360 (t0) REVERT: E 190 GLU cc_start: 0.8254 (mp0) cc_final: 0.7919 (mt-10) REVERT: B 129 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7378 (tm-30) REVERT: B 226 ASP cc_start: 0.8301 (m-30) cc_final: 0.7521 (m-30) REVERT: B 303 ILE cc_start: 0.8607 (mp) cc_final: 0.8322 (tp) REVERT: F 210 GLU cc_start: 0.8316 (tt0) cc_final: 0.7540 (tt0) REVERT: F 300 ASP cc_start: 0.7703 (t70) cc_final: 0.7309 (t70) REVERT: C 151 LYS cc_start: 0.7927 (ptpt) cc_final: 0.7545 (ttpt) REVERT: C 284 ASP cc_start: 0.8320 (t0) cc_final: 0.8042 (t0) REVERT: C 294 ILE cc_start: 0.8820 (pt) cc_final: 0.8467 (mt) REVERT: D 129 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7284 (tm-30) REVERT: D 226 ASP cc_start: 0.8148 (m-30) cc_final: 0.7533 (m-30) REVERT: D 303 ILE cc_start: 0.8624 (mp) cc_final: 0.8328 (tp) REVERT: D 310 TYR cc_start: 0.8392 (t80) cc_final: 0.7704 (t80) REVERT: H 210 GLU cc_start: 0.8336 (tt0) cc_final: 0.7564 (tt0) REVERT: H 300 ASP cc_start: 0.7666 (t70) cc_final: 0.7287 (t70) outliers start: 27 outliers final: 16 residues processed: 312 average time/residue: 0.2882 time to fit residues: 124.4910 Evaluate side-chains 292 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 276 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 107 optimal weight: 0.2980 chunk 160 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13400 Z= 0.231 Angle : 0.442 4.825 18152 Z= 0.236 Chirality : 0.046 0.135 2174 Planarity : 0.003 0.036 2360 Dihedral : 3.388 16.548 1942 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.10 % Allowed : 15.53 % Favored : 82.37 % 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: -0.76 (0.19), residues: 1766 helix: -0.47 (0.18), residues: 838 sheet: 0.70 (0.26), residues: 336 loop : -1.05 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 123 HIS 0.005 0.001 HIS G 193 PHE 0.006 0.001 PHE A 232 TYR 0.018 0.002 TYR E 333 ARG 0.004 0.000 ARG H 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 277 time to evaluate : 1.420 Fit side-chains REVERT: A 151 LYS cc_start: 0.8139 (ptpt) cc_final: 0.7760 (ttpt) REVERT: A 263 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.7263 (mtt180) REVERT: A 284 ASP cc_start: 0.8348 (t0) cc_final: 0.8075 (t0) REVERT: E 129 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8727 (mm-30) REVERT: E 190 GLU cc_start: 0.8250 (mp0) cc_final: 0.7880 (mt-10) REVERT: B 169 ASP cc_start: 0.8673 (t70) cc_final: 0.8353 (t0) REVERT: B 226 ASP cc_start: 0.8311 (m-30) cc_final: 0.7497 (m-30) REVERT: B 303 ILE cc_start: 0.8605 (mp) cc_final: 0.8332 (tp) REVERT: F 300 ASP cc_start: 0.7730 (t70) cc_final: 0.7345 (t70) REVERT: C 151 LYS cc_start: 0.7976 (ptpt) cc_final: 0.7609 (ttpt) REVERT: C 264 MET cc_start: 0.8594 (ttm) cc_final: 0.8388 (ttm) REVERT: C 284 ASP cc_start: 0.8391 (t0) cc_final: 0.7871 (t0) REVERT: D 169 ASP cc_start: 0.8664 (t70) cc_final: 0.8379 (t0) REVERT: D 226 ASP cc_start: 0.8217 (m-30) cc_final: 0.7546 (m-30) REVERT: D 303 ILE cc_start: 0.8617 (mp) cc_final: 0.8347 (tp) REVERT: H 300 ASP cc_start: 0.7689 (t70) cc_final: 0.7294 (t70) outliers start: 27 outliers final: 20 residues processed: 287 average time/residue: 0.2529 time to fit residues: 104.0470 Evaluate side-chains 290 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 270 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN G 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13400 Z= 0.269 Angle : 0.460 5.361 18152 Z= 0.245 Chirality : 0.047 0.135 2174 Planarity : 0.003 0.036 2360 Dihedral : 3.427 16.380 1942 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.90 % Allowed : 16.84 % Favored : 80.26 % 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: -0.48 (0.20), residues: 1766 helix: -0.20 (0.18), residues: 830 sheet: 0.70 (0.26), residues: 336 loop : -0.88 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 123 HIS 0.004 0.001 HIS G 193 PHE 0.006 0.001 PHE C 312 TYR 0.024 0.002 TYR F 333 ARG 0.004 0.000 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 263 time to evaluate : 1.745 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8122 (ptpt) cc_final: 0.7733 (ttpt) REVERT: A 210 GLU cc_start: 0.7721 (tt0) cc_final: 0.7268 (tt0) REVERT: A 254 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7495 (m-30) REVERT: A 263 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.7196 (mtt180) REVERT: A 284 ASP cc_start: 0.8427 (t0) cc_final: 0.7909 (t0) REVERT: A 333 TYR cc_start: 0.8408 (t80) cc_final: 0.8164 (t80) REVERT: E 129 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8735 (mm-30) REVERT: E 190 GLU cc_start: 0.8282 (mp0) cc_final: 0.7965 (mt-10) REVERT: B 169 ASP cc_start: 0.8705 (t70) cc_final: 0.8370 (t0) REVERT: B 226 ASP cc_start: 0.8360 (m-30) cc_final: 0.7534 (m-30) REVERT: B 239 MET cc_start: 0.8915 (mtp) cc_final: 0.8506 (mtt) REVERT: B 303 ILE cc_start: 0.8607 (mp) cc_final: 0.8342 (tp) REVERT: F 300 ASP cc_start: 0.7755 (t70) cc_final: 0.7362 (t70) REVERT: C 151 LYS cc_start: 0.7985 (ptpt) cc_final: 0.7614 (ttpt) REVERT: C 284 ASP cc_start: 0.8450 (t0) cc_final: 0.7938 (t0) REVERT: C 333 TYR cc_start: 0.8366 (t80) cc_final: 0.8081 (t80) REVERT: D 169 ASP cc_start: 0.8713 (t70) cc_final: 0.8391 (t0) REVERT: D 226 ASP cc_start: 0.8279 (m-30) cc_final: 0.7594 (m-30) REVERT: D 239 MET cc_start: 0.8921 (mtp) cc_final: 0.8525 (mtt) REVERT: D 303 ILE cc_start: 0.8629 (mp) cc_final: 0.8357 (tp) REVERT: H 266 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: H 300 ASP cc_start: 0.7696 (t70) cc_final: 0.7332 (t70) outliers start: 38 outliers final: 25 residues processed: 274 average time/residue: 0.2564 time to fit residues: 100.9837 Evaluate side-chains 288 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 261 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 170 optimal weight: 0.2980 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13400 Z= 0.259 Angle : 0.454 5.596 18152 Z= 0.241 Chirality : 0.047 0.137 2174 Planarity : 0.003 0.036 2360 Dihedral : 3.415 16.195 1942 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.76 % Allowed : 17.13 % Favored : 80.12 % 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: -0.29 (0.20), residues: 1766 helix: -0.02 (0.19), residues: 830 sheet: 0.71 (0.27), residues: 336 loop : -0.76 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 123 HIS 0.004 0.001 HIS G 193 PHE 0.006 0.001 PHE C 312 TYR 0.020 0.002 TYR F 333 ARG 0.004 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 272 time to evaluate : 1.497 Fit side-chains REVERT: A 151 LYS cc_start: 0.8111 (ptpt) cc_final: 0.7720 (ttpt) REVERT: A 210 GLU cc_start: 0.7767 (tt0) cc_final: 0.7316 (tt0) REVERT: A 254 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: A 284 ASP cc_start: 0.8485 (t0) cc_final: 0.7971 (t0) REVERT: A 333 TYR cc_start: 0.8389 (t80) cc_final: 0.8171 (t80) REVERT: E 129 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8744 (mm-30) REVERT: E 190 GLU cc_start: 0.8335 (mp0) cc_final: 0.7971 (mt-10) REVERT: B 169 ASP cc_start: 0.8722 (t70) cc_final: 0.8410 (t0) REVERT: B 226 ASP cc_start: 0.8368 (m-30) cc_final: 0.7532 (m-30) REVERT: B 303 ILE cc_start: 0.8574 (mp) cc_final: 0.8316 (tp) REVERT: F 266 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: F 300 ASP cc_start: 0.7889 (t70) cc_final: 0.7494 (t70) REVERT: C 151 LYS cc_start: 0.7985 (ptpt) cc_final: 0.7610 (ttpt) REVERT: C 169 ASP cc_start: 0.8298 (m-30) cc_final: 0.7895 (m-30) REVERT: C 284 ASP cc_start: 0.8499 (t0) cc_final: 0.7992 (t0) REVERT: C 333 TYR cc_start: 0.8421 (t80) cc_final: 0.8161 (t80) REVERT: D 169 ASP cc_start: 0.8721 (t70) cc_final: 0.8397 (t0) REVERT: D 210 GLU cc_start: 0.8326 (tt0) cc_final: 0.8073 (tt0) REVERT: D 213 ARG cc_start: 0.8235 (mtt-85) cc_final: 0.7662 (mtp85) REVERT: D 226 ASP cc_start: 0.8227 (m-30) cc_final: 0.7535 (m-30) REVERT: D 239 MET cc_start: 0.8944 (mtp) cc_final: 0.8492 (mtt) REVERT: D 303 ILE cc_start: 0.8613 (mp) cc_final: 0.8348 (tp) REVERT: H 266 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: H 300 ASP cc_start: 0.7870 (t70) cc_final: 0.7469 (t70) outliers start: 37 outliers final: 31 residues processed: 282 average time/residue: 0.2570 time to fit residues: 103.6247 Evaluate side-chains 296 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 262 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.0030 chunk 97 optimal weight: 3.9990 chunk 124 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 169 optimal weight: 0.0470 chunk 106 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 overall best weight: 0.5890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13400 Z= 0.143 Angle : 0.412 5.788 18152 Z= 0.218 Chirality : 0.045 0.136 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.165 15.218 1942 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.03 % Allowed : 18.36 % Favored : 79.61 % 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: 0.04 (0.20), residues: 1766 helix: 0.29 (0.19), residues: 830 sheet: 0.83 (0.27), residues: 336 loop : -0.65 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 123 HIS 0.002 0.000 HIS G 193 PHE 0.006 0.001 PHE B 140 TYR 0.019 0.001 TYR E 333 ARG 0.003 0.000 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 270 time to evaluate : 1.389 Fit side-chains REVERT: A 151 LYS cc_start: 0.8048 (ptpt) cc_final: 0.7742 (ttpt) REVERT: A 263 ARG cc_start: 0.7482 (mtm-85) cc_final: 0.7213 (mtt180) REVERT: A 284 ASP cc_start: 0.8450 (t0) cc_final: 0.7938 (t0) REVERT: E 190 GLU cc_start: 0.8273 (mp0) cc_final: 0.7919 (mt-10) REVERT: E 318 ILE cc_start: 0.8340 (mt) cc_final: 0.8016 (pt) REVERT: B 169 ASP cc_start: 0.8674 (t70) cc_final: 0.8363 (t0) REVERT: B 226 ASP cc_start: 0.8287 (m-30) cc_final: 0.7475 (m-30) REVERT: B 303 ILE cc_start: 0.8568 (mp) cc_final: 0.8367 (tp) REVERT: F 266 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: F 300 ASP cc_start: 0.7943 (t70) cc_final: 0.7549 (t70) REVERT: C 151 LYS cc_start: 0.7976 (ptpt) cc_final: 0.7565 (ttpt) REVERT: C 169 ASP cc_start: 0.8209 (m-30) cc_final: 0.7830 (m-30) REVERT: C 263 ARG cc_start: 0.7578 (mtm-85) cc_final: 0.7249 (mtt180) REVERT: C 284 ASP cc_start: 0.8462 (t0) cc_final: 0.7951 (t0) REVERT: C 333 TYR cc_start: 0.8388 (t80) cc_final: 0.8185 (t80) REVERT: D 169 ASP cc_start: 0.8684 (t70) cc_final: 0.8381 (t0) REVERT: D 226 ASP cc_start: 0.8189 (m-30) cc_final: 0.7527 (m-30) REVERT: D 239 MET cc_start: 0.8929 (mtp) cc_final: 0.8584 (mtt) REVERT: H 266 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: H 300 ASP cc_start: 0.7870 (t70) cc_final: 0.7474 (t70) outliers start: 27 outliers final: 21 residues processed: 279 average time/residue: 0.2718 time to fit residues: 107.5003 Evaluate side-chains 284 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 261 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 107 optimal weight: 0.0970 chunk 115 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13400 Z= 0.212 Angle : 0.444 6.378 18152 Z= 0.233 Chirality : 0.046 0.135 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.211 15.236 1942 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.98 % Allowed : 17.63 % Favored : 79.39 % 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: 0.14 (0.20), residues: 1766 helix: 0.40 (0.19), residues: 822 sheet: 0.80 (0.26), residues: 336 loop : -0.59 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 123 HIS 0.004 0.001 HIS G 193 PHE 0.006 0.001 PHE C 232 TYR 0.022 0.001 TYR A 333 ARG 0.004 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 266 time to evaluate : 1.508 Fit side-chains REVERT: A 151 LYS cc_start: 0.8057 (ptpt) cc_final: 0.7714 (ttpt) REVERT: A 169 ASP cc_start: 0.8266 (m-30) cc_final: 0.7885 (m-30) REVERT: A 263 ARG cc_start: 0.7496 (mtm-85) cc_final: 0.7202 (mtt180) REVERT: A 284 ASP cc_start: 0.8464 (t0) cc_final: 0.7951 (t0) REVERT: E 129 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8755 (mm-30) REVERT: E 318 ILE cc_start: 0.8323 (mt) cc_final: 0.7988 (pt) REVERT: B 169 ASP cc_start: 0.8706 (t70) cc_final: 0.8400 (t0) REVERT: B 226 ASP cc_start: 0.8289 (m-30) cc_final: 0.7477 (m-30) REVERT: F 266 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: F 300 ASP cc_start: 0.7959 (t70) cc_final: 0.7573 (t70) REVERT: C 151 LYS cc_start: 0.7989 (ptpt) cc_final: 0.7579 (ttpt) REVERT: C 169 ASP cc_start: 0.8260 (m-30) cc_final: 0.7873 (m-30) REVERT: C 263 ARG cc_start: 0.7489 (mtm-85) cc_final: 0.7238 (mtt180) REVERT: C 284 ASP cc_start: 0.8476 (t0) cc_final: 0.7960 (t0) REVERT: C 294 ILE cc_start: 0.8801 (pt) cc_final: 0.8549 (mt) REVERT: C 334 ILE cc_start: 0.8303 (pt) cc_final: 0.8103 (tp) REVERT: D 169 ASP cc_start: 0.8714 (t70) cc_final: 0.8382 (t0) REVERT: D 210 GLU cc_start: 0.8336 (tt0) cc_final: 0.8077 (tt0) REVERT: D 226 ASP cc_start: 0.8196 (m-30) cc_final: 0.7529 (m-30) REVERT: D 239 MET cc_start: 0.8917 (mtp) cc_final: 0.8512 (mtt) REVERT: H 266 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: H 300 ASP cc_start: 0.7916 (t70) cc_final: 0.7533 (t70) outliers start: 40 outliers final: 29 residues processed: 280 average time/residue: 0.2528 time to fit residues: 101.6116 Evaluate side-chains 292 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 261 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13400 Z= 0.276 Angle : 0.486 7.375 18152 Z= 0.254 Chirality : 0.048 0.179 2174 Planarity : 0.003 0.036 2360 Dihedral : 3.354 15.369 1942 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.76 % Allowed : 19.01 % 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: -0.01 (0.20), residues: 1766 helix: 0.35 (0.19), residues: 822 sheet: 0.48 (0.27), residues: 320 loop : -0.57 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 123 HIS 0.005 0.001 HIS G 193 PHE 0.006 0.001 PHE B 140 TYR 0.025 0.002 TYR H 333 ARG 0.004 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 258 time to evaluate : 1.497 Fit side-chains REVERT: A 151 LYS cc_start: 0.8004 (ptpt) cc_final: 0.7673 (ttpt) REVERT: A 263 ARG cc_start: 0.7516 (mtm-85) cc_final: 0.7219 (mtt180) REVERT: A 284 ASP cc_start: 0.8505 (t0) cc_final: 0.7969 (t0) REVERT: E 129 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8763 (mm-30) REVERT: E 318 ILE cc_start: 0.8347 (mt) cc_final: 0.7977 (pt) REVERT: B 169 ASP cc_start: 0.8722 (t70) cc_final: 0.8376 (t0) REVERT: B 226 ASP cc_start: 0.8292 (m-30) cc_final: 0.7475 (m-30) REVERT: F 266 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: F 300 ASP cc_start: 0.7981 (t70) cc_final: 0.7596 (t70) REVERT: C 151 LYS cc_start: 0.7973 (ptpt) cc_final: 0.7603 (ttpt) REVERT: C 169 ASP cc_start: 0.8290 (m-30) cc_final: 0.7899 (m-30) REVERT: C 254 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: C 284 ASP cc_start: 0.8525 (t0) cc_final: 0.7995 (t0) REVERT: D 169 ASP cc_start: 0.8738 (t70) cc_final: 0.8400 (t0) REVERT: D 210 GLU cc_start: 0.8354 (tt0) cc_final: 0.8084 (tt0) REVERT: D 226 ASP cc_start: 0.8198 (m-30) cc_final: 0.7529 (m-30) REVERT: D 239 MET cc_start: 0.8943 (mtp) cc_final: 0.8538 (mtt) REVERT: H 266 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: H 300 ASP cc_start: 0.7927 (t70) cc_final: 0.7549 (t70) outliers start: 37 outliers final: 29 residues processed: 271 average time/residue: 0.2548 time to fit residues: 99.3909 Evaluate side-chains 279 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 247 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 175 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 0.0030 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13400 Z= 0.146 Angle : 0.438 6.194 18152 Z= 0.229 Chirality : 0.046 0.136 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.149 14.601 1942 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.81 % Allowed : 19.88 % Favored : 78.30 % 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: 0.33 (0.20), residues: 1766 helix: 0.60 (0.19), residues: 822 sheet: 0.80 (0.26), residues: 336 loop : -0.50 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 123 HIS 0.003 0.000 HIS G 193 PHE 0.005 0.001 PHE B 140 TYR 0.025 0.001 TYR H 333 ARG 0.004 0.000 ARG F 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 262 time to evaluate : 1.520 Fit side-chains REVERT: A 151 LYS cc_start: 0.7996 (ptpt) cc_final: 0.7603 (ttpt) REVERT: A 169 ASP cc_start: 0.8292 (m-30) cc_final: 0.7924 (m-30) REVERT: A 263 ARG cc_start: 0.7512 (mtm-85) cc_final: 0.7222 (mtt180) REVERT: A 284 ASP cc_start: 0.8521 (t0) cc_final: 0.7999 (t0) REVERT: E 129 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8768 (mm-30) REVERT: E 318 ILE cc_start: 0.8270 (mt) cc_final: 0.7960 (pt) REVERT: B 169 ASP cc_start: 0.8657 (t70) cc_final: 0.8372 (t70) REVERT: B 226 ASP cc_start: 0.8282 (m-30) cc_final: 0.7455 (m-30) REVERT: F 266 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: F 300 ASP cc_start: 0.7977 (t70) cc_final: 0.7604 (t70) REVERT: F 303 ILE cc_start: 0.8204 (pt) cc_final: 0.7999 (pt) REVERT: C 151 LYS cc_start: 0.7858 (ptpt) cc_final: 0.7572 (ttpt) REVERT: C 169 ASP cc_start: 0.8194 (m-30) cc_final: 0.7831 (m-30) REVERT: C 263 ARG cc_start: 0.7541 (mtm-85) cc_final: 0.7334 (mtt180) REVERT: C 284 ASP cc_start: 0.8524 (t0) cc_final: 0.8000 (t0) REVERT: C 294 ILE cc_start: 0.8769 (pt) cc_final: 0.8538 (mt) REVERT: C 310 TYR cc_start: 0.7500 (t80) cc_final: 0.7277 (t80) REVERT: D 129 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7373 (tm-30) REVERT: D 169 ASP cc_start: 0.8677 (t70) cc_final: 0.8366 (t70) REVERT: D 210 GLU cc_start: 0.8295 (tt0) cc_final: 0.8063 (tt0) REVERT: D 226 ASP cc_start: 0.8181 (m-30) cc_final: 0.7522 (m-30) REVERT: D 239 MET cc_start: 0.8930 (mtp) cc_final: 0.8619 (mtt) REVERT: H 266 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: H 300 ASP cc_start: 0.7917 (t70) cc_final: 0.7555 (t70) outliers start: 24 outliers final: 21 residues processed: 272 average time/residue: 0.2525 time to fit residues: 99.2119 Evaluate side-chains 280 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 257 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 143 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.169427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132625 restraints weight = 28235.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.136714 restraints weight = 17044.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.139159 restraints weight = 9253.572| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13400 Z= 0.209 Angle : 0.474 13.420 18152 Z= 0.244 Chirality : 0.047 0.179 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.193 14.843 1942 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.18 % Allowed : 20.03 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1766 helix: 0.56 (0.19), residues: 822 sheet: 0.80 (0.26), residues: 336 loop : -0.46 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 123 HIS 0.003 0.001 HIS G 193 PHE 0.006 0.001 PHE D 140 TYR 0.024 0.002 TYR H 333 ARG 0.004 0.000 ARG B 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2807.25 seconds wall clock time: 51 minutes 20.86 seconds (3080.86 seconds total)