Starting phenix.real_space_refine on Sat Sep 12 02:48:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uwn_20925/09_2026/6uwn_20925.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uwn_20925/09_2026/6uwn_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 { model { file = "/net/cci-nas-00/data/ceres_data/6uwn_20925/09_2026/6uwn_20925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uwn_20925/09_2026/6uwn_20925.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uwn_20925/09_2026/6uwn_20925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uwn_20925/09_2026/6uwn_20925.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6uwn_20925/09_2026/6uwn_20925.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uwn_20925/09_2026/6uwn_20925.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 68 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'ARG:plan': 3, 'GLU:plan': 9, '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: {'ARG:plan': 3, 'GLU:plan': 9, '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: 3.79, per 1000 atoms: 0.29 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 - 3.00 Amino acid : True - 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: 0.99 Conformation dependent library (CDL) restraints added in 785.5 milliseconds 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: 0.25 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: 1.58 Time building geometry restraints manager: 1.36 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: 0.00 - 1.79: 17594 1.79 - 3.59: 507 3.59 - 5.38: 47 5.38 - 7.17: 1 7.17 - 8.96: 3 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 3.040 nonbonded pdb=" OD1 ASP E 184 " pdb=" O HOH E 501 " model vdw 2.286 3.040 nonbonded pdb=" O ILE F 285 " pdb=" OG1 THR F 289 " model vdw 2.286 3.040 nonbonded pdb=" O ILE H 285 " pdb=" OG1 THR H 289 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASP G 184 " pdb=" O HOH G 501 " model vdw 2.289 3.040 ... (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 Time spend for trying shortcut: 0.02 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 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 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 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 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 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 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 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 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: 0.890 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.370 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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= 0.305 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.001 ARG H 166 TYR 0.020 0.002 TYR D 247 PHE 0.013 0.002 PHE A 232 TRP 0.003 0.001 TRP E 123 HIS 0.009 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00737 / 0.30 (13400) covalent geometry : angle 0.72821 / 0.43 (18152) hydrogen bonds : bond 0.27641 / 18.96 ( 563) hydrogen bonds : angle 8.69561 / 6.27 ( 1600) *********************** 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 to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.513 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: 0.8653 (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: 0.7844 (t80) REVERT: F 125 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8477 (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: 0.7967 (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: 0.7919 (mtpt) REVERT: C 151 LYS cc_start: 0.8013 (ptpt) cc_final: 0.7586 (ttpt) REVERT: G 154 ARG cc_start: 0.7834 (ttp-110) cc_final: 0.7634 (mtm110) REVERT: G 210 GLU cc_start: 0.8411 (tt0) cc_final: 0.8076 (tt0) REVERT: G 239 MET cc_start: 0.8667 (mtt) cc_final: 0.8452 (mtt) REVERT: G 325 GLU cc_start: 0.8441 (tt0) cc_final: 0.8211 (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: 0.7878 (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: 0.1518 time to fit residues: 74.1922 Evaluate side-chains 284 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.0070 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.0870 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN B 227 GLN F 332 ASN C 219 GLN C 253 GLN D 227 GLN H 117 HIS H 332 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.174604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.139338 restraints weight = 34191.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.144261 restraints weight = 14926.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.147266 restraints weight = 9518.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.148076 restraints weight = 6896.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.151732 restraints weight = 5559.064| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1919 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= 0.100 Angle : 0.454 5.055 18152 Z= 0.250 Chirality : 0.046 0.143 2174 Planarity : 0.004 0.038 2360 Dihedral : 3.834 17.767 1942 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.45 % Allowed : 12.05 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.17), residues: 1766 helix: -2.31 (0.15), residues: 830 sheet: 0.52 (0.26), residues: 336 loop : -1.89 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 213 TYR 0.016 0.001 TYR E 333 PHE 0.007 0.001 PHE G 251 TRP 0.004 0.001 TRP H 123 HIS 0.004 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (13400) covalent geometry : angle 0.45393 / 0.25 (18152) hydrogen bonds : bond 0.04042 / 2.74 ( 563) hydrogen bonds : angle 5.06339 / 3.58 ( 1600) *********************** 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 319 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 301 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7968 (ptpt) cc_final: 0.7602 (ttpt) REVERT: A 284 ASP cc_start: 0.8198 (t0) cc_final: 0.7961 (t0) REVERT: A 294 ILE cc_start: 0.8822 (pt) cc_final: 0.8403 (mt) REVERT: E 129 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8754 (mm-30) REVERT: E 190 GLU cc_start: 0.8268 (mp0) cc_final: 0.7893 (mt-10) REVERT: B 226 ASP cc_start: 0.8194 (m-30) cc_final: 0.7552 (m-30) REVERT: B 303 ILE cc_start: 0.8581 (mp) cc_final: 0.8236 (tp) REVERT: B 310 TYR cc_start: 0.8573 (t80) cc_final: 0.7587 (t80) REVERT: F 184 ASP cc_start: 0.8333 (t70) cc_final: 0.7933 (t0) REVERT: F 210 GLU cc_start: 0.8293 (tt0) cc_final: 0.7948 (tt0) REVERT: F 300 ASP cc_start: 0.7476 (t70) cc_final: 0.7044 (t70) REVERT: C 151 LYS cc_start: 0.7814 (ptpt) cc_final: 0.7525 (ttpt) REVERT: C 284 ASP cc_start: 0.8226 (t0) cc_final: 0.7991 (t0) REVERT: C 294 ILE cc_start: 0.8850 (pt) cc_final: 0.8405 (mt) REVERT: D 226 ASP cc_start: 0.8192 (m-30) cc_final: 0.7566 (m-30) REVERT: D 303 ILE cc_start: 0.8582 (mp) cc_final: 0.8208 (tp) REVERT: D 310 TYR cc_start: 0.8574 (t80) cc_final: 0.7960 (t80) REVERT: H 184 ASP cc_start: 0.8326 (t70) cc_final: 0.7938 (t0) REVERT: H 210 GLU cc_start: 0.8323 (tt0) cc_final: 0.7981 (tt0) REVERT: H 300 ASP cc_start: 0.7536 (t70) cc_final: 0.7108 (t70) outliers start: 18 outliers final: 11 residues processed: 309 average time/residue: 0.1232 time to fit residues: 54.2311 Evaluate side-chains 280 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 269 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain G residue 304 ILE 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 153 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.0040 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.171300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136043 restraints weight = 35558.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.141695 restraints weight = 15987.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.143010 restraints weight = 9389.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.144490 restraints weight = 6953.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.147894 restraints weight = 5964.078| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13400 Z= 0.160 Angle : 0.473 4.412 18152 Z= 0.255 Chirality : 0.047 0.138 2174 Planarity : 0.004 0.039 2360 Dihedral : 3.639 17.289 1942 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.32 % Allowed : 14.59 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.18), residues: 1766 helix: -1.08 (0.17), residues: 822 sheet: 0.52 (0.26), residues: 336 loop : -1.49 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 213 TYR 0.019 0.002 TYR A 333 PHE 0.006 0.001 PHE A 312 TRP 0.002 0.000 TRP D 123 HIS 0.005 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (13400) covalent geometry : angle 0.47326 / 0.26 (18152) hydrogen bonds : bond 0.03911 / 2.66 ( 563) hydrogen bonds : angle 4.63361 / 3.29 ( 1600) *********************** 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 315 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 285 time to evaluate : 0.524 Fit side-chains REVERT: A 140 PHE cc_start: 0.8561 (m-80) cc_final: 0.8250 (m-80) REVERT: A 151 LYS cc_start: 0.8062 (ptpt) cc_final: 0.7676 (ttpt) REVERT: A 284 ASP cc_start: 0.8307 (t0) cc_final: 0.8052 (t0) REVERT: E 129 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8792 (mm-30) REVERT: E 145 ASP cc_start: 0.8537 (t70) cc_final: 0.8314 (t0) REVERT: E 190 GLU cc_start: 0.8247 (mp0) cc_final: 0.7778 (mt-10) REVERT: B 226 ASP cc_start: 0.8371 (m-30) cc_final: 0.7508 (m-30) REVERT: B 303 ILE cc_start: 0.8627 (mp) cc_final: 0.8249 (tp) REVERT: F 300 ASP cc_start: 0.7600 (t70) cc_final: 0.7195 (t70) REVERT: F 323 LYS cc_start: 0.8266 (mttm) cc_final: 0.7924 (mtpt) REVERT: C 151 LYS cc_start: 0.7994 (ptpt) cc_final: 0.7597 (ttpt) REVERT: C 284 ASP cc_start: 0.8346 (t0) cc_final: 0.8089 (t0) REVERT: D 226 ASP cc_start: 0.8363 (m-30) cc_final: 0.7510 (m-30) REVERT: D 303 ILE cc_start: 0.8639 (mp) cc_final: 0.8280 (tp) REVERT: D 310 TYR cc_start: 0.8599 (t80) cc_final: 0.7892 (t80) REVERT: H 300 ASP cc_start: 0.7597 (t70) cc_final: 0.7203 (t70) REVERT: H 323 LYS cc_start: 0.8274 (mttm) cc_final: 0.7935 (mtpt) outliers start: 30 outliers final: 20 residues processed: 298 average time/residue: 0.1268 time to fit residues: 54.0800 Evaluate side-chains 290 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 270 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 325 GLU 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 255 VAL 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 158 ASN 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 255 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain H residue 265 VAL 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 75 optimal weight: 0.2980 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 0.0470 chunk 149 optimal weight: 0.3980 chunk 135 optimal weight: 0.1980 chunk 172 optimal weight: 0.9990 chunk 134 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.170338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133816 restraints weight = 27947.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.137010 restraints weight = 18582.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.140762 restraints weight = 10022.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.143934 restraints weight = 6879.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.145427 restraints weight = 5345.589| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13400 Z= 0.080 Angle : 0.413 7.086 18152 Z= 0.222 Chirality : 0.045 0.136 2174 Planarity : 0.003 0.033 2360 Dihedral : 3.291 15.702 1942 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.81 % Allowed : 15.75 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.19), residues: 1766 helix: -0.38 (0.18), residues: 830 sheet: 0.58 (0.26), residues: 336 loop : -1.19 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 313 TYR 0.018 0.001 TYR E 333 PHE 0.005 0.001 PHE D 140 TRP 0.003 0.000 TRP F 123 HIS 0.003 0.000 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.08 (13400) covalent geometry : angle 0.41274 / 0.22 (18152) hydrogen bonds : bond 0.02829 / 1.92 ( 563) hydrogen bonds : angle 4.24221 / 3.01 ( 1600) *********************** 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 311 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 288 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8389 (m-80) cc_final: 0.8170 (m-80) REVERT: A 151 LYS cc_start: 0.8076 (ptpt) cc_final: 0.7693 (ttpt) REVERT: A 284 ASP cc_start: 0.8186 (t0) cc_final: 0.7958 (t0) REVERT: A 294 ILE cc_start: 0.8758 (pt) cc_final: 0.8500 (mt) REVERT: A 333 TYR cc_start: 0.8328 (t80) cc_final: 0.8054 (t80) REVERT: E 129 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8618 (mm-30) REVERT: E 145 ASP cc_start: 0.8571 (t70) cc_final: 0.8331 (t0) REVERT: E 190 GLU cc_start: 0.8179 (mp0) cc_final: 0.7764 (mt-10) REVERT: B 129 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7374 (tm-30) REVERT: B 169 ASP cc_start: 0.8572 (t70) cc_final: 0.8321 (t0) REVERT: B 226 ASP cc_start: 0.8291 (m-30) cc_final: 0.7498 (m-30) REVERT: B 239 MET cc_start: 0.8804 (mtp) cc_final: 0.8569 (mtt) REVERT: B 303 ILE cc_start: 0.8595 (mp) cc_final: 0.8370 (tp) REVERT: F 266 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7777 (mt-10) REVERT: F 300 ASP cc_start: 0.7513 (t70) cc_final: 0.7097 (t70) REVERT: F 323 LYS cc_start: 0.8286 (mttm) cc_final: 0.7945 (mtpt) REVERT: C 140 PHE cc_start: 0.8365 (m-80) cc_final: 0.8149 (m-80) REVERT: C 151 LYS cc_start: 0.7911 (ptpt) cc_final: 0.7574 (ttpt) REVERT: C 284 ASP cc_start: 0.8220 (t0) cc_final: 0.7989 (t0) REVERT: C 294 ILE cc_start: 0.8726 (pt) cc_final: 0.8431 (mt) REVERT: D 129 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7376 (tm-30) REVERT: D 169 ASP cc_start: 0.8552 (t70) cc_final: 0.8311 (t0) REVERT: D 226 ASP cc_start: 0.8323 (m-30) cc_final: 0.7437 (m-30) REVERT: D 303 ILE cc_start: 0.8605 (mp) cc_final: 0.8381 (tp) REVERT: H 266 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: H 300 ASP cc_start: 0.7510 (t70) cc_final: 0.7096 (t70) REVERT: H 323 LYS cc_start: 0.8289 (mttm) cc_final: 0.7948 (mtpt) outliers start: 23 outliers final: 14 residues processed: 300 average time/residue: 0.1211 time to fit residues: 52.2312 Evaluate side-chains 286 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 270 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 294 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 91 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 253 GLN D 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.173449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.138810 restraints weight = 40659.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.145252 restraints weight = 19667.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.146458 restraints weight = 10466.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.149512 restraints weight = 7048.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.151838 restraints weight = 5338.423| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13400 Z= 0.118 Angle : 0.431 4.913 18152 Z= 0.230 Chirality : 0.046 0.135 2174 Planarity : 0.003 0.039 2360 Dihedral : 3.241 15.793 1942 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.54 % Allowed : 16.84 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1766 helix: -0.11 (0.18), residues: 838 sheet: 0.65 (0.26), residues: 336 loop : -0.93 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.024 0.002 TYR H 333 PHE 0.005 0.001 PHE A 232 TRP 0.003 0.000 TRP B 123 HIS 0.004 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (13400) covalent geometry : angle 0.43069 / 0.23 (18152) hydrogen bonds : bond 0.03060 / 2.09 ( 563) hydrogen bonds : angle 4.20721 / 2.99 ( 1600) *********************** 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 319 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 0.461 Fit side-chains REVERT: A 140 PHE cc_start: 0.8466 (m-80) cc_final: 0.8258 (m-80) REVERT: A 151 LYS cc_start: 0.7923 (ptpt) cc_final: 0.7717 (ttpt) REVERT: A 284 ASP cc_start: 0.8197 (t0) cc_final: 0.7780 (t0) REVERT: A 333 TYR cc_start: 0.8307 (t80) cc_final: 0.8091 (t80) REVERT: E 129 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8638 (mm-30) REVERT: E 190 GLU cc_start: 0.8218 (mp0) cc_final: 0.7840 (mt-10) REVERT: B 129 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7390 (tm-30) REVERT: B 169 ASP cc_start: 0.8596 (t70) cc_final: 0.8381 (t0) REVERT: B 226 ASP cc_start: 0.8232 (m-30) cc_final: 0.7527 (m-30) REVERT: B 239 MET cc_start: 0.8883 (mtp) cc_final: 0.8471 (mtt) REVERT: F 266 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: F 300 ASP cc_start: 0.7406 (t70) cc_final: 0.7005 (t70) REVERT: F 323 LYS cc_start: 0.8318 (mttm) cc_final: 0.8034 (mtpt) REVERT: C 151 LYS cc_start: 0.7858 (ptpt) cc_final: 0.7647 (ttpt) REVERT: C 169 ASP cc_start: 0.8135 (m-30) cc_final: 0.7802 (m-30) REVERT: C 284 ASP cc_start: 0.8214 (t0) cc_final: 0.7794 (t0) REVERT: G 210 GLU cc_start: 0.8512 (tt0) cc_final: 0.8140 (tt0) REVERT: D 169 ASP cc_start: 0.8599 (t70) cc_final: 0.8388 (t0) REVERT: D 226 ASP cc_start: 0.8241 (m-30) cc_final: 0.7525 (m-30) REVERT: D 310 TYR cc_start: 0.8549 (t80) cc_final: 0.7908 (t80) REVERT: H 142 LEU cc_start: 0.8746 (tp) cc_final: 0.8509 (tt) REVERT: H 300 ASP cc_start: 0.7523 (t70) cc_final: 0.7118 (t70) REVERT: H 323 LYS cc_start: 0.8316 (mttm) cc_final: 0.8044 (mtpt) outliers start: 33 outliers final: 22 residues processed: 299 average time/residue: 0.1119 time to fit residues: 48.9720 Evaluate side-chains 277 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 254 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 325 GLU 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 255 VAL Chi-restraints excluded: chain B residue 275 LEU 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 325 GLU 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 255 VAL 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 294 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 75 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.168808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129710 restraints weight = 34539.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.136445 restraints weight = 14143.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.141609 restraints weight = 7177.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.142595 restraints weight = 4967.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.143254 restraints weight = 4131.721| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13400 Z= 0.109 Angle : 0.434 6.773 18152 Z= 0.231 Chirality : 0.046 0.190 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.203 15.357 1942 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.18 % Allowed : 17.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.20), residues: 1766 helix: 0.17 (0.19), residues: 830 sheet: 0.72 (0.26), residues: 336 loop : -0.86 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.025 0.001 TYR H 333 PHE 0.006 0.001 PHE C 140 TRP 0.002 0.000 TRP D 123 HIS 0.003 0.000 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (13400) covalent geometry : angle 0.43403 / 0.23 (18152) hydrogen bonds : bond 0.02966 / 2.02 ( 563) hydrogen bonds : angle 4.14662 / 2.95 ( 1600) *********************** 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 295 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 267 time to evaluate : 0.508 Fit side-chains REVERT: A 140 PHE cc_start: 0.8433 (m-80) cc_final: 0.8149 (m-80) REVERT: A 151 LYS cc_start: 0.7967 (ptpt) cc_final: 0.7664 (ttpt) REVERT: A 169 ASP cc_start: 0.8176 (m-30) cc_final: 0.7761 (m-30) REVERT: A 284 ASP cc_start: 0.8325 (t0) cc_final: 0.7817 (t0) REVERT: A 333 TYR cc_start: 0.8384 (t80) cc_final: 0.8175 (t80) REVERT: E 129 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8617 (mm-30) REVERT: E 190 GLU cc_start: 0.8278 (mp0) cc_final: 0.7803 (mt-10) REVERT: B 129 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7381 (tm-30) REVERT: B 169 ASP cc_start: 0.8703 (t70) cc_final: 0.8403 (t0) REVERT: B 226 ASP cc_start: 0.8328 (m-30) cc_final: 0.7561 (m-30) REVERT: B 239 MET cc_start: 0.8903 (mtp) cc_final: 0.8475 (mtt) REVERT: F 142 LEU cc_start: 0.8687 (tp) cc_final: 0.8449 (tt) REVERT: F 266 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: F 300 ASP cc_start: 0.7778 (t70) cc_final: 0.7345 (t70) REVERT: F 323 LYS cc_start: 0.8244 (mttm) cc_final: 0.7920 (mtpt) REVERT: C 151 LYS cc_start: 0.7932 (ptpt) cc_final: 0.7575 (ttpt) REVERT: C 169 ASP cc_start: 0.8213 (m-30) cc_final: 0.7798 (m-30) REVERT: C 284 ASP cc_start: 0.8311 (t0) cc_final: 0.7793 (t0) REVERT: D 129 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7395 (tm-30) REVERT: D 169 ASP cc_start: 0.8701 (t70) cc_final: 0.8395 (t0) REVERT: D 226 ASP cc_start: 0.8347 (m-30) cc_final: 0.7560 (m-30) REVERT: H 142 LEU cc_start: 0.8674 (tp) cc_final: 0.8444 (tt) REVERT: H 266 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: H 300 ASP cc_start: 0.7730 (t70) cc_final: 0.7322 (t70) REVERT: H 323 LYS cc_start: 0.8231 (mttm) cc_final: 0.7925 (mtpt) outliers start: 28 outliers final: 22 residues processed: 278 average time/residue: 0.1208 time to fit residues: 48.4875 Evaluate side-chains 287 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 263 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 325 GLU 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 275 LEU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 296 VAL 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 245 ASP Chi-restraints excluded: chain C residue 325 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 35 optimal weight: 4.9990 chunk 146 optimal weight: 0.0020 chunk 127 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 117 optimal weight: 0.0980 chunk 85 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 139 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.150937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.117567 restraints weight = 31233.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.120692 restraints weight = 27160.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.121608 restraints weight = 15805.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.124194 restraints weight = 8816.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.126821 restraints weight = 6627.377| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13400 Z= 0.085 Angle : 0.428 8.244 18152 Z= 0.226 Chirality : 0.046 0.209 2174 Planarity : 0.003 0.033 2360 Dihedral : 3.081 14.597 1942 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.81 % Allowed : 18.29 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.20), residues: 1766 helix: 0.40 (0.19), residues: 830 sheet: 0.84 (0.26), residues: 336 loop : -0.73 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.025 0.001 TYR H 333 PHE 0.005 0.001 PHE B 140 TRP 0.003 0.000 TRP B 123 HIS 0.002 0.000 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.08 (13400) covalent geometry : angle 0.42782 / 0.23 (18152) hydrogen bonds : bond 0.02658 / 1.80 ( 563) hydrogen bonds : angle 4.04686 / 2.87 ( 1600) *********************** 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 298 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 275 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8380 (m-80) cc_final: 0.8142 (m-80) REVERT: A 151 LYS cc_start: 0.7915 (ptpt) cc_final: 0.7593 (ttpt) REVERT: A 169 ASP cc_start: 0.8118 (m-30) cc_final: 0.7722 (m-30) REVERT: A 284 ASP cc_start: 0.8280 (t0) cc_final: 0.7806 (t0) REVERT: E 129 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8663 (mm-30) REVERT: E 190 GLU cc_start: 0.8200 (mp0) cc_final: 0.7658 (mt-10) REVERT: B 129 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7382 (tm-30) REVERT: B 169 ASP cc_start: 0.8678 (t70) cc_final: 0.8315 (t0) REVERT: B 226 ASP cc_start: 0.8337 (m-30) cc_final: 0.7444 (m-30) REVERT: B 239 MET cc_start: 0.8878 (mtp) cc_final: 0.8519 (mtt) REVERT: F 142 LEU cc_start: 0.8655 (tp) cc_final: 0.8440 (tt) REVERT: F 266 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: F 300 ASP cc_start: 0.7823 (t70) cc_final: 0.7395 (t70) REVERT: F 323 LYS cc_start: 0.8231 (mttm) cc_final: 0.7915 (mtpt) REVERT: C 151 LYS cc_start: 0.7908 (ptpt) cc_final: 0.7542 (ttpt) REVERT: C 284 ASP cc_start: 0.8312 (t0) cc_final: 0.7832 (t0) REVERT: G 210 GLU cc_start: 0.8561 (tt0) cc_final: 0.8090 (tt0) REVERT: D 129 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7397 (tm-30) REVERT: D 163 ASP cc_start: 0.8109 (t70) cc_final: 0.7784 (t70) REVERT: D 169 ASP cc_start: 0.8686 (t70) cc_final: 0.8344 (t0) REVERT: D 226 ASP cc_start: 0.8360 (m-30) cc_final: 0.7461 (m-30) REVERT: H 142 LEU cc_start: 0.8645 (tp) cc_final: 0.8417 (tt) REVERT: H 266 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7751 (mt-10) REVERT: H 300 ASP cc_start: 0.7844 (t70) cc_final: 0.7421 (t70) REVERT: H 323 LYS cc_start: 0.8226 (mttm) cc_final: 0.7903 (mtpt) outliers start: 23 outliers final: 18 residues processed: 288 average time/residue: 0.1143 time to fit residues: 47.5379 Evaluate side-chains 283 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 263 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 325 GLU 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 303 ILE 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 325 GLU 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 296 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 17 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.148374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.113732 restraints weight = 30608.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.115010 restraints weight = 26487.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.116252 restraints weight = 18096.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.118837 restraints weight = 10306.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.121815 restraints weight = 7682.037| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13400 Z= 0.161 Angle : 0.491 10.237 18152 Z= 0.255 Chirality : 0.048 0.227 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.256 15.232 1942 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.18 % Allowed : 18.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.20), residues: 1766 helix: 0.38 (0.19), residues: 822 sheet: 0.55 (0.27), residues: 304 loop : -0.62 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.022 0.001 TYR H 333 PHE 0.007 0.001 PHE C 232 TRP 0.002 0.000 TRP G 123 HIS 0.004 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (13400) covalent geometry : angle 0.49060 / 0.25 (18152) hydrogen bonds : bond 0.03324 / 2.28 ( 563) hydrogen bonds : angle 4.18124 / 2.99 ( 1600) *********************** 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 288 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 0.493 Fit side-chains REVERT: A 140 PHE cc_start: 0.8575 (m-80) cc_final: 0.8324 (m-80) REVERT: A 151 LYS cc_start: 0.7893 (ptpt) cc_final: 0.7550 (ttpt) REVERT: A 284 ASP cc_start: 0.8353 (t0) cc_final: 0.7890 (t0) REVERT: E 129 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8633 (mm-30) REVERT: B 169 ASP cc_start: 0.8779 (t70) cc_final: 0.8422 (t0) REVERT: B 226 ASP cc_start: 0.8324 (m-30) cc_final: 0.7470 (m-30) REVERT: B 239 MET cc_start: 0.8926 (mtp) cc_final: 0.8509 (mtt) REVERT: F 142 LEU cc_start: 0.8746 (tp) cc_final: 0.8466 (tt) REVERT: F 266 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: F 300 ASP cc_start: 0.7887 (t70) cc_final: 0.7487 (t70) REVERT: F 323 LYS cc_start: 0.8241 (mttm) cc_final: 0.7944 (mtpt) REVERT: C 151 LYS cc_start: 0.7965 (ptpt) cc_final: 0.7654 (ttpt) REVERT: C 169 ASP cc_start: 0.8389 (m-30) cc_final: 0.8009 (m-30) REVERT: C 284 ASP cc_start: 0.8336 (t0) cc_final: 0.7876 (t0) REVERT: D 163 ASP cc_start: 0.8279 (t70) cc_final: 0.7962 (t70) REVERT: D 169 ASP cc_start: 0.8779 (t70) cc_final: 0.8436 (t0) REVERT: D 226 ASP cc_start: 0.8386 (m-30) cc_final: 0.7531 (m-30) REVERT: H 142 LEU cc_start: 0.8762 (tp) cc_final: 0.8495 (tt) REVERT: H 300 ASP cc_start: 0.7874 (t70) cc_final: 0.7466 (t70) REVERT: H 323 LYS cc_start: 0.8222 (mttm) cc_final: 0.7942 (mtpt) outliers start: 28 outliers final: 20 residues processed: 273 average time/residue: 0.1188 time to fit residues: 47.1471 Evaluate side-chains 271 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 325 GLU 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 303 ILE Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 325 GLU 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 296 VAL Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain H residue 240 SER 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 49 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 162 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.147870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.114410 restraints weight = 35891.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.116371 restraints weight = 32619.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.118458 restraints weight = 17271.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.121944 restraints weight = 10039.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.122519 restraints weight = 7086.308| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13400 Z= 0.133 Angle : 0.486 11.115 18152 Z= 0.250 Chirality : 0.048 0.267 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.224 15.079 1942 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.96 % Allowed : 19.01 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1766 helix: 0.44 (0.19), residues: 822 sheet: 0.51 (0.27), residues: 304 loop : -0.56 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.027 0.001 TYR H 333 PHE 0.006 0.001 PHE B 140 TRP 0.001 0.000 TRP B 123 HIS 0.003 0.000 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (13400) covalent geometry : angle 0.48585 / 0.25 (18152) hydrogen bonds : bond 0.03106 / 2.12 ( 563) hydrogen bonds : angle 4.14505 / 2.95 ( 1600) *********************** 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 283 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 0.522 Fit side-chains REVERT: A 140 PHE cc_start: 0.8523 (m-80) cc_final: 0.8316 (m-80) REVERT: A 151 LYS cc_start: 0.7820 (ptpt) cc_final: 0.7548 (ttpt) REVERT: A 284 ASP cc_start: 0.8327 (t0) cc_final: 0.7916 (t0) REVERT: B 169 ASP cc_start: 0.8728 (t70) cc_final: 0.8419 (t70) REVERT: B 212 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7887 (mm-30) REVERT: B 226 ASP cc_start: 0.8299 (m-30) cc_final: 0.7467 (m-30) REVERT: B 239 MET cc_start: 0.8914 (mtp) cc_final: 0.8562 (mtt) REVERT: F 142 LEU cc_start: 0.8763 (tp) cc_final: 0.8495 (tt) REVERT: F 266 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: F 300 ASP cc_start: 0.7803 (t70) cc_final: 0.7409 (t70) REVERT: F 323 LYS cc_start: 0.8243 (mttm) cc_final: 0.7965 (mtpt) REVERT: C 151 LYS cc_start: 0.7928 (ptpt) cc_final: 0.7648 (ttpt) REVERT: C 169 ASP cc_start: 0.8344 (m-30) cc_final: 0.8005 (m-30) REVERT: C 263 ARG cc_start: 0.7537 (mtm-85) cc_final: 0.7311 (mtt180) REVERT: C 284 ASP cc_start: 0.8346 (t0) cc_final: 0.7932 (t0) REVERT: D 163 ASP cc_start: 0.8245 (t70) cc_final: 0.7907 (t70) REVERT: D 169 ASP cc_start: 0.8729 (t70) cc_final: 0.8410 (t0) REVERT: D 226 ASP cc_start: 0.8334 (m-30) cc_final: 0.7531 (m-30) REVERT: H 142 LEU cc_start: 0.8775 (tp) cc_final: 0.8518 (tt) REVERT: H 266 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: H 300 ASP cc_start: 0.7821 (t70) cc_final: 0.7416 (t70) REVERT: H 323 LYS cc_start: 0.8224 (mttm) cc_final: 0.7967 (mtpt) outliers start: 25 outliers final: 21 residues processed: 271 average time/residue: 0.1186 time to fit residues: 46.7846 Evaluate side-chains 276 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 253 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 325 GLU 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 282 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 325 GLU 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 296 VAL Chi-restraints excluded: chain D residue 303 ILE 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 135 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 113 optimal weight: 0.0070 chunk 7 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 169 optimal weight: 0.0170 chunk 10 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.151815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.118167 restraints weight = 36202.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.120276 restraints weight = 30738.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.121678 restraints weight = 15422.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.125822 restraints weight = 8626.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.127992 restraints weight = 5667.607| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13400 Z= 0.089 Angle : 0.466 10.911 18152 Z= 0.240 Chirality : 0.046 0.258 2174 Planarity : 0.003 0.032 2360 Dihedral : 3.080 14.584 1942 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.67 % Allowed : 19.52 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.20), residues: 1766 helix: 0.58 (0.19), residues: 830 sheet: 0.56 (0.28), residues: 304 loop : -0.50 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.026 0.001 TYR H 333 PHE 0.006 0.001 PHE B 140 TRP 0.003 0.000 TRP F 123 HIS 0.002 0.000 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (13400) covalent geometry : angle 0.46568 / 0.24 (18152) hydrogen bonds : bond 0.02735 / 1.86 ( 563) hydrogen bonds : angle 4.05764 / 2.89 ( 1600) ********************** 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 284 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 263 time to evaluate : 0.536 Fit side-chains REVERT: A 140 PHE cc_start: 0.8376 (m-80) cc_final: 0.8149 (m-80) REVERT: A 151 LYS cc_start: 0.7684 (ptpt) cc_final: 0.7420 (ttpt) REVERT: A 284 ASP cc_start: 0.8373 (t0) cc_final: 0.7919 (t0) REVERT: E 129 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8555 (mm-30) REVERT: E 318 ILE cc_start: 0.8244 (mt) cc_final: 0.7942 (pt) REVERT: B 129 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7476 (tm-30) REVERT: B 163 ASP cc_start: 0.8194 (t70) cc_final: 0.7901 (t0) REVERT: B 169 ASP cc_start: 0.8715 (t70) cc_final: 0.8383 (t0) REVERT: B 212 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7856 (mm-30) REVERT: B 226 ASP cc_start: 0.8269 (m-30) cc_final: 0.7424 (m-30) REVERT: B 239 MET cc_start: 0.8885 (mtp) cc_final: 0.8590 (mtt) REVERT: F 266 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: F 300 ASP cc_start: 0.7831 (t70) cc_final: 0.7459 (t70) REVERT: F 323 LYS cc_start: 0.8227 (mttm) cc_final: 0.7903 (mtpt) REVERT: C 151 LYS cc_start: 0.7776 (ptpt) cc_final: 0.7564 (ttpt) REVERT: C 169 ASP cc_start: 0.8298 (m-30) cc_final: 0.7901 (m-30) REVERT: C 284 ASP cc_start: 0.8391 (t0) cc_final: 0.7939 (t0) REVERT: D 129 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7473 (tm-30) REVERT: D 163 ASP cc_start: 0.8250 (t70) cc_final: 0.7885 (t0) REVERT: D 169 ASP cc_start: 0.8720 (t70) cc_final: 0.8395 (t0) REVERT: D 226 ASP cc_start: 0.8312 (m-30) cc_final: 0.7461 (m-30) REVERT: H 142 LEU cc_start: 0.8694 (tp) cc_final: 0.8453 (tt) REVERT: H 266 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: H 300 ASP cc_start: 0.7840 (t70) cc_final: 0.7457 (t70) REVERT: H 323 LYS cc_start: 0.8240 (mttm) cc_final: 0.7916 (mtpt) outliers start: 21 outliers final: 19 residues processed: 275 average time/residue: 0.1256 time to fit residues: 50.0306 Evaluate side-chains 279 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 258 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 325 GLU 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 303 ILE Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 325 GLU 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 296 VAL Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain H residue 158 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 4 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 219 GLN D 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.145253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.107514 restraints weight = 46130.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.110375 restraints weight = 25476.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.111888 restraints weight = 15823.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.114434 restraints weight = 9861.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.115525 restraints weight = 7699.287| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13400 Z= 0.234 Angle : 0.567 12.200 18152 Z= 0.292 Chirality : 0.050 0.281 2174 Planarity : 0.004 0.036 2360 Dihedral : 3.488 15.918 1942 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.32 % Allowed : 19.30 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1766 helix: 0.27 (0.19), residues: 822 sheet: 0.31 (0.27), residues: 304 loop : -0.53 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 263 TYR 0.024 0.002 TYR H 333 PHE 0.009 0.001 PHE A 232 TRP 0.006 0.001 TRP E 123 HIS 0.006 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.23 (13400) covalent geometry : angle 0.56656 / 0.29 (18152) hydrogen bonds : bond 0.03810 / 2.61 ( 563) hydrogen bonds : angle 4.32420 / 3.08 ( 1600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2385.83 seconds wall clock time: 41 minutes 45.76 seconds (2505.76 seconds total)