Starting phenix.real_space_refine on Wed Mar 4 11:18:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uwn_20925/03_2026/6uwn_20925.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uwn_20925/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6uwn_20925/03_2026/6uwn_20925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uwn_20925/03_2026/6uwn_20925.map" model { file = "/net/cci-nas-00/data/ceres_data/6uwn_20925/03_2026/6uwn_20925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uwn_20925/03_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-dev-5986/lib/python3.9/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: 3.98, per 1000 atoms: 0.30 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: 1.03 Conformation dependent library (CDL) restraints added in 893.5 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: 0.51 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: 2.26 Time building geometry restraints manager: 1.45 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: 0.01 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: 1.280 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.260 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 13400 Z= 0.305 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 covalent geometry : bond 0.00737 (13400) covalent geometry : angle 0.72821 (18152) hydrogen bonds : bond 0.27641 ( 563) hydrogen bonds : angle 8.69561 ( 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 : 0.524 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: 0.8107 (t0) REVERT: F 210 GLU cc_start: 0.8351 (tt0) cc_final: 0.7977 (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: 0.7584 (ttpt) REVERT: G 154 ARG cc_start: 0.7834 (ttp-110) cc_final: 0.7633 (mtm110) REVERT: G 210 GLU cc_start: 0.8411 (tt0) cc_final: 0.8075 (tt0) REVERT: G 239 MET cc_start: 0.8667 (mtt) cc_final: 0.8454 (mtt) REVERT: G 325 GLU cc_start: 0.8441 (tt0) cc_final: 0.8210 (tp30) REVERT: D 226 ASP cc_start: 0.8258 (m-30) cc_final: 0.7777 (m-30) REVERT: D 310 TYR cc_start: 0.8532 (t80) cc_final: 0.7878 (t80) REVERT: H 125 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8404 (mm-30) REVERT: H 210 GLU cc_start: 0.8337 (tt0) cc_final: 0.7991 (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: 0.1446 time to fit residues: 69.8785 Evaluate side-chains 290 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.0870 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN B 227 GLN F 332 ASN C 219 GLN C 253 GLN D 227 GLN H 117 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.173385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.137881 restraints weight = 34493.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.144132 restraints weight = 15846.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.145415 restraints weight = 8995.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.148666 restraints weight = 6517.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.149960 restraints weight = 5190.708| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13400 Z= 0.111 Angle : 0.468 4.715 18152 Z= 0.258 Chirality : 0.046 0.142 2174 Planarity : 0.004 0.038 2360 Dihedral : 3.911 18.260 1942 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.60 % Allowed : 12.55 % Favored : 85.85 % 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: -2.57 (0.17), residues: 1766 helix: -2.26 (0.15), residues: 830 sheet: 0.48 (0.26), residues: 336 loop : -1.91 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 213 TYR 0.015 0.001 TYR E 333 PHE 0.006 0.001 PHE G 251 TRP 0.003 0.001 TRP H 123 HIS 0.004 0.000 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00242 (13400) covalent geometry : angle 0.46782 (18152) hydrogen bonds : bond 0.04475 ( 563) hydrogen bonds : angle 5.13222 ( 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 312 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 292 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7935 (ptpt) cc_final: 0.7598 (ttpt) REVERT: A 284 ASP cc_start: 0.8138 (t0) cc_final: 0.7905 (t0) REVERT: E 129 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8720 (mm-30) REVERT: E 190 GLU cc_start: 0.8310 (mp0) cc_final: 0.8028 (mt-10) REVERT: B 226 ASP cc_start: 0.8264 (m-30) cc_final: 0.7647 (m-30) REVERT: B 303 ILE cc_start: 0.8616 (mp) cc_final: 0.8274 (tp) REVERT: B 310 TYR cc_start: 0.8592 (t80) cc_final: 0.7662 (t80) REVERT: F 184 ASP cc_start: 0.8356 (t70) cc_final: 0.8033 (t0) REVERT: F 210 GLU cc_start: 0.8361 (tt0) cc_final: 0.7916 (tt0) REVERT: F 300 ASP cc_start: 0.7457 (t70) cc_final: 0.7014 (t70) REVERT: C 151 LYS cc_start: 0.7831 (ptpt) cc_final: 0.7536 (ttpt) REVERT: C 284 ASP cc_start: 0.8225 (t0) cc_final: 0.7991 (t0) REVERT: G 254 ASP cc_start: 0.8086 (m-30) cc_final: 0.7829 (m-30) REVERT: D 226 ASP cc_start: 0.8225 (m-30) cc_final: 0.7613 (m-30) REVERT: D 303 ILE cc_start: 0.8617 (mp) cc_final: 0.8259 (tp) REVERT: D 310 TYR cc_start: 0.8584 (t80) cc_final: 0.7630 (t80) REVERT: H 184 ASP cc_start: 0.8186 (t0) cc_final: 0.7956 (t0) REVERT: H 210 GLU cc_start: 0.8428 (tt0) cc_final: 0.8043 (tt0) REVERT: H 300 ASP cc_start: 0.7497 (t70) cc_final: 0.7063 (t70) outliers start: 20 outliers final: 11 residues processed: 301 average time/residue: 0.1158 time to fit residues: 49.2488 Evaluate side-chains 287 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 276 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain F residue 190 GLU 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 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: 2.9990 chunk 102 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.0040 chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.165352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124703 restraints weight = 35243.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131451 restraints weight = 15351.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.137440 restraints weight = 7523.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.138210 restraints weight = 4852.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.138660 restraints weight = 4269.621| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13400 Z= 0.195 Angle : 0.502 4.722 18152 Z= 0.270 Chirality : 0.048 0.139 2174 Planarity : 0.004 0.041 2360 Dihedral : 3.783 17.565 1942 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.25 % Allowed : 14.51 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.55 (0.18), residues: 1766 helix: -1.14 (0.17), residues: 822 sheet: 0.44 (0.26), residues: 336 loop : -1.50 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 213 TYR 0.019 0.002 TYR A 333 PHE 0.008 0.001 PHE C 312 TRP 0.003 0.001 TRP E 123 HIS 0.006 0.001 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00471 (13400) covalent geometry : angle 0.50175 (18152) hydrogen bonds : bond 0.04169 ( 563) hydrogen bonds : angle 4.70953 ( 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 304 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 275 time to evaluate : 0.466 Fit side-chains REVERT: A 151 LYS cc_start: 0.8047 (ptpt) cc_final: 0.7679 (ttpt) REVERT: A 210 GLU cc_start: 0.7905 (tt0) cc_final: 0.7218 (tt0) REVERT: A 284 ASP cc_start: 0.8355 (t0) cc_final: 0.8102 (t0) REVERT: E 129 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8720 (mm-30) REVERT: E 190 GLU cc_start: 0.8333 (mp0) cc_final: 0.7983 (mt-10) REVERT: B 226 ASP cc_start: 0.8305 (m-30) cc_final: 0.7517 (m-30) REVERT: B 298 ARG cc_start: 0.6643 (ttp-110) cc_final: 0.6038 (mtp180) REVERT: B 303 ILE cc_start: 0.8596 (mp) cc_final: 0.8194 (tp) REVERT: F 300 ASP cc_start: 0.7641 (t70) cc_final: 0.7244 (t70) REVERT: F 323 LYS cc_start: 0.8327 (mttm) cc_final: 0.7969 (mtpt) REVERT: C 151 LYS cc_start: 0.7969 (ptpt) cc_final: 0.7595 (ttpt) REVERT: C 284 ASP cc_start: 0.8368 (t0) cc_final: 0.7867 (t0) REVERT: D 226 ASP cc_start: 0.8302 (m-30) cc_final: 0.7545 (m-30) REVERT: D 303 ILE cc_start: 0.8604 (mp) cc_final: 0.8187 (tp) REVERT: H 300 ASP cc_start: 0.7654 (t70) cc_final: 0.7252 (t70) REVERT: H 323 LYS cc_start: 0.8333 (mttm) cc_final: 0.7980 (mtpt) outliers start: 29 outliers final: 18 residues processed: 284 average time/residue: 0.1253 time to fit residues: 49.5325 Evaluate side-chains 293 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 275 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 F residue 240 SER Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 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 D residue 275 LEU Chi-restraints excluded: chain D residue 282 ASP 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: 3.9990 chunk 36 optimal weight: 0.0060 chunk 38 optimal weight: 0.0170 chunk 149 optimal weight: 0.0050 chunk 135 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 overall best weight: 0.1446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.175921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.139930 restraints weight = 28332.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.144191 restraints weight = 16812.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.146955 restraints weight = 9321.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.150137 restraints weight = 6653.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.150672 restraints weight = 4985.362| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13400 Z= 0.077 Angle : 0.412 4.827 18152 Z= 0.222 Chirality : 0.045 0.136 2174 Planarity : 0.003 0.033 2360 Dihedral : 3.333 15.849 1942 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.60 % Allowed : 15.53 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.82 (0.19), residues: 1766 helix: -0.43 (0.18), residues: 830 sheet: 0.61 (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 0.006 0.001 PHE D 140 TRP 0.004 0.001 TRP F 123 HIS 0.003 0.000 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00161 (13400) covalent geometry : angle 0.41206 (18152) hydrogen bonds : bond 0.02846 ( 563) hydrogen bonds : angle 4.26024 ( 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 322 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 302 time to evaluate : 0.470 Fit side-chains REVERT: A 140 PHE cc_start: 0.8393 (m-80) cc_final: 0.8134 (m-80) REVERT: A 151 LYS cc_start: 0.8082 (ptpt) cc_final: 0.7707 (ttpt) REVERT: A 284 ASP cc_start: 0.8250 (t0) cc_final: 0.8011 (t0) REVERT: E 145 ASP cc_start: 0.8564 (t70) cc_final: 0.8361 (t0) REVERT: E 190 GLU cc_start: 0.8179 (mp0) cc_final: 0.7742 (mt-10) REVERT: B 129 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7389 (tm-30) REVERT: B 226 ASP cc_start: 0.8298 (m-30) cc_final: 0.7510 (m-30) REVERT: B 239 MET cc_start: 0.8793 (mtp) cc_final: 0.8583 (mtt) REVERT: B 298 ARG cc_start: 0.6571 (ttp-110) cc_final: 0.6126 (ttm110) REVERT: B 303 ILE cc_start: 0.8594 (mp) cc_final: 0.8370 (tp) REVERT: F 221 ARG cc_start: 0.7987 (ttm110) cc_final: 0.7761 (ttp-170) REVERT: F 300 ASP cc_start: 0.7543 (t70) cc_final: 0.7173 (t70) REVERT: F 323 LYS cc_start: 0.8321 (mttm) cc_final: 0.7961 (mtpt) REVERT: C 140 PHE cc_start: 0.8327 (m-80) cc_final: 0.8101 (m-80) REVERT: C 151 LYS cc_start: 0.7937 (ptpt) cc_final: 0.7581 (ttpt) REVERT: C 284 ASP cc_start: 0.8291 (t0) cc_final: 0.8047 (t0) REVERT: D 129 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7380 (tm-30) REVERT: D 226 ASP cc_start: 0.8318 (m-30) cc_final: 0.7465 (m-30) REVERT: D 239 MET cc_start: 0.8808 (mtp) cc_final: 0.8590 (mtt) REVERT: D 303 ILE cc_start: 0.8562 (mp) cc_final: 0.8303 (tp) REVERT: H 266 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: H 300 ASP cc_start: 0.7540 (t70) cc_final: 0.7143 (t70) REVERT: H 323 LYS cc_start: 0.8302 (mttm) cc_final: 0.7950 (mtpt) outliers start: 20 outliers final: 12 residues processed: 310 average time/residue: 0.1282 time to fit residues: 55.3922 Evaluate side-chains 289 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 276 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 91 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.165564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.125805 restraints weight = 40443.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.131784 restraints weight = 14857.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.137153 restraints weight = 8023.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.137930 restraints weight = 5594.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.139081 restraints weight = 4790.468| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13400 Z= 0.189 Angle : 0.480 5.640 18152 Z= 0.256 Chirality : 0.048 0.138 2174 Planarity : 0.004 0.041 2360 Dihedral : 3.470 16.394 1942 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.76 % Allowed : 15.38 % Favored : 81.86 % 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: -0.61 (0.20), residues: 1766 helix: -0.28 (0.18), residues: 830 sheet: 0.60 (0.26), residues: 336 loop : -0.97 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 206 TYR 0.020 0.001 TYR C 333 PHE 0.007 0.001 PHE A 232 TRP 0.002 0.001 TRP E 123 HIS 0.008 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00457 (13400) covalent geometry : angle 0.48049 (18152) hydrogen bonds : bond 0.03609 ( 563) hydrogen bonds : angle 4.36833 ( 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 312 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 276 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8610 (m-80) cc_final: 0.8313 (m-80) REVERT: A 151 LYS cc_start: 0.7961 (ptpt) cc_final: 0.7665 (ttpt) REVERT: A 210 GLU cc_start: 0.7910 (tt0) cc_final: 0.7234 (tt0) REVERT: A 284 ASP cc_start: 0.8367 (t0) cc_final: 0.7868 (t0) REVERT: A 333 TYR cc_start: 0.8419 (t80) cc_final: 0.8157 (t80) REVERT: E 129 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8745 (mm-30) REVERT: E 190 GLU cc_start: 0.8299 (mp0) cc_final: 0.7930 (mt-10) REVERT: B 138 GLU cc_start: 0.7912 (tp30) cc_final: 0.7658 (tp30) REVERT: B 169 ASP cc_start: 0.8662 (t0) cc_final: 0.8261 (t0) REVERT: B 226 ASP cc_start: 0.8312 (m-30) cc_final: 0.7594 (m-30) REVERT: B 303 ILE cc_start: 0.8605 (mp) cc_final: 0.8353 (tp) REVERT: F 142 LEU cc_start: 0.8747 (tp) cc_final: 0.8486 (tt) REVERT: F 266 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: F 300 ASP cc_start: 0.7629 (t70) cc_final: 0.7260 (t70) REVERT: F 323 LYS cc_start: 0.8349 (mttm) cc_final: 0.8030 (mtpt) REVERT: C 140 PHE cc_start: 0.8592 (m-80) cc_final: 0.8326 (m-80) REVERT: C 151 LYS cc_start: 0.7980 (ptpt) cc_final: 0.7612 (ttpt) REVERT: C 284 ASP cc_start: 0.8395 (t0) cc_final: 0.7900 (t0) REVERT: C 333 TYR cc_start: 0.8414 (t80) cc_final: 0.8214 (t80) REVERT: D 169 ASP cc_start: 0.8616 (t0) cc_final: 0.8181 (t0) REVERT: D 184 ASP cc_start: 0.8794 (t70) cc_final: 0.8590 (t0) REVERT: D 226 ASP cc_start: 0.8302 (m-30) cc_final: 0.7524 (m-30) REVERT: D 303 ILE cc_start: 0.8595 (mp) cc_final: 0.8323 (tp) REVERT: H 294 ILE cc_start: 0.9275 (pt) cc_final: 0.9007 (pt) REVERT: H 300 ASP cc_start: 0.7621 (t70) cc_final: 0.7248 (t70) REVERT: H 323 LYS cc_start: 0.8334 (mttm) cc_final: 0.8015 (mtpt) outliers start: 36 outliers final: 26 residues processed: 288 average time/residue: 0.1224 time to fit residues: 50.6141 Evaluate side-chains 287 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 260 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 245 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 266 GLU Chi-restraints excluded: chain E residue 280 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 158 ASN Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain D residue 275 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 75 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 286 HIS H 286 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.170515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.135273 restraints weight = 35188.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.139843 restraints weight = 16991.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.141437 restraints weight = 10325.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.144884 restraints weight = 7497.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.146628 restraints weight = 6043.221| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13400 Z= 0.173 Angle : 0.474 4.575 18152 Z= 0.253 Chirality : 0.047 0.139 2174 Planarity : 0.004 0.040 2360 Dihedral : 3.472 16.466 1942 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.05 % Allowed : 17.13 % Favored : 79.83 % 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: -0.58 (0.20), residues: 1766 helix: -0.15 (0.18), residues: 830 sheet: 0.34 (0.27), residues: 320 loop : -0.90 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.019 0.001 TYR C 333 PHE 0.006 0.001 PHE A 312 TRP 0.002 0.001 TRP E 123 HIS 0.004 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00423 (13400) covalent geometry : angle 0.47374 (18152) hydrogen bonds : bond 0.03455 ( 563) hydrogen bonds : angle 4.32542 ( 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 306 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8618 (m-80) cc_final: 0.8393 (m-80) REVERT: A 151 LYS cc_start: 0.7920 (ptpt) cc_final: 0.7705 (ttpt) REVERT: A 210 GLU cc_start: 0.7900 (tt0) cc_final: 0.7281 (tt0) REVERT: A 284 ASP cc_start: 0.8400 (t0) cc_final: 0.7948 (t0) REVERT: A 333 TYR cc_start: 0.8350 (t80) cc_final: 0.8146 (t80) REVERT: E 129 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8748 (mm-30) REVERT: B 169 ASP cc_start: 0.8599 (t70) cc_final: 0.8277 (t0) REVERT: B 226 ASP cc_start: 0.8279 (m-30) cc_final: 0.7573 (m-30) REVERT: B 303 ILE cc_start: 0.8650 (mp) cc_final: 0.8421 (tp) REVERT: F 266 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: F 300 ASP cc_start: 0.7717 (t70) cc_final: 0.7296 (t70) REVERT: F 323 LYS cc_start: 0.8404 (mttm) cc_final: 0.8106 (mtpt) REVERT: C 151 LYS cc_start: 0.7936 (ptpt) cc_final: 0.7658 (ttpt) REVERT: C 284 ASP cc_start: 0.8417 (t0) cc_final: 0.7966 (t0) REVERT: G 170 LEU cc_start: 0.8833 (mt) cc_final: 0.8630 (tp) REVERT: D 169 ASP cc_start: 0.8612 (t70) cc_final: 0.8254 (t0) REVERT: D 226 ASP cc_start: 0.8269 (m-30) cc_final: 0.7542 (m-30) REVERT: D 303 ILE cc_start: 0.8624 (mp) cc_final: 0.8390 (tp) REVERT: H 266 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: H 300 ASP cc_start: 0.7679 (t70) cc_final: 0.7255 (t70) REVERT: H 323 LYS cc_start: 0.8375 (mttm) cc_final: 0.8080 (mtpt) outliers start: 40 outliers final: 30 residues processed: 286 average time/residue: 0.1190 time to fit residues: 48.0425 Evaluate side-chains 282 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 250 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain D residue 275 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 35 optimal weight: 0.6980 chunk 146 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 139 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.172604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.135814 restraints weight = 32455.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.143211 restraints weight = 14882.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.145792 restraints weight = 7422.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.146383 restraints weight = 6467.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.149303 restraints weight = 5326.164| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13400 Z= 0.114 Angle : 0.445 6.725 18152 Z= 0.234 Chirality : 0.046 0.137 2174 Planarity : 0.003 0.037 2360 Dihedral : 3.329 15.903 1942 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.32 % Allowed : 18.00 % Favored : 79.68 % 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: -0.35 (0.20), residues: 1766 helix: 0.12 (0.19), residues: 822 sheet: 0.34 (0.27), residues: 320 loop : -0.84 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.019 0.001 TYR E 333 PHE 0.006 0.001 PHE D 140 TRP 0.002 0.000 TRP D 123 HIS 0.008 0.001 HIS H 161 Details of bonding type rmsd covalent geometry : bond 0.00272 (13400) covalent geometry : angle 0.44463 (18152) hydrogen bonds : bond 0.03054 ( 563) hydrogen bonds : angle 4.19055 ( 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 297 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 266 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8531 (m-80) cc_final: 0.8309 (m-80) REVERT: A 151 LYS cc_start: 0.7918 (ptpt) cc_final: 0.7690 (ttpt) REVERT: A 284 ASP cc_start: 0.8350 (t0) cc_final: 0.7929 (t0) REVERT: E 129 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8726 (mm-30) REVERT: B 169 ASP cc_start: 0.8613 (t70) cc_final: 0.8309 (t0) REVERT: B 226 ASP cc_start: 0.8200 (m-30) cc_final: 0.7493 (m-30) REVERT: B 239 MET cc_start: 0.8869 (mtp) cc_final: 0.8633 (mtt) REVERT: F 142 LEU cc_start: 0.8783 (tp) cc_final: 0.8505 (tt) REVERT: F 266 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: F 300 ASP cc_start: 0.7733 (t70) cc_final: 0.7314 (t70) REVERT: F 323 LYS cc_start: 0.8417 (mttm) cc_final: 0.8127 (mtpt) REVERT: C 151 LYS cc_start: 0.7930 (ptpt) cc_final: 0.7621 (ttpt) REVERT: C 169 ASP cc_start: 0.8205 (m-30) cc_final: 0.7832 (m-30) REVERT: C 210 GLU cc_start: 0.7769 (tt0) cc_final: 0.7351 (tt0) REVERT: C 284 ASP cc_start: 0.8399 (t0) cc_final: 0.7979 (t0) REVERT: D 169 ASP cc_start: 0.8612 (t70) cc_final: 0.8257 (t0) REVERT: D 226 ASP cc_start: 0.8289 (m-30) cc_final: 0.7498 (m-30) REVERT: D 239 MET cc_start: 0.8888 (mtp) cc_final: 0.8473 (mtt) REVERT: H 142 LEU cc_start: 0.8774 (tp) cc_final: 0.8510 (tt) REVERT: H 266 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: H 300 ASP cc_start: 0.7673 (t70) cc_final: 0.7258 (t70) REVERT: H 323 LYS cc_start: 0.8371 (mttm) cc_final: 0.8078 (mtpt) outliers start: 31 outliers final: 25 residues processed: 279 average time/residue: 0.1176 time to fit residues: 46.6704 Evaluate side-chains 276 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 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 275 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain F residue 158 ASN 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 287 ASP Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain H residue 158 ASN 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: 0.4980 chunk 79 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 0.0030 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.158190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.123044 restraints weight = 29398.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.127656 restraints weight = 19879.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.127362 restraints weight = 15596.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.131807 restraints weight = 9018.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.131953 restraints weight = 5911.463| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13400 Z= 0.096 Angle : 0.431 6.982 18152 Z= 0.226 Chirality : 0.046 0.138 2174 Planarity : 0.003 0.036 2360 Dihedral : 3.194 15.184 1942 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.39 % Allowed : 18.58 % 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: -0.14 (0.20), residues: 1766 helix: 0.29 (0.19), residues: 830 sheet: 0.38 (0.27), residues: 320 loop : -0.70 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.020 0.001 TYR E 333 PHE 0.006 0.001 PHE C 140 TRP 0.003 0.000 TRP B 123 HIS 0.005 0.001 HIS H 161 Details of bonding type rmsd covalent geometry : bond 0.00226 (13400) covalent geometry : angle 0.43072 (18152) hydrogen bonds : bond 0.02814 ( 563) hydrogen bonds : angle 4.07026 ( 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 298 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 266 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8482 (m-80) cc_final: 0.8231 (m-80) REVERT: A 151 LYS cc_start: 0.7928 (ptpt) cc_final: 0.7593 (ttpt) REVERT: A 284 ASP cc_start: 0.8319 (t0) cc_final: 0.7899 (t0) REVERT: E 129 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8718 (mm-30) REVERT: B 169 ASP cc_start: 0.8651 (t70) cc_final: 0.8276 (t0) REVERT: B 226 ASP cc_start: 0.8291 (m-30) cc_final: 0.7450 (m-30) REVERT: B 239 MET cc_start: 0.8864 (mtp) cc_final: 0.8585 (mtt) REVERT: F 142 LEU cc_start: 0.8764 (tp) cc_final: 0.8528 (tt) REVERT: F 266 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: F 300 ASP cc_start: 0.7888 (t70) cc_final: 0.7488 (t70) REVERT: F 323 LYS cc_start: 0.8319 (mttm) cc_final: 0.8023 (mtpt) REVERT: C 151 LYS cc_start: 0.7951 (ptpt) cc_final: 0.7628 (ttpt) REVERT: C 263 ARG cc_start: 0.7508 (mtm-85) cc_final: 0.7235 (mtt180) REVERT: C 284 ASP cc_start: 0.8393 (t0) cc_final: 0.7965 (t0) REVERT: C 294 ILE cc_start: 0.8808 (pt) cc_final: 0.8592 (mt) REVERT: C 298 ARG cc_start: 0.6345 (ttp-170) cc_final: 0.6136 (ttm110) REVERT: D 169 ASP cc_start: 0.8667 (t70) cc_final: 0.8269 (t0) REVERT: D 226 ASP cc_start: 0.8282 (m-30) cc_final: 0.7520 (m-30) REVERT: D 239 MET cc_start: 0.8930 (mtp) cc_final: 0.8532 (mtt) REVERT: H 142 LEU cc_start: 0.8762 (tp) cc_final: 0.8508 (tt) REVERT: H 266 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: H 300 ASP cc_start: 0.7863 (t70) cc_final: 0.7464 (t70) REVERT: H 323 LYS cc_start: 0.8245 (mttm) cc_final: 0.7951 (mtpt) outliers start: 32 outliers final: 25 residues processed: 279 average time/residue: 0.1138 time to fit residues: 45.4261 Evaluate side-chains 283 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 256 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 281 LEU Chi-restraints excluded: chain F residue 158 ASN 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 287 ASP Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 49 optimal weight: 0.8980 chunk 128 optimal weight: 0.3980 chunk 38 optimal weight: 0.1980 chunk 162 optimal weight: 0.8980 chunk 119 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.161408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.127821 restraints weight = 35219.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.131441 restraints weight = 26517.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.132521 restraints weight = 14254.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.137032 restraints weight = 8181.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.139506 restraints weight = 5428.502| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13400 Z= 0.095 Angle : 0.454 8.073 18152 Z= 0.237 Chirality : 0.046 0.195 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.135 14.900 1942 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.10 % Allowed : 19.09 % 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: 0.01 (0.20), residues: 1766 helix: 0.40 (0.19), residues: 830 sheet: 0.41 (0.28), residues: 304 loop : -0.54 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.020 0.001 TYR E 333 PHE 0.006 0.001 PHE D 140 TRP 0.002 0.000 TRP B 123 HIS 0.004 0.001 HIS H 161 Details of bonding type rmsd covalent geometry : bond 0.00221 (13400) covalent geometry : angle 0.45448 (18152) hydrogen bonds : bond 0.02786 ( 563) hydrogen bonds : angle 4.03342 ( 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 289 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8420 (m-80) cc_final: 0.8181 (m-80) REVERT: A 151 LYS cc_start: 0.7844 (ptpt) cc_final: 0.7571 (ttpt) REVERT: A 284 ASP cc_start: 0.8337 (t0) cc_final: 0.7898 (t0) REVERT: E 129 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8717 (mm-30) REVERT: E 215 GLU cc_start: 0.8177 (pm20) cc_final: 0.7863 (pt0) REVERT: E 318 ILE cc_start: 0.8284 (mt) cc_final: 0.8080 (pt) REVERT: B 129 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7435 (tm-30) REVERT: B 169 ASP cc_start: 0.8726 (t70) cc_final: 0.8353 (t0) REVERT: B 226 ASP cc_start: 0.8268 (m-30) cc_final: 0.7438 (m-30) REVERT: B 239 MET cc_start: 0.8871 (mtp) cc_final: 0.8616 (mtt) REVERT: F 142 LEU cc_start: 0.8742 (tp) cc_final: 0.8504 (tt) REVERT: F 266 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: F 300 ASP cc_start: 0.7840 (t70) cc_final: 0.7465 (t70) REVERT: F 323 LYS cc_start: 0.8334 (mttm) cc_final: 0.8027 (mtpt) REVERT: C 151 LYS cc_start: 0.7903 (ptpt) cc_final: 0.7609 (ttpt) REVERT: C 169 ASP cc_start: 0.8174 (m-30) cc_final: 0.7796 (m-30) REVERT: C 210 GLU cc_start: 0.7812 (tt0) cc_final: 0.7367 (tt0) REVERT: C 250 MET cc_start: 0.8860 (mtp) cc_final: 0.8524 (mtp) REVERT: C 263 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.7239 (mtt180) REVERT: C 284 ASP cc_start: 0.8372 (t0) cc_final: 0.7939 (t0) REVERT: G 318 ILE cc_start: 0.8287 (mt) cc_final: 0.8083 (pt) REVERT: D 129 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7439 (tm-30) REVERT: D 169 ASP cc_start: 0.8679 (t70) cc_final: 0.8251 (t0) REVERT: D 226 ASP cc_start: 0.8286 (m-30) cc_final: 0.7480 (m-30) REVERT: D 239 MET cc_start: 0.8928 (mtp) cc_final: 0.8557 (mtt) REVERT: H 142 LEU cc_start: 0.8750 (tp) cc_final: 0.8486 (tt) REVERT: H 266 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7737 (mt-10) REVERT: H 300 ASP cc_start: 0.7773 (t70) cc_final: 0.7380 (t70) REVERT: H 323 LYS cc_start: 0.8227 (mttm) cc_final: 0.7956 (mtpt) outliers start: 28 outliers final: 22 residues processed: 275 average time/residue: 0.1178 time to fit residues: 46.2525 Evaluate side-chains 280 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 256 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 281 LEU Chi-restraints excluded: chain F residue 158 ASN 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 287 ASP Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE 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: 2.9990 chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.146058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.110538 restraints weight = 36588.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.116314 restraints weight = 27199.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.115126 restraints weight = 13315.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.117268 restraints weight = 7939.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.120503 restraints weight = 6033.771| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13400 Z= 0.195 Angle : 0.524 10.606 18152 Z= 0.275 Chirality : 0.049 0.144 2174 Planarity : 0.004 0.036 2360 Dihedral : 3.442 15.954 1942 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.25 % Allowed : 19.09 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.17 (0.20), residues: 1766 helix: 0.24 (0.19), residues: 822 sheet: 0.24 (0.28), residues: 304 loop : -0.58 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.018 0.001 TYR E 333 PHE 0.008 0.001 PHE A 232 TRP 0.004 0.001 TRP F 123 HIS 0.005 0.001 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00473 (13400) covalent geometry : angle 0.52357 (18152) hydrogen bonds : bond 0.03588 ( 563) hydrogen bonds : angle 4.23797 ( 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: 30 poor density : 254 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8558 (m-80) cc_final: 0.8261 (m-80) REVERT: A 151 LYS cc_start: 0.7909 (ptpt) cc_final: 0.7537 (ttpt) REVERT: A 210 GLU cc_start: 0.7882 (tt0) cc_final: 0.7213 (tt0) REVERT: A 284 ASP cc_start: 0.8445 (t0) cc_final: 0.7935 (t0) REVERT: E 129 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8731 (mm-30) REVERT: E 318 ILE cc_start: 0.8266 (mt) cc_final: 0.7918 (pt) REVERT: B 169 ASP cc_start: 0.8773 (t70) cc_final: 0.8271 (t0) REVERT: B 226 ASP cc_start: 0.8398 (m-30) cc_final: 0.7545 (m-30) REVERT: B 239 MET cc_start: 0.8950 (mtp) cc_final: 0.8558 (mtt) REVERT: F 142 LEU cc_start: 0.8794 (tp) cc_final: 0.8496 (tt) REVERT: F 266 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: F 300 ASP cc_start: 0.8019 (t70) cc_final: 0.7641 (t70) REVERT: F 323 LYS cc_start: 0.8260 (mttm) cc_final: 0.7949 (mtpt) REVERT: C 151 LYS cc_start: 0.7989 (ptpt) cc_final: 0.7650 (ttpt) REVERT: C 284 ASP cc_start: 0.8498 (t0) cc_final: 0.8006 (t0) REVERT: D 169 ASP cc_start: 0.8765 (t70) cc_final: 0.8265 (t0) REVERT: D 226 ASP cc_start: 0.8324 (m-30) cc_final: 0.7487 (m-30) REVERT: D 239 MET cc_start: 0.8930 (mtp) cc_final: 0.8412 (mtt) REVERT: H 142 LEU cc_start: 0.8773 (tp) cc_final: 0.8485 (tt) REVERT: H 266 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: H 300 ASP cc_start: 0.7937 (t70) cc_final: 0.7576 (t70) REVERT: H 323 LYS cc_start: 0.8253 (mttm) cc_final: 0.7945 (mtpt) outliers start: 30 outliers final: 23 residues processed: 268 average time/residue: 0.1164 time to fit residues: 44.3922 Evaluate side-chains 273 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 281 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE 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: 1.9990 chunk 138 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 124 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.149963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.108695 restraints weight = 45010.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.111670 restraints weight = 21785.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.115731 restraints weight = 13614.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.116776 restraints weight = 10076.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.117276 restraints weight = 8189.384| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13400 Z= 0.119 Angle : 0.485 9.402 18152 Z= 0.250 Chirality : 0.047 0.145 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.269 15.460 1942 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.81 % Allowed : 19.96 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.02 (0.20), residues: 1766 helix: 0.40 (0.19), residues: 822 sheet: 0.29 (0.28), residues: 304 loop : -0.52 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.019 0.001 TYR E 333 PHE 0.006 0.001 PHE F 251 TRP 0.002 0.000 TRP D 123 HIS 0.004 0.001 HIS H 161 Details of bonding type rmsd covalent geometry : bond 0.00286 (13400) covalent geometry : angle 0.48474 (18152) hydrogen bonds : bond 0.03065 ( 563) hydrogen bonds : angle 4.12164 ( 1600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2223.91 seconds wall clock time: 38 minutes 56.47 seconds (2336.47 seconds total)