Starting phenix.real_space_refine on Sat Sep 12 02:44:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u5n_20650/09_2026/6u5n_20650.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u5n_20650/09_2026/6u5n_20650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u5n_20650/09_2026/6u5n_20650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u5n_20650/09_2026/6u5n_20650.map" model { file = "/net/cci-nas-00/data/ceres_data/6u5n_20650/09_2026/6u5n_20650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u5n_20650/09_2026/6u5n_20650.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6u5n_20650/09_2026/6u5n_20650.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u5n_20650/09_2026/6u5n_20650.cif" } resolution = 3.2 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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 2506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13262 Number of models: 1 Model: "" Number of chains: 16 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: "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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: C, G, D, H 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: 3.75, per 1000 atoms: 0.28 Number of scatterers: 13262 At special positions: 0 Unit cell: (141.384, 137, 69.048, 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 2506 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: 1.07 Conformation dependent library (CDL) restraints added in 838.2 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: 88 helices and 16 sheets defined 45.9% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 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 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.623A pdb=" N ALA A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.530A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'E' and resid 124 through 133 Processing helix chain 'E' and resid 148 through 155 removed outlier: 3.521A pdb=" N SER E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.566A pdb=" N ALA E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.659A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.617A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.586A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.799A pdb=" N LEU E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 289 removed outlier: 3.594A pdb=" N VAL E 288 " --> pdb=" O ASP E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 334 Processing helix chain 'B' and resid 124 through 134 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 173 Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.512A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.582A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.555A pdb=" N VAL B 288 " --> pdb=" O ASP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 148 through 155 removed outlier: 3.857A pdb=" N SER F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.637A pdb=" N ALA F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.627A pdb=" N ILE F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.559A pdb=" N GLY F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 241 Processing helix chain 'F' and resid 246 through 256 removed outlier: 3.596A pdb=" N MET F 250 " --> pdb=" O GLY F 246 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU F 256 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.689A pdb=" N ASP F 284 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.565A pdb=" N VAL F 288 " --> pdb=" O ASP F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 334 Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.623A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.530A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 242 Processing helix chain 'C' and resid 246 through 256 Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 323 through 334 Processing helix chain 'G' and resid 124 through 133 Processing helix chain 'G' and resid 148 through 155 removed outlier: 3.521A pdb=" N SER G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 173 removed outlier: 3.566A pdb=" N ALA G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.659A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.616A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 241 removed outlier: 3.586A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 256 removed outlier: 3.799A pdb=" N LEU G 256 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 289 removed outlier: 3.594A pdb=" N VAL G 288 " --> pdb=" O ASP G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 334 Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 148 through 155 Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.512A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.582A pdb=" N ILE D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 256 Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.555A pdb=" N VAL D 288 " --> pdb=" O ASP D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 148 through 155 removed outlier: 3.857A pdb=" N SER H 155 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 173 removed outlier: 3.637A pdb=" N ALA H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 removed outlier: 3.628A pdb=" N ILE H 201 " --> pdb=" O GLY H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 224 removed outlier: 3.558A pdb=" N GLY H 224 " --> pdb=" O LEU H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 241 Processing helix chain 'H' and resid 246 through 256 removed outlier: 3.596A pdb=" N MET H 250 " --> pdb=" O GLY H 246 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU H 256 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.689A pdb=" N ASP H 284 " --> pdb=" O VAL H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.566A pdb=" N VAL H 288 " --> pdb=" O ASP H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.501A pdb=" N VAL A 139 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL A 160 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL A 141 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 207 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE A 229 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA A 209 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 7.220A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.508A 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: 3.552A pdb=" N ALA E 143 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL E 118 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU E 142 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE E 120 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL E 181 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLU E 210 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL E 183 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE E 207 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE E 229 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA E 209 " --> pdb=" O ILE E 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 263 through 268 removed outlier: 7.515A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 3.512A 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: 6.402A pdb=" N VAL B 139 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS B 117 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA B 180 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE B 208 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 181 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N GLU B 210 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL B 183 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 263 through 268 removed outlier: 7.185A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.482A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL F 118 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU F 142 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE F 120 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N HIS F 117 " --> pdb=" O ALA F 178 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA F 180 " --> pdb=" O HIS F 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 263 through 268 removed outlier: 7.258A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.500A pdb=" N VAL C 139 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL C 160 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL C 141 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE C 207 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE C 229 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA C 209 " --> pdb=" O ILE C 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 263 through 268 removed outlier: 7.220A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.507A 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: 3.551A pdb=" N ALA G 143 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL G 118 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU G 142 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE G 120 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL G 181 " --> pdb=" O ILE G 208 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU G 210 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL G 183 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE G 207 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE G 229 " --> pdb=" O ILE G 207 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA G 209 " --> pdb=" O ILE G 229 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 263 through 268 removed outlier: 7.515A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) removed outlier: 3.512A 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: 6.401A pdb=" N VAL D 139 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS D 117 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA D 180 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE D 208 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL D 181 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLU D 210 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL D 183 " --> pdb=" O GLU D 210 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 263 through 268 removed outlier: 7.185A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.482A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL H 118 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU H 142 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE H 120 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N HIS H 117 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA H 180 " --> pdb=" O HIS H 117 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 7.258A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1718 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: 2.30 Time building geometry restraints manager: 1.47 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: 4523 1.34 - 1.45: 1252 1.45 - 1.57: 7537 1.57 - 1.69: 0 1.69 - 1.80: 88 Bond restraints: 13400 Sorted by residual: bond pdb=" N PRO C 324 " pdb=" CD PRO C 324 " ideal model delta sigma weight residual 1.473 1.408 0.065 1.40e-02 5.10e+03 2.15e+01 bond pdb=" N PRO A 324 " pdb=" CD PRO A 324 " ideal model delta sigma weight residual 1.473 1.408 0.065 1.40e-02 5.10e+03 2.15e+01 bond pdb=" CA GLU B 212 " pdb=" C GLU B 212 " ideal model delta sigma weight residual 1.524 1.556 -0.033 1.26e-02 6.30e+03 6.69e+00 bond pdb=" CA GLU D 212 " pdb=" C GLU D 212 " ideal model delta sigma weight residual 1.524 1.556 -0.032 1.26e-02 6.30e+03 6.63e+00 bond pdb=" CG1 ILE C 195 " pdb=" CD1 ILE C 195 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.03e+00 ... (remaining 13395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 17615 1.91 - 3.81: 497 3.81 - 5.72: 32 5.72 - 7.62: 6 7.62 - 9.53: 2 Bond angle restraints: 18152 Sorted by residual: angle pdb=" N ARG D 298 " pdb=" CA ARG D 298 " pdb=" C ARG D 298 " ideal model delta sigma weight residual 109.07 118.60 -9.53 1.61e+00 3.86e-01 3.50e+01 angle pdb=" N ARG B 298 " pdb=" CA ARG B 298 " pdb=" C ARG B 298 " ideal model delta sigma weight residual 109.07 118.56 -9.49 1.61e+00 3.86e-01 3.47e+01 angle pdb=" N PRO A 324 " pdb=" CA PRO A 324 " pdb=" C PRO A 324 " ideal model delta sigma weight residual 113.65 119.91 -6.26 1.35e+00 5.49e-01 2.15e+01 angle pdb=" N PRO C 324 " pdb=" CA PRO C 324 " pdb=" C PRO C 324 " ideal model delta sigma weight residual 113.65 119.91 -6.26 1.35e+00 5.49e-01 2.15e+01 angle pdb=" N GLU D 212 " pdb=" CA GLU D 212 " pdb=" C GLU D 212 " ideal model delta sigma weight residual 111.14 115.20 -4.06 1.08e+00 8.57e-01 1.42e+01 ... (remaining 18147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 7345 17.29 - 34.58: 679 34.58 - 51.87: 106 51.87 - 69.16: 36 69.16 - 86.45: 14 Dihedral angle restraints: 8180 sinusoidal: 3108 harmonic: 5072 Sorted by residual: dihedral pdb=" CA ASP G 284 " pdb=" C ASP G 284 " pdb=" N ILE G 285 " pdb=" CA ILE G 285 " ideal model delta harmonic sigma weight residual -180.00 -162.03 -17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP E 284 " pdb=" C ASP E 284 " pdb=" N ILE E 285 " pdb=" CA ILE E 285 " ideal model delta harmonic sigma weight residual -180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP G 245 " pdb=" C ASP G 245 " pdb=" N GLY G 246 " pdb=" CA GLY G 246 " ideal model delta harmonic sigma weight residual -180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 8177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1456 0.047 - 0.095: 470 0.095 - 0.142: 223 0.142 - 0.189: 19 0.189 - 0.237: 6 Chirality restraints: 2174 Sorted by residual: chirality pdb=" CA PRO C 324 " pdb=" N PRO C 324 " pdb=" C PRO C 324 " pdb=" CB PRO C 324 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO A 324 " pdb=" N PRO A 324 " pdb=" C PRO A 324 " pdb=" CB PRO A 324 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB VAL B 278 " pdb=" CA VAL B 278 " pdb=" CG1 VAL B 278 " pdb=" CG2 VAL B 278 " 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 LYS D 323 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO D 324 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 324 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 324 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 323 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO B 324 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 324 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 324 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 267 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO D 268 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 268 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 268 " -0.027 5.00e-02 4.00e+02 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 83 2.51 - 3.10: 8642 3.10 - 3.70: 19374 3.70 - 4.30: 28296 4.30 - 4.90: 49370 Nonbonded interactions: 105765 Sorted by model distance: nonbonded pdb=" O ASP C 244 " pdb=" OD1 ASP C 245 " model vdw 1.907 3.040 nonbonded pdb=" O ASP A 244 " pdb=" OD1 ASP A 245 " model vdw 1.907 3.040 nonbonded pdb=" O GLY E 290 " pdb="CA CA E 402 " model vdw 2.034 2.510 nonbonded pdb=" O GLY G 290 " pdb="CA CA G 402 " model vdw 2.034 2.510 nonbonded pdb=" O GLY C 290 " pdb="CA CA C 403 " model vdw 2.058 2.510 ... (remaining 105760 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'H' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.670 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 13400 Z= 0.255 Angle : 0.759 9.527 18152 Z= 0.466 Chirality : 0.055 0.237 2174 Planarity : 0.005 0.055 2360 Dihedral : 14.130 86.454 4912 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.15 % Allowed : 5.95 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.16), residues: 1766 helix: -2.90 (0.12), residues: 838 sheet: 1.11 (0.27), residues: 304 loop : -2.23 (0.18), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 132 TYR 0.011 0.002 TYR E 247 PHE 0.010 0.002 PHE C 232 TRP 0.002 0.001 TRP B 123 HIS 0.013 0.002 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.26 (13400) covalent geometry : angle 0.75902 / 0.47 (18152) hydrogen bonds : bond 0.18162 / 12.63 ( 600) hydrogen bonds : angle 6.92110 / 4.97 ( 1718) *********************** 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 319 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ILE cc_start: 0.8941 (mm) cc_final: 0.8609 (mm) REVERT: E 184 ASP cc_start: 0.8009 (t0) cc_final: 0.7696 (t0) REVERT: E 294 ILE cc_start: 0.8905 (pt) cc_final: 0.8666 (pt) REVERT: E 317 ILE cc_start: 0.9106 (mm) cc_final: 0.8888 (mm) REVERT: E 323 LYS cc_start: 0.7931 (mtpp) cc_final: 0.7684 (mtpp) REVERT: B 172 LYS cc_start: 0.8272 (mtpt) cc_final: 0.8039 (mtpt) REVERT: B 303 ILE cc_start: 0.8565 (mt) cc_final: 0.8288 (mm) REVERT: F 218 GLU cc_start: 0.7598 (pt0) cc_final: 0.7346 (pt0) REVERT: C 317 ILE cc_start: 0.8963 (mm) cc_final: 0.8672 (mm) REVERT: G 184 ASP cc_start: 0.7993 (t0) cc_final: 0.7694 (t0) REVERT: G 247 TYR cc_start: 0.8825 (m-80) cc_final: 0.8344 (m-80) REVERT: G 294 ILE cc_start: 0.8894 (pt) cc_final: 0.8657 (pt) REVERT: G 317 ILE cc_start: 0.9045 (mm) cc_final: 0.8782 (mm) REVERT: D 172 LYS cc_start: 0.8291 (mtpt) cc_final: 0.8060 (mtpt) REVERT: D 184 ASP cc_start: 0.8134 (t0) cc_final: 0.7740 (t70) REVERT: D 285 ILE cc_start: 0.8922 (mm) cc_final: 0.8717 (mm) REVERT: D 303 ILE cc_start: 0.8544 (mt) cc_final: 0.8270 (mm) REVERT: D 333 TYR cc_start: 0.8695 (t80) cc_final: 0.8483 (t80) REVERT: H 218 GLU cc_start: 0.7676 (pt0) cc_final: 0.7426 (pt0) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.1789 time to fit residues: 74.6593 Evaluate side-chains 248 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.148750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.102534 restraints weight = 32630.022| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.89 r_work: 0.2776 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1544 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= 0.115 Angle : 0.444 3.555 18152 Z= 0.243 Chirality : 0.046 0.138 2174 Planarity : 0.004 0.037 2360 Dihedral : 3.699 14.054 1942 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.94 % Allowed : 10.30 % Favored : 88.75 % 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: -1.46 (0.18), residues: 1766 helix: -1.10 (0.17), residues: 838 sheet: 1.04 (0.27), residues: 304 loop : -1.64 (0.20), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 116 TYR 0.017 0.001 TYR B 333 PHE 0.005 0.001 PHE C 232 TRP 0.002 0.000 TRP F 123 HIS 0.005 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (13400) covalent geometry : angle 0.44439 / 0.24 (18152) hydrogen bonds : bond 0.04088 / 2.80 ( 600) hydrogen bonds : angle 4.65048 / 3.33 ( 1718) *********************** 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 269 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 258 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8565 (m-30) cc_final: 0.7832 (t0) REVERT: A 153 LEU cc_start: 0.8151 (mt) cc_final: 0.7925 (mm) REVERT: A 212 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8069 (mt-10) REVERT: A 221 ARG cc_start: 0.8729 (ttm110) cc_final: 0.8456 (mtm-85) REVERT: A 222 MET cc_start: 0.8802 (mmm) cc_final: 0.8590 (mmm) REVERT: A 317 ILE cc_start: 0.8758 (mm) cc_final: 0.8429 (mm) REVERT: E 210 GLU cc_start: 0.8386 (tt0) cc_final: 0.8089 (tt0) REVERT: E 323 LYS cc_start: 0.7525 (mtpp) cc_final: 0.7250 (mtpp) REVERT: B 172 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7901 (mtpt) REVERT: B 264 MET cc_start: 0.8637 (ttp) cc_final: 0.8314 (ttm) REVERT: B 303 ILE cc_start: 0.8076 (mt) cc_final: 0.7682 (mm) REVERT: B 313 ARG cc_start: 0.7326 (mtp85) cc_final: 0.6907 (mtp180) REVERT: F 218 GLU cc_start: 0.8341 (pt0) cc_final: 0.8014 (pt0) REVERT: F 222 MET cc_start: 0.8679 (mtm) cc_final: 0.8468 (mtm) REVERT: C 212 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8094 (mt-10) REVERT: C 221 ARG cc_start: 0.8732 (ttm110) cc_final: 0.8468 (mtm-85) REVERT: C 222 MET cc_start: 0.8816 (mmm) cc_final: 0.8604 (mmm) REVERT: C 317 ILE cc_start: 0.8793 (mm) cc_final: 0.8462 (mm) REVERT: G 210 GLU cc_start: 0.8356 (tt0) cc_final: 0.8059 (tt0) REVERT: D 172 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7927 (mtpt) REVERT: D 264 MET cc_start: 0.8637 (ttp) cc_final: 0.8323 (ttm) REVERT: D 285 ILE cc_start: 0.8120 (mm) cc_final: 0.7904 (mm) REVERT: D 303 ILE cc_start: 0.8064 (mt) cc_final: 0.7675 (mm) REVERT: D 313 ARG cc_start: 0.7379 (mtp85) cc_final: 0.6911 (mtp180) REVERT: D 333 TYR cc_start: 0.8133 (t80) cc_final: 0.7930 (t80) REVERT: H 218 GLU cc_start: 0.8444 (pt0) cc_final: 0.8146 (pt0) outliers start: 11 outliers final: 7 residues processed: 264 average time/residue: 0.1572 time to fit residues: 56.5416 Evaluate side-chains 238 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 231 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 280 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 3 optimal weight: 0.0170 chunk 15 optimal weight: 5.9990 chunk 109 optimal weight: 0.4980 chunk 141 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN C 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.149516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.113570 restraints weight = 27283.209| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 4.89 r_work: 0.2790 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13400 Z= 0.097 Angle : 0.404 3.185 18152 Z= 0.220 Chirality : 0.046 0.140 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.426 13.211 1942 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.23 % Allowed : 11.97 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.62 (0.19), residues: 1766 helix: -0.30 (0.18), residues: 846 sheet: 1.05 (0.27), residues: 304 loop : -1.17 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 116 TYR 0.013 0.001 TYR G 333 PHE 0.005 0.001 PHE G 251 TRP 0.003 0.001 TRP D 123 HIS 0.004 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (13400) covalent geometry : angle 0.40354 / 0.22 (18152) hydrogen bonds : bond 0.03427 / 2.33 ( 600) hydrogen bonds : angle 4.32897 / 3.12 ( 1718) *********************** 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 255 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 240 time to evaluate : 0.546 Fit side-chains REVERT: A 138 GLU cc_start: 0.7219 (tt0) cc_final: 0.6888 (mt-10) REVERT: A 145 ASP cc_start: 0.8497 (m-30) cc_final: 0.7776 (t0) REVERT: A 153 LEU cc_start: 0.8073 (mt) cc_final: 0.7865 (mm) REVERT: E 210 GLU cc_start: 0.8482 (tt0) cc_final: 0.8165 (tt0) REVERT: E 247 TYR cc_start: 0.8746 (m-80) cc_final: 0.8222 (m-80) REVERT: B 116 ARG cc_start: 0.7901 (mmm160) cc_final: 0.7641 (mtp85) REVERT: B 172 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7974 (mtpp) REVERT: B 226 ASP cc_start: 0.8740 (m-30) cc_final: 0.8532 (m-30) REVERT: B 303 ILE cc_start: 0.7910 (mt) cc_final: 0.7615 (mm) REVERT: B 313 ARG cc_start: 0.7324 (mtp85) cc_final: 0.6844 (mtp180) REVERT: F 146 GLU cc_start: 0.6928 (tp30) cc_final: 0.6712 (tp30) REVERT: F 218 GLU cc_start: 0.8385 (pt0) cc_final: 0.8069 (pt0) REVERT: F 245 ASP cc_start: 0.7755 (p0) cc_final: 0.7255 (p0) REVERT: C 145 ASP cc_start: 0.8523 (m-30) cc_final: 0.7798 (t0) REVERT: G 210 GLU cc_start: 0.8468 (tt0) cc_final: 0.8144 (tt0) REVERT: G 313 ARG cc_start: 0.6591 (mtm180) cc_final: 0.6121 (mtm180) REVERT: D 116 ARG cc_start: 0.7885 (mmm160) cc_final: 0.7679 (mtp85) REVERT: D 226 ASP cc_start: 0.8738 (m-30) cc_final: 0.8533 (m-30) REVERT: D 285 ILE cc_start: 0.8081 (mm) cc_final: 0.7868 (mm) REVERT: D 303 ILE cc_start: 0.7896 (mt) cc_final: 0.7584 (mm) REVERT: D 333 TYR cc_start: 0.8024 (t80) cc_final: 0.7791 (t80) REVERT: H 146 GLU cc_start: 0.6938 (tp30) cc_final: 0.6730 (tp30) REVERT: H 218 GLU cc_start: 0.8412 (pt0) cc_final: 0.8133 (pt0) REVERT: H 245 ASP cc_start: 0.7763 (p0) cc_final: 0.7276 (p0) REVERT: H 250 MET cc_start: 0.9091 (mtm) cc_final: 0.8887 (mtp) outliers start: 15 outliers final: 10 residues processed: 248 average time/residue: 0.1528 time to fit residues: 51.4392 Evaluate side-chains 235 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 225 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 9 optimal weight: 0.0050 chunk 120 optimal weight: 0.6980 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.148357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.105203 restraints weight = 32572.972| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.55 r_work: 0.2809 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13400 Z= 0.112 Angle : 0.406 3.424 18152 Z= 0.220 Chirality : 0.046 0.135 2174 Planarity : 0.003 0.036 2360 Dihedral : 3.347 14.366 1942 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.16 % Allowed : 13.72 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.20 (0.19), residues: 1766 helix: 0.05 (0.18), residues: 846 sheet: 1.10 (0.28), residues: 304 loop : -0.87 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 116 TYR 0.010 0.001 TYR G 333 PHE 0.007 0.001 PHE C 232 TRP 0.001 0.000 TRP D 123 HIS 0.004 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.11 (13400) covalent geometry : angle 0.40649 / 0.22 (18152) hydrogen bonds : bond 0.03364 / 2.29 ( 600) hydrogen bonds : angle 4.23286 / 3.05 ( 1718) *********************** 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 241 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 227 time to evaluate : 0.450 Fit side-chains REVERT: A 138 GLU cc_start: 0.7253 (tt0) cc_final: 0.7002 (mt-10) REVERT: A 145 ASP cc_start: 0.8463 (m-30) cc_final: 0.7888 (t0) REVERT: E 210 GLU cc_start: 0.8408 (tt0) cc_final: 0.8108 (tt0) REVERT: E 247 TYR cc_start: 0.8768 (m-80) cc_final: 0.8345 (m-80) REVERT: E 313 ARG cc_start: 0.6619 (mtm180) cc_final: 0.6217 (mtm180) REVERT: B 116 ARG cc_start: 0.7903 (mmm160) cc_final: 0.7674 (mtp85) REVERT: B 226 ASP cc_start: 0.8675 (m-30) cc_final: 0.8443 (m-30) REVERT: B 303 ILE cc_start: 0.8049 (mt) cc_final: 0.7772 (mm) REVERT: F 218 GLU cc_start: 0.8328 (pt0) cc_final: 0.8039 (pt0) REVERT: F 245 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7115 (p0) REVERT: F 298 ARG cc_start: 0.5027 (mtm180) cc_final: 0.4818 (mtt180) REVERT: C 145 ASP cc_start: 0.8510 (m-30) cc_final: 0.7920 (t0) REVERT: G 210 GLU cc_start: 0.8444 (tt0) cc_final: 0.8121 (tt0) REVERT: G 247 TYR cc_start: 0.8800 (m-80) cc_final: 0.8376 (m-80) REVERT: D 116 ARG cc_start: 0.7913 (mmm160) cc_final: 0.7701 (mtp85) REVERT: D 226 ASP cc_start: 0.8681 (m-30) cc_final: 0.8450 (m-30) REVERT: D 285 ILE cc_start: 0.8231 (mm) cc_final: 0.8016 (mm) REVERT: D 303 ILE cc_start: 0.8032 (mt) cc_final: 0.7762 (mm) REVERT: H 172 LYS cc_start: 0.7685 (mtmt) cc_final: 0.7440 (mtmt) REVERT: H 218 GLU cc_start: 0.8407 (pt0) cc_final: 0.8163 (pt0) REVERT: H 298 ARG cc_start: 0.5001 (mtm180) cc_final: 0.4798 (mtt180) outliers start: 14 outliers final: 10 residues processed: 235 average time/residue: 0.1420 time to fit residues: 45.9223 Evaluate side-chains 226 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 215 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 36 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 156 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 169 optimal weight: 0.0980 chunk 155 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.149333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.106034 restraints weight = 34470.937| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.67 r_work: 0.2812 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13400 Z= 0.090 Angle : 0.390 4.037 18152 Z= 0.211 Chirality : 0.046 0.140 2174 Planarity : 0.003 0.041 2360 Dihedral : 3.244 12.877 1942 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.16 % Allowed : 15.67 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.20 (0.19), residues: 1766 helix: 0.39 (0.18), residues: 846 sheet: 1.16 (0.28), residues: 304 loop : -0.61 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 116 TYR 0.025 0.001 TYR D 333 PHE 0.006 0.001 PHE G 251 TRP 0.001 0.000 TRP E 123 HIS 0.003 0.000 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 (13400) covalent geometry : angle 0.39003 / 0.21 (18152) hydrogen bonds : bond 0.02994 / 2.03 ( 600) hydrogen bonds : angle 4.10901 / 2.97 ( 1718) *********************** 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 238 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 224 time to evaluate : 0.523 Fit side-chains REVERT: A 138 GLU cc_start: 0.7271 (tt0) cc_final: 0.7047 (mt-10) REVERT: A 145 ASP cc_start: 0.8409 (m-30) cc_final: 0.7871 (t0) REVERT: E 210 GLU cc_start: 0.8448 (tt0) cc_final: 0.8148 (tt0) REVERT: E 247 TYR cc_start: 0.8702 (m-80) cc_final: 0.8300 (m-80) REVERT: B 116 ARG cc_start: 0.7882 (mmm160) cc_final: 0.7661 (mtp85) REVERT: B 226 ASP cc_start: 0.8689 (m-30) cc_final: 0.8434 (m-30) REVERT: B 264 MET cc_start: 0.8890 (ttp) cc_final: 0.8532 (ttm) REVERT: B 303 ILE cc_start: 0.8052 (mt) cc_final: 0.7758 (mm) REVERT: B 313 ARG cc_start: 0.7432 (mtp85) cc_final: 0.6832 (mtp180) REVERT: F 218 GLU cc_start: 0.8345 (pt0) cc_final: 0.8089 (pt0) REVERT: F 245 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7053 (p0) REVERT: C 145 ASP cc_start: 0.8414 (m-30) cc_final: 0.7885 (t0) REVERT: G 210 GLU cc_start: 0.8454 (tt0) cc_final: 0.8140 (tt0) REVERT: G 247 TYR cc_start: 0.8758 (m-80) cc_final: 0.8370 (m-80) REVERT: D 226 ASP cc_start: 0.8696 (m-30) cc_final: 0.8447 (m-30) REVERT: D 264 MET cc_start: 0.8877 (ttp) cc_final: 0.8523 (ttm) REVERT: D 285 ILE cc_start: 0.8187 (mm) cc_final: 0.7963 (mm) REVERT: D 303 ILE cc_start: 0.8035 (mt) cc_final: 0.7751 (mm) REVERT: H 172 LYS cc_start: 0.7609 (mtmt) cc_final: 0.7391 (mtmt) REVERT: H 218 GLU cc_start: 0.8352 (pt0) cc_final: 0.8079 (pt0) REVERT: H 245 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7135 (p0) REVERT: H 250 MET cc_start: 0.9118 (mtm) cc_final: 0.8846 (mtp) outliers start: 14 outliers final: 11 residues processed: 230 average time/residue: 0.1475 time to fit residues: 46.7401 Evaluate side-chains 220 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 207 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 280 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 128 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.148173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.103881 restraints weight = 30467.549| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.86 r_work: 0.2764 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13400 Z= 0.114 Angle : 0.406 3.601 18152 Z= 0.219 Chirality : 0.046 0.140 2174 Planarity : 0.003 0.040 2360 Dihedral : 3.287 13.983 1942 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.52 % Allowed : 16.62 % 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: 0.31 (0.20), residues: 1766 helix: 0.44 (0.18), residues: 846 sheet: 1.21 (0.28), residues: 304 loop : -0.49 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 116 TYR 0.008 0.001 TYR G 333 PHE 0.007 0.001 PHE A 232 TRP 0.001 0.000 TRP B 123 HIS 0.004 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.11 (13400) covalent geometry : angle 0.40632 / 0.22 (18152) hydrogen bonds : bond 0.03265 / 2.23 ( 600) hydrogen bonds : angle 4.16880 / 3.00 ( 1718) *********************** 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 234 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 0.533 Fit side-chains REVERT: A 138 GLU cc_start: 0.7312 (tt0) cc_final: 0.7012 (mt-10) REVERT: A 145 ASP cc_start: 0.8452 (m-30) cc_final: 0.7900 (t0) REVERT: E 210 GLU cc_start: 0.8511 (tt0) cc_final: 0.8200 (tt0) REVERT: E 247 TYR cc_start: 0.8733 (m-80) cc_final: 0.8311 (m-80) REVERT: B 116 ARG cc_start: 0.7969 (mmm160) cc_final: 0.7751 (mtp85) REVERT: B 134 LEU cc_start: 0.7588 (mt) cc_final: 0.7382 (mt) REVERT: B 226 ASP cc_start: 0.8747 (m-30) cc_final: 0.8518 (m-30) REVERT: B 303 ILE cc_start: 0.8053 (mt) cc_final: 0.7760 (mm) REVERT: B 313 ARG cc_start: 0.7359 (mtp85) cc_final: 0.6932 (mtp180) REVERT: F 218 GLU cc_start: 0.8463 (pt0) cc_final: 0.8151 (pt0) REVERT: F 222 MET cc_start: 0.8780 (mtp) cc_final: 0.8536 (mtm) REVERT: F 245 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7054 (p0) REVERT: C 145 ASP cc_start: 0.8470 (m-30) cc_final: 0.7934 (t0) REVERT: G 210 GLU cc_start: 0.8492 (tt0) cc_final: 0.8181 (tt0) REVERT: G 247 TYR cc_start: 0.8808 (m-80) cc_final: 0.8395 (m-80) REVERT: D 226 ASP cc_start: 0.8762 (m-30) cc_final: 0.8534 (m-30) REVERT: D 285 ILE cc_start: 0.8083 (mm) cc_final: 0.7844 (mm) REVERT: D 303 ILE cc_start: 0.8041 (mt) cc_final: 0.7760 (mm) REVERT: H 172 LYS cc_start: 0.7607 (mtmt) cc_final: 0.7367 (mtmt) REVERT: H 218 GLU cc_start: 0.8376 (pt0) cc_final: 0.7995 (pt0) REVERT: H 222 MET cc_start: 0.8752 (mtm) cc_final: 0.8468 (mtm) REVERT: H 245 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7117 (p0) outliers start: 19 outliers final: 10 residues processed: 226 average time/residue: 0.1476 time to fit residues: 45.3697 Evaluate side-chains 225 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 213 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 280 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 90 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 158 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.147480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.103861 restraints weight = 32633.988| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.73 r_work: 0.2779 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13400 Z= 0.130 Angle : 0.423 5.392 18152 Z= 0.226 Chirality : 0.047 0.151 2174 Planarity : 0.004 0.041 2360 Dihedral : 3.346 14.419 1942 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.45 % Allowed : 16.62 % Favored : 81.93 % 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: 0.39 (0.20), residues: 1766 helix: 0.48 (0.18), residues: 846 sheet: 1.21 (0.28), residues: 304 loop : -0.40 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 116 TYR 0.008 0.001 TYR G 333 PHE 0.008 0.001 PHE G 251 TRP 0.001 0.000 TRP A 123 HIS 0.005 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 (13400) covalent geometry : angle 0.42344 / 0.23 (18152) hydrogen bonds : bond 0.03369 / 2.29 ( 600) hydrogen bonds : angle 4.17049 / 3.01 ( 1718) *********************** 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 249 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 0.528 Fit side-chains REVERT: A 138 GLU cc_start: 0.7321 (tt0) cc_final: 0.7031 (mt-10) REVERT: A 145 ASP cc_start: 0.8450 (m-30) cc_final: 0.7965 (t0) REVERT: E 116 ARG cc_start: 0.8020 (mtt90) cc_final: 0.6939 (mmm-85) REVERT: E 210 GLU cc_start: 0.8439 (tt0) cc_final: 0.8105 (tt0) REVERT: E 213 ARG cc_start: 0.8467 (mtp180) cc_final: 0.8109 (mtp180) REVERT: B 116 ARG cc_start: 0.7966 (mmm160) cc_final: 0.7700 (mtp85) REVERT: B 154 ARG cc_start: 0.8394 (ttp80) cc_final: 0.8119 (ttp-110) REVERT: B 303 ILE cc_start: 0.8120 (mt) cc_final: 0.7823 (mm) REVERT: B 313 ARG cc_start: 0.7397 (mtp85) cc_final: 0.6957 (mtp180) REVERT: F 218 GLU cc_start: 0.8361 (pt0) cc_final: 0.8026 (pt0) REVERT: F 222 MET cc_start: 0.8724 (mtp) cc_final: 0.8466 (mtm) REVERT: F 317 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8030 (mm) REVERT: C 145 ASP cc_start: 0.8427 (m-30) cc_final: 0.7943 (t0) REVERT: G 116 ARG cc_start: 0.8005 (mtt90) cc_final: 0.6938 (mmm-85) REVERT: G 210 GLU cc_start: 0.8416 (tt0) cc_final: 0.8081 (tt0) REVERT: G 213 ARG cc_start: 0.8465 (mtp180) cc_final: 0.8105 (mtp180) REVERT: G 247 TYR cc_start: 0.8822 (m-80) cc_final: 0.8427 (m-80) REVERT: D 154 ARG cc_start: 0.8403 (ttp80) cc_final: 0.8135 (ttp-110) REVERT: D 285 ILE cc_start: 0.8194 (mm) cc_final: 0.7929 (mm) REVERT: D 303 ILE cc_start: 0.8078 (mt) cc_final: 0.7800 (mm) REVERT: D 313 ARG cc_start: 0.7423 (mtp85) cc_final: 0.6978 (mtp180) REVERT: H 172 LYS cc_start: 0.7641 (mtmt) cc_final: 0.7394 (mtmt) REVERT: H 218 GLU cc_start: 0.8382 (pt0) cc_final: 0.7997 (pt0) REVERT: H 222 MET cc_start: 0.8751 (mtm) cc_final: 0.8471 (mtm) REVERT: H 245 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7074 (p0) outliers start: 18 outliers final: 14 residues processed: 240 average time/residue: 0.1409 time to fit residues: 46.5267 Evaluate side-chains 231 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 264 MET Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 119 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.149119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.104660 restraints weight = 42424.291| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.97 r_work: 0.2759 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2358 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= 0.099 Angle : 0.411 7.601 18152 Z= 0.217 Chirality : 0.046 0.157 2174 Planarity : 0.003 0.038 2360 Dihedral : 3.253 13.268 1942 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.45 % Allowed : 16.69 % 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: 0.55 (0.20), residues: 1766 helix: 0.66 (0.19), residues: 846 sheet: 1.19 (0.28), residues: 304 loop : -0.33 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 116 TYR 0.008 0.001 TYR G 333 PHE 0.007 0.001 PHE G 251 TRP 0.001 0.000 TRP F 123 HIS 0.003 0.000 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (13400) covalent geometry : angle 0.41064 / 0.22 (18152) hydrogen bonds : bond 0.03044 / 2.06 ( 600) hydrogen bonds : angle 4.10665 / 2.97 ( 1718) *********************** 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 249 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 0.556 Fit side-chains REVERT: A 138 GLU cc_start: 0.7353 (tt0) cc_final: 0.7058 (mt-10) REVERT: A 145 ASP cc_start: 0.8484 (m-30) cc_final: 0.8102 (t0) REVERT: E 116 ARG cc_start: 0.8056 (mtt90) cc_final: 0.6987 (mmm-85) REVERT: E 210 GLU cc_start: 0.8509 (tt0) cc_final: 0.8198 (tt0) REVERT: E 213 ARG cc_start: 0.8499 (mtp180) cc_final: 0.8129 (mtp180) REVERT: B 116 ARG cc_start: 0.7959 (mmm160) cc_final: 0.7750 (mtp85) REVERT: B 154 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8153 (ttp-110) REVERT: B 303 ILE cc_start: 0.8085 (mt) cc_final: 0.7783 (mm) REVERT: B 313 ARG cc_start: 0.7376 (mtp85) cc_final: 0.6942 (mtp180) REVERT: F 218 GLU cc_start: 0.8327 (pt0) cc_final: 0.8045 (pt0) REVERT: F 245 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7060 (p0) REVERT: C 145 ASP cc_start: 0.8462 (m-30) cc_final: 0.7958 (t0) REVERT: C 317 ILE cc_start: 0.8744 (mm) cc_final: 0.8507 (mm) REVERT: G 116 ARG cc_start: 0.8029 (mtt90) cc_final: 0.6940 (mmm-85) REVERT: G 210 GLU cc_start: 0.8486 (tt0) cc_final: 0.8172 (tt0) REVERT: G 213 ARG cc_start: 0.8486 (mtp180) cc_final: 0.8111 (mtp180) REVERT: D 154 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8160 (ttp-110) REVERT: D 285 ILE cc_start: 0.8194 (mm) cc_final: 0.7933 (mm) REVERT: D 303 ILE cc_start: 0.8069 (mt) cc_final: 0.7791 (mm) REVERT: D 313 ARG cc_start: 0.7402 (mtp85) cc_final: 0.6964 (mtp180) REVERT: H 172 LYS cc_start: 0.7584 (mtmt) cc_final: 0.7358 (mtmt) REVERT: H 218 GLU cc_start: 0.8430 (pt0) cc_final: 0.8144 (pt0) REVERT: H 245 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7080 (p0) REVERT: H 250 MET cc_start: 0.9110 (mtm) cc_final: 0.8882 (mtp) outliers start: 18 outliers final: 15 residues processed: 238 average time/residue: 0.1520 time to fit residues: 49.0939 Evaluate side-chains 243 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 226 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 280 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 107 optimal weight: 0.0470 chunk 71 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.149368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.102972 restraints weight = 30675.957| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.28 r_work: 0.2797 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13400 Z= 0.095 Angle : 0.404 6.950 18152 Z= 0.214 Chirality : 0.046 0.148 2174 Planarity : 0.003 0.038 2360 Dihedral : 3.189 12.856 1942 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.60 % Allowed : 17.05 % Favored : 81.35 % 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: 0.64 (0.20), residues: 1766 helix: 0.75 (0.19), residues: 846 sheet: 1.22 (0.28), residues: 304 loop : -0.29 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 116 TYR 0.007 0.001 TYR G 333 PHE 0.007 0.001 PHE E 251 TRP 0.001 0.000 TRP G 123 HIS 0.003 0.000 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.09 (13400) covalent geometry : angle 0.40386 / 0.21 (18152) hydrogen bonds : bond 0.02990 / 2.03 ( 600) hydrogen bonds : angle 4.08980 / 2.95 ( 1718) *********************** 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 243 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.630 Fit side-chains REVERT: A 138 GLU cc_start: 0.7330 (tt0) cc_final: 0.7046 (mt-10) REVERT: A 145 ASP cc_start: 0.8458 (m-30) cc_final: 0.8110 (t0) REVERT: E 210 GLU cc_start: 0.8504 (tt0) cc_final: 0.8202 (tt0) REVERT: E 213 ARG cc_start: 0.8424 (mtp180) cc_final: 0.8074 (mtp180) REVERT: B 154 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8154 (ttp-110) REVERT: B 303 ILE cc_start: 0.8059 (mt) cc_final: 0.7753 (mm) REVERT: B 313 ARG cc_start: 0.7407 (mtp85) cc_final: 0.6978 (mtp180) REVERT: F 218 GLU cc_start: 0.8307 (pt0) cc_final: 0.8023 (pt0) REVERT: F 245 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.6986 (p0) REVERT: C 145 ASP cc_start: 0.8458 (m-30) cc_final: 0.8113 (t0) REVERT: G 210 GLU cc_start: 0.8476 (tt0) cc_final: 0.8176 (tt0) REVERT: G 213 ARG cc_start: 0.8423 (mtp180) cc_final: 0.8077 (mtp180) REVERT: D 154 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8160 (ttp-110) REVERT: D 285 ILE cc_start: 0.8219 (mm) cc_final: 0.7955 (mm) REVERT: D 303 ILE cc_start: 0.8061 (mt) cc_final: 0.7782 (mm) REVERT: D 313 ARG cc_start: 0.7438 (mtp85) cc_final: 0.7007 (mtp180) REVERT: H 172 LYS cc_start: 0.7554 (mtmt) cc_final: 0.7332 (mtmt) REVERT: H 218 GLU cc_start: 0.8406 (pt0) cc_final: 0.8008 (pt0) REVERT: H 222 MET cc_start: 0.8752 (mtp) cc_final: 0.8483 (mtm) REVERT: H 245 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7004 (p0) REVERT: H 250 MET cc_start: 0.9080 (mtm) cc_final: 0.8842 (mtp) outliers start: 20 outliers final: 18 residues processed: 230 average time/residue: 0.1341 time to fit residues: 42.7703 Evaluate side-chains 237 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 264 MET Chi-restraints excluded: chain H residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 8 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 51 optimal weight: 0.0980 chunk 165 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.148917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.112060 restraints weight = 21915.549| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.13 r_work: 0.2877 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13400 Z= 0.102 Angle : 0.413 7.040 18152 Z= 0.218 Chirality : 0.046 0.150 2174 Planarity : 0.003 0.045 2360 Dihedral : 3.213 13.256 1942 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.60 % Allowed : 17.13 % Favored : 81.28 % 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: 0.69 (0.20), residues: 1766 helix: 0.77 (0.19), residues: 846 sheet: 1.26 (0.28), residues: 304 loop : -0.25 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 241 TYR 0.007 0.001 TYR G 333 PHE 0.007 0.001 PHE E 251 TRP 0.001 0.000 TRP G 123 HIS 0.003 0.000 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.10 (13400) covalent geometry : angle 0.41283 / 0.22 (18152) hydrogen bonds : bond 0.03038 / 2.06 ( 600) hydrogen bonds : angle 4.07302 / 2.93 ( 1718) ********************** 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 243 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7248 (tt0) cc_final: 0.7026 (mt-10) REVERT: E 116 ARG cc_start: 0.8038 (mtt90) cc_final: 0.7065 (mmm-85) REVERT: E 210 GLU cc_start: 0.8349 (tt0) cc_final: 0.8040 (tt0) REVERT: E 213 ARG cc_start: 0.8359 (mtp180) cc_final: 0.8015 (mtp180) REVERT: B 154 ARG cc_start: 0.8360 (ttp80) cc_final: 0.8103 (ttp-110) REVERT: B 303 ILE cc_start: 0.8123 (mt) cc_final: 0.7821 (mm) REVERT: B 313 ARG cc_start: 0.7485 (mtp85) cc_final: 0.7049 (mtp180) REVERT: F 218 GLU cc_start: 0.8262 (pt0) cc_final: 0.7984 (pt0) REVERT: F 245 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.6935 (p0) REVERT: F 317 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8141 (mm) REVERT: G 210 GLU cc_start: 0.8327 (tt0) cc_final: 0.8014 (tt0) REVERT: G 213 ARG cc_start: 0.8349 (mtp180) cc_final: 0.8004 (mtp180) REVERT: D 154 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8112 (ttp-110) REVERT: D 285 ILE cc_start: 0.8274 (mm) cc_final: 0.8003 (mm) REVERT: D 303 ILE cc_start: 0.8108 (mt) cc_final: 0.7830 (mm) REVERT: D 313 ARG cc_start: 0.7505 (mtp85) cc_final: 0.7066 (mtp180) REVERT: H 218 GLU cc_start: 0.8278 (pt0) cc_final: 0.8002 (pt0) REVERT: H 245 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.6962 (p0) REVERT: H 250 MET cc_start: 0.9052 (mtm) cc_final: 0.8799 (mtp) outliers start: 20 outliers final: 17 residues processed: 231 average time/residue: 0.1381 time to fit residues: 43.9213 Evaluate side-chains 241 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 82 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 33 optimal weight: 0.0270 chunk 151 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.147418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.111057 restraints weight = 30679.543| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 4.97 r_work: 0.2720 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13400 Z= 0.134 Angle : 0.437 7.091 18152 Z= 0.230 Chirality : 0.047 0.147 2174 Planarity : 0.004 0.047 2360 Dihedral : 3.335 14.534 1942 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.74 % Allowed : 17.20 % Favored : 81.06 % 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: 0.60 (0.20), residues: 1766 helix: 0.67 (0.18), residues: 846 sheet: 1.24 (0.28), residues: 304 loop : -0.26 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 241 TYR 0.007 0.001 TYR H 333 PHE 0.008 0.001 PHE G 251 TRP 0.002 0.001 TRP H 123 HIS 0.004 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.13 (13400) covalent geometry : angle 0.43710 / 0.23 (18152) hydrogen bonds : bond 0.03406 / 2.32 ( 600) hydrogen bonds : angle 4.12148 / 2.96 ( 1718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3474.87 seconds wall clock time: 60 minutes 3.37 seconds (3603.37 seconds total)