Starting phenix.real_space_refine on Thu Jul 31 07:11:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u5n_20650/07_2025/6u5n_20650.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u5n_20650/07_2025/6u5n_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_20650/07_2025/6u5n_20650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u5n_20650/07_2025/6u5n_20650.map" model { file = "/net/cci-nas-00/data/ceres_data/6u5n_20650/07_2025/6u5n_20650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u5n_20650/07_2025/6u5n_20650.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1647 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "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: G, C, H, D 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: 9.20, per 1000 atoms: 0.69 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: 2.77 Conformation dependent library (CDL) restraints added in 2.5 seconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3268 Finding SS restraints... Secondary structure from input PDB file: 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: 1.99 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: 3.94 Time building geometry restraints manager: 3.32 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: 0.07 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.010 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 34.310 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (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 TRP 0.002 0.001 TRP B 123 HIS 0.013 0.002 HIS E 193 PHE 0.010 0.002 PHE C 232 TYR 0.011 0.002 TYR E 247 ARG 0.003 0.001 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.18162 ( 600) hydrogen bonds : angle 6.92110 ( 1718) covalent geometry : bond 0.00585 (13400) covalent geometry : angle 0.75902 (18152) *********************** 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 : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ILE cc_start: 0.8941 (mm) cc_final: 0.8610 (mm) REVERT: E 184 ASP cc_start: 0.8009 (t0) cc_final: 0.7693 (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: 0.8887 (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: 0.8033 (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: 0.7345 (pt0) REVERT: C 317 ILE cc_start: 0.8963 (mm) cc_final: 0.8673 (mm) REVERT: G 184 ASP cc_start: 0.7993 (t0) cc_final: 0.7690 (t0) REVERT: G 247 TYR cc_start: 0.8825 (m-80) cc_final: 0.8343 (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: 0.8781 (mm) REVERT: D 172 LYS cc_start: 0.8291 (mtpt) cc_final: 0.8054 (mtpt) REVERT: D 184 ASP cc_start: 0.8135 (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: 0.8482 (t80) REVERT: H 218 GLU cc_start: 0.7676 (pt0) cc_final: 0.7425 (pt0) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.3755 time to fit residues: 155.0188 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 : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 7.9990 chunk 133 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.148155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.108044 restraints weight = 37987.543| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.73 r_work: 0.2788 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 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 = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13400 Z= 0.109 Angle : 0.435 3.491 18152 Z= 0.238 Chirality : 0.046 0.137 2174 Planarity : 0.004 0.036 2360 Dihedral : 3.670 13.951 1942 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.94 % Allowed : 10.01 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 1766 helix: -1.08 (0.17), residues: 838 sheet: 1.04 (0.27), residues: 304 loop : -1.63 (0.20), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 123 HIS 0.004 0.001 HIS E 193 PHE 0.005 0.001 PHE G 251 TYR 0.017 0.001 TYR B 333 ARG 0.006 0.000 ARG G 116 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 600) hydrogen bonds : angle 4.63979 ( 1718) covalent geometry : bond 0.00247 (13400) covalent geometry : angle 0.43525 (18152) *********************** 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 270 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 259 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8563 (m-30) cc_final: 0.7837 (t0) REVERT: A 153 LEU cc_start: 0.8141 (mt) cc_final: 0.7934 (mm) REVERT: A 212 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8067 (mt-10) REVERT: A 221 ARG cc_start: 0.8729 (ttm110) cc_final: 0.8459 (mtm-85) REVERT: A 222 MET cc_start: 0.8805 (mmm) cc_final: 0.8594 (mmm) REVERT: A 317 ILE cc_start: 0.8772 (mm) cc_final: 0.8440 (mm) REVERT: E 210 GLU cc_start: 0.8356 (tt0) cc_final: 0.8044 (tt0) REVERT: E 323 LYS cc_start: 0.7500 (mtpp) cc_final: 0.7220 (mtpp) REVERT: B 172 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7897 (mtpt) REVERT: B 264 MET cc_start: 0.8630 (ttp) cc_final: 0.8300 (ttm) REVERT: B 303 ILE cc_start: 0.8072 (mt) cc_final: 0.7680 (mm) REVERT: B 313 ARG cc_start: 0.7376 (mtp85) cc_final: 0.6949 (mtp180) REVERT: F 218 GLU cc_start: 0.8336 (pt0) cc_final: 0.8014 (pt0) REVERT: F 222 MET cc_start: 0.8700 (mtm) cc_final: 0.8477 (mtm) REVERT: C 212 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8088 (mt-10) REVERT: C 221 ARG cc_start: 0.8722 (ttm110) cc_final: 0.8456 (mtm-85) REVERT: C 222 MET cc_start: 0.8816 (mmm) cc_final: 0.8606 (mmm) REVERT: C 317 ILE cc_start: 0.8789 (mm) cc_final: 0.8463 (mm) REVERT: G 210 GLU cc_start: 0.8336 (tt0) cc_final: 0.8021 (tt0) REVERT: D 172 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7924 (mtpt) REVERT: D 264 MET cc_start: 0.8629 (ttp) cc_final: 0.8308 (ttm) REVERT: D 285 ILE cc_start: 0.8163 (mm) cc_final: 0.7951 (mm) REVERT: D 303 ILE cc_start: 0.8052 (mt) cc_final: 0.7667 (mm) REVERT: D 313 ARG cc_start: 0.7399 (mtp85) cc_final: 0.6920 (mtp180) REVERT: D 333 TYR cc_start: 0.8212 (t80) cc_final: 0.8007 (t80) REVERT: H 218 GLU cc_start: 0.8432 (pt0) cc_final: 0.8142 (pt0) outliers start: 11 outliers final: 7 residues processed: 265 average time/residue: 0.3302 time to fit residues: 117.4018 Evaluate side-chains 239 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 232 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 2 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 122 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 0.0970 chunk 91 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3551 r_free = 0.3551 target = 0.148968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.104370 restraints weight = 34257.818| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.73 r_work: 0.2796 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13400 Z= 0.106 Angle : 0.410 3.218 18152 Z= 0.222 Chirality : 0.046 0.141 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.457 13.712 1942 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.23 % Allowed : 11.90 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.19), residues: 1766 helix: -0.37 (0.18), residues: 838 sheet: 1.03 (0.27), residues: 304 loop : -1.20 (0.21), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 123 HIS 0.004 0.001 HIS E 193 PHE 0.006 0.001 PHE C 232 TYR 0.013 0.001 TYR G 333 ARG 0.007 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 600) hydrogen bonds : angle 4.35594 ( 1718) covalent geometry : bond 0.00254 (13400) covalent geometry : angle 0.40969 (18152) *********************** 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 252 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 237 time to evaluate : 1.519 Fit side-chains REVERT: A 138 GLU cc_start: 0.7195 (tt0) cc_final: 0.6879 (mt-10) REVERT: A 145 ASP cc_start: 0.8492 (m-30) cc_final: 0.7792 (t0) REVERT: A 153 LEU cc_start: 0.8114 (mt) cc_final: 0.7898 (mm) REVERT: A 222 MET cc_start: 0.8862 (mmm) cc_final: 0.8641 (mmm) REVERT: E 210 GLU cc_start: 0.8457 (tt0) cc_final: 0.8131 (tt0) REVERT: E 247 TYR cc_start: 0.8785 (m-80) cc_final: 0.8257 (m-80) REVERT: B 116 ARG cc_start: 0.7881 (mmm160) cc_final: 0.7558 (mtp85) REVERT: B 172 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7998 (mtpp) REVERT: B 303 ILE cc_start: 0.7973 (mt) cc_final: 0.7655 (mm) REVERT: B 313 ARG cc_start: 0.7423 (mtp85) cc_final: 0.6940 (mtp180) REVERT: F 146 GLU cc_start: 0.6945 (tp30) cc_final: 0.6741 (tp30) REVERT: F 218 GLU cc_start: 0.8338 (pt0) cc_final: 0.8016 (pt0) REVERT: F 245 ASP cc_start: 0.7622 (p0) cc_final: 0.7096 (p0) REVERT: C 145 ASP cc_start: 0.8513 (m-30) cc_final: 0.7815 (t0) REVERT: G 210 GLU cc_start: 0.8444 (tt0) cc_final: 0.8114 (tt0) REVERT: D 172 LYS cc_start: 0.8221 (mtpt) cc_final: 0.8010 (mtpp) REVERT: D 285 ILE cc_start: 0.8198 (mm) cc_final: 0.7985 (mm) REVERT: D 303 ILE cc_start: 0.7938 (mt) cc_final: 0.7626 (mm) REVERT: D 333 TYR cc_start: 0.8134 (t80) cc_final: 0.7900 (t80) REVERT: H 146 GLU cc_start: 0.6965 (tp30) cc_final: 0.6753 (tp30) REVERT: H 218 GLU cc_start: 0.8386 (pt0) cc_final: 0.8102 (pt0) REVERT: H 245 ASP cc_start: 0.7768 (p0) cc_final: 0.7276 (p0) REVERT: H 250 MET cc_start: 0.9092 (mtm) cc_final: 0.8876 (mtp) outliers start: 15 outliers final: 9 residues processed: 245 average time/residue: 0.3604 time to fit residues: 122.5412 Evaluate side-chains 225 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 216 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.0670 chunk 36 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN C 219 GLN D 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.148795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.104391 restraints weight = 35159.912| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.91 r_work: 0.2780 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13400 Z= 0.108 Angle : 0.405 3.290 18152 Z= 0.220 Chirality : 0.046 0.144 2174 Planarity : 0.003 0.037 2360 Dihedral : 3.344 14.416 1942 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.16 % Allowed : 13.50 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.19), residues: 1766 helix: 0.08 (0.18), residues: 846 sheet: 1.07 (0.27), residues: 304 loop : -0.82 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 123 HIS 0.004 0.001 HIS E 193 PHE 0.006 0.001 PHE C 232 TYR 0.011 0.001 TYR G 333 ARG 0.010 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 600) hydrogen bonds : angle 4.20244 ( 1718) covalent geometry : bond 0.00265 (13400) covalent geometry : angle 0.40509 (18152) *********************** 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 245 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 231 time to evaluate : 2.122 Fit side-chains REVERT: A 138 GLU cc_start: 0.7263 (tt0) cc_final: 0.6987 (mt-10) REVERT: A 145 ASP cc_start: 0.8512 (m-30) cc_final: 0.7892 (t0) REVERT: E 210 GLU cc_start: 0.8489 (tt0) cc_final: 0.8176 (tt0) REVERT: E 247 TYR cc_start: 0.8778 (m-80) cc_final: 0.8332 (m-80) REVERT: E 313 ARG cc_start: 0.6613 (mtm180) cc_final: 0.6205 (mtm180) REVERT: B 116 ARG cc_start: 0.7867 (mmm160) cc_final: 0.7650 (mtp85) REVERT: B 303 ILE cc_start: 0.8014 (mt) cc_final: 0.7722 (mm) REVERT: F 146 GLU cc_start: 0.6909 (tp30) cc_final: 0.6700 (tp30) REVERT: F 218 GLU cc_start: 0.8367 (pt0) cc_final: 0.8082 (pt0) REVERT: F 245 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.6971 (p0) REVERT: C 145 ASP cc_start: 0.8538 (m-30) cc_final: 0.7910 (t0) REVERT: G 210 GLU cc_start: 0.8491 (tt0) cc_final: 0.8167 (tt0) REVERT: G 247 TYR cc_start: 0.8768 (m-80) cc_final: 0.8388 (m-80) REVERT: G 313 ARG cc_start: 0.6604 (mtm180) cc_final: 0.6193 (mtm180) REVERT: D 285 ILE cc_start: 0.8181 (mm) cc_final: 0.7961 (mm) REVERT: D 303 ILE cc_start: 0.7994 (mt) cc_final: 0.7708 (mm) REVERT: D 333 TYR cc_start: 0.8070 (t80) cc_final: 0.7827 (t80) REVERT: H 146 GLU cc_start: 0.6916 (tp30) cc_final: 0.6703 (tp30) REVERT: H 218 GLU cc_start: 0.8339 (pt0) cc_final: 0.8060 (pt0) REVERT: H 250 MET cc_start: 0.9104 (mtm) cc_final: 0.8854 (mtp) outliers start: 14 outliers final: 10 residues processed: 239 average time/residue: 0.3309 time to fit residues: 108.0577 Evaluate side-chains 228 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 217 time to evaluate : 1.568 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.145858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.100305 restraints weight = 38201.697| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.95 r_work: 0.2737 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13400 Z= 0.178 Angle : 0.464 4.274 18152 Z= 0.248 Chirality : 0.048 0.145 2174 Planarity : 0.004 0.039 2360 Dihedral : 3.555 16.586 1942 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.60 % Allowed : 15.09 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 1766 helix: 0.05 (0.18), residues: 846 sheet: 1.12 (0.28), residues: 304 loop : -0.64 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 123 HIS 0.007 0.001 HIS G 193 PHE 0.010 0.001 PHE A 232 TYR 0.009 0.001 TYR G 333 ARG 0.009 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 600) hydrogen bonds : angle 4.32168 ( 1718) covalent geometry : bond 0.00454 (13400) covalent geometry : angle 0.46440 (18152) *********************** 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 236 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 1.617 Fit side-chains REVERT: A 138 GLU cc_start: 0.7291 (tt0) cc_final: 0.6947 (mt-10) REVERT: A 145 ASP cc_start: 0.8517 (m-30) cc_final: 0.8000 (t0) REVERT: E 116 ARG cc_start: 0.7995 (mtt90) cc_final: 0.6956 (mmm-85) REVERT: E 210 GLU cc_start: 0.8471 (tt0) cc_final: 0.8175 (tt0) REVERT: E 247 TYR cc_start: 0.8823 (m-80) cc_final: 0.8350 (m-80) REVERT: E 323 LYS cc_start: 0.7653 (mtpp) cc_final: 0.7339 (mtpp) REVERT: B 116 ARG cc_start: 0.7997 (mmm160) cc_final: 0.7715 (mtp85) REVERT: B 226 ASP cc_start: 0.8707 (m-30) cc_final: 0.8426 (m-30) REVERT: B 303 ILE cc_start: 0.8136 (mt) cc_final: 0.7858 (mm) REVERT: F 146 GLU cc_start: 0.7003 (tp30) cc_final: 0.6788 (tp30) REVERT: F 218 GLU cc_start: 0.8445 (pt0) cc_final: 0.8184 (pt0) REVERT: C 145 ASP cc_start: 0.8497 (m-30) cc_final: 0.7993 (t0) REVERT: G 210 GLU cc_start: 0.8448 (tt0) cc_final: 0.8149 (tt0) REVERT: G 213 ARG cc_start: 0.8554 (mtp180) cc_final: 0.8162 (mtp180) REVERT: G 247 TYR cc_start: 0.8865 (m-80) cc_final: 0.8420 (m-80) REVERT: D 285 ILE cc_start: 0.8169 (mm) cc_final: 0.7908 (mm) REVERT: D 303 ILE cc_start: 0.8117 (mt) cc_final: 0.7839 (mm) REVERT: H 146 GLU cc_start: 0.7019 (tp30) cc_final: 0.6818 (tp30) REVERT: H 218 GLU cc_start: 0.8443 (pt0) cc_final: 0.8165 (pt0) REVERT: H 245 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7196 (p0) outliers start: 20 outliers final: 17 residues processed: 227 average time/residue: 0.3147 time to fit residues: 97.1114 Evaluate side-chains 220 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR 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 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 Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 134 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 149 optimal weight: 0.0010 chunk 121 optimal weight: 0.0050 chunk 157 optimal weight: 0.9990 overall best weight: 0.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.147878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.104364 restraints weight = 32368.332| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.89 r_work: 0.2781 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13400 Z= 0.103 Angle : 0.406 5.470 18152 Z= 0.218 Chirality : 0.046 0.150 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.354 13.638 1942 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.38 % Allowed : 16.18 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.20), residues: 1766 helix: 0.40 (0.18), residues: 846 sheet: 1.15 (0.28), residues: 304 loop : -0.52 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP G 123 HIS 0.003 0.000 HIS G 193 PHE 0.007 0.001 PHE G 251 TYR 0.028 0.001 TYR D 333 ARG 0.009 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 600) hydrogen bonds : angle 4.18310 ( 1718) covalent geometry : bond 0.00255 (13400) covalent geometry : angle 0.40592 (18152) *********************** 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 238 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 1.627 Fit side-chains REVERT: A 138 GLU cc_start: 0.7294 (tt0) cc_final: 0.7083 (mt-10) REVERT: A 145 ASP cc_start: 0.8439 (m-30) cc_final: 0.7939 (t0) REVERT: E 210 GLU cc_start: 0.8469 (tt0) cc_final: 0.8149 (tt0) REVERT: E 247 TYR cc_start: 0.8724 (m-80) cc_final: 0.8318 (m-80) REVERT: B 116 ARG cc_start: 0.7925 (mmm160) cc_final: 0.7718 (mtp85) REVERT: B 226 ASP cc_start: 0.8637 (m-30) cc_final: 0.8400 (m-30) REVERT: B 303 ILE cc_start: 0.8110 (mt) cc_final: 0.7810 (mm) REVERT: F 146 GLU cc_start: 0.6947 (tp30) cc_final: 0.6704 (tp30) REVERT: F 218 GLU cc_start: 0.8298 (pt0) cc_final: 0.7956 (pt0) REVERT: F 222 MET cc_start: 0.8789 (mtp) cc_final: 0.8542 (mtm) REVERT: F 245 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7126 (p0) REVERT: C 145 ASP cc_start: 0.8457 (m-30) cc_final: 0.7958 (t0) REVERT: G 210 GLU cc_start: 0.8439 (tt0) cc_final: 0.8102 (tt0) REVERT: G 247 TYR cc_start: 0.8783 (m-80) cc_final: 0.8407 (m-80) REVERT: D 285 ILE cc_start: 0.8208 (mm) cc_final: 0.7971 (mm) REVERT: D 303 ILE cc_start: 0.8072 (mt) cc_final: 0.7783 (mm) REVERT: H 146 GLU cc_start: 0.6955 (tp30) cc_final: 0.6723 (tp30) REVERT: H 218 GLU cc_start: 0.8353 (pt0) cc_final: 0.8061 (pt0) REVERT: H 245 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7125 (p0) REVERT: H 250 MET cc_start: 0.9114 (mtm) cc_final: 0.8863 (mtp) outliers start: 17 outliers final: 11 residues processed: 229 average time/residue: 0.3323 time to fit residues: 102.9341 Evaluate side-chains 226 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 213 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 245 ASP Chi-restraints excluded: chain F residue 280 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 66 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 121 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 108 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.145042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.108963 restraints weight = 29418.934| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 5.25 r_work: 0.2704 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13400 Z= 0.202 Angle : 0.479 5.225 18152 Z= 0.254 Chirality : 0.049 0.141 2174 Planarity : 0.004 0.036 2360 Dihedral : 3.599 17.075 1942 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.52 % Allowed : 16.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1766 helix: 0.20 (0.18), residues: 846 sheet: 1.10 (0.29), residues: 304 loop : -0.50 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 123 HIS 0.007 0.001 HIS G 193 PHE 0.010 0.001 PHE C 232 TYR 0.026 0.002 TYR D 333 ARG 0.008 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 600) hydrogen bonds : angle 4.33447 ( 1718) covalent geometry : bond 0.00516 (13400) covalent geometry : angle 0.47905 (18152) *********************** 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: 19 poor density : 230 time to evaluate : 1.586 Fit side-chains REVERT: A 138 GLU cc_start: 0.7376 (tt0) cc_final: 0.7065 (mt-10) REVERT: A 145 ASP cc_start: 0.8541 (m-30) cc_final: 0.7996 (t0) REVERT: E 116 ARG cc_start: 0.8030 (mtt90) cc_final: 0.6906 (mmm-85) REVERT: E 210 GLU cc_start: 0.8543 (tt0) cc_final: 0.8259 (tt0) REVERT: E 213 ARG cc_start: 0.8467 (mtp180) cc_final: 0.8095 (mtp180) REVERT: E 247 TYR cc_start: 0.8809 (m-80) cc_final: 0.8322 (m-80) REVERT: E 323 LYS cc_start: 0.7589 (mtpp) cc_final: 0.7345 (mtpp) REVERT: B 116 ARG cc_start: 0.8002 (mmm160) cc_final: 0.7725 (mtp85) REVERT: B 154 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8174 (ttp-110) REVERT: B 226 ASP cc_start: 0.8814 (m-30) cc_final: 0.8559 (m-30) REVERT: B 303 ILE cc_start: 0.8062 (mt) cc_final: 0.7757 (mm) REVERT: F 150 LYS cc_start: 0.7934 (mtmt) cc_final: 0.7426 (mptt) REVERT: F 218 GLU cc_start: 0.8375 (pt0) cc_final: 0.8025 (pt0) REVERT: F 222 MET cc_start: 0.8647 (mtp) cc_final: 0.8402 (mtm) REVERT: F 245 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7113 (p0) REVERT: C 145 ASP cc_start: 0.8514 (m-30) cc_final: 0.7977 (t0) REVERT: G 210 GLU cc_start: 0.8523 (tt0) cc_final: 0.8239 (tt0) REVERT: G 213 ARG cc_start: 0.8452 (mtp180) cc_final: 0.8074 (mtp180) REVERT: D 154 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8168 (ttp-110) REVERT: D 285 ILE cc_start: 0.8058 (mm) cc_final: 0.7789 (mm) REVERT: D 303 ILE cc_start: 0.8032 (mt) cc_final: 0.7734 (mm) REVERT: H 150 LYS cc_start: 0.7958 (mtmt) cc_final: 0.7457 (mptt) REVERT: H 218 GLU cc_start: 0.8382 (pt0) cc_final: 0.8007 (pt0) REVERT: H 222 MET cc_start: 0.8667 (mtp) cc_final: 0.8418 (mtm) REVERT: H 245 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7118 (p0) REVERT: H 250 MET cc_start: 0.9169 (mtm) cc_final: 0.8919 (mtp) outliers start: 19 outliers final: 17 residues processed: 240 average time/residue: 0.3132 time to fit residues: 102.1129 Evaluate side-chains 241 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain E residue 245 ASP 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 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 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 Chi-restraints excluded: chain H residue 317 ILE 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 146 optimal weight: 5.9990 chunk 6 optimal weight: 0.0970 chunk 137 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 172 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 158 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.149025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.112610 restraints weight = 26720.027| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 4.54 r_work: 0.2800 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13400 Z= 0.076 Angle : 0.387 5.259 18152 Z= 0.209 Chirality : 0.045 0.137 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.237 12.467 1942 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.16 % Allowed : 17.05 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.20), residues: 1766 helix: 0.67 (0.19), residues: 846 sheet: 1.12 (0.28), residues: 304 loop : -0.39 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 123 HIS 0.001 0.000 HIS G 193 PHE 0.006 0.001 PHE E 251 TYR 0.026 0.001 TYR D 333 ARG 0.008 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.02771 ( 600) hydrogen bonds : angle 4.09109 ( 1718) covalent geometry : bond 0.00171 (13400) covalent geometry : angle 0.38673 (18152) *********************** 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 246 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 232 time to evaluate : 1.480 Fit side-chains REVERT: A 138 GLU cc_start: 0.7321 (tt0) cc_final: 0.7055 (mt-10) REVERT: A 145 ASP cc_start: 0.8482 (m-30) cc_final: 0.8123 (t0) REVERT: E 210 GLU cc_start: 0.8465 (tt0) cc_final: 0.8148 (tt0) REVERT: E 213 ARG cc_start: 0.8409 (mtp180) cc_final: 0.8009 (mtp180) REVERT: B 154 ARG cc_start: 0.8403 (ttp80) cc_final: 0.8113 (ttp-110) REVERT: B 226 ASP cc_start: 0.8674 (m-30) cc_final: 0.8464 (m-30) REVERT: B 303 ILE cc_start: 0.8049 (mt) cc_final: 0.7750 (mm) REVERT: B 313 ARG cc_start: 0.7293 (mtp85) cc_final: 0.6846 (mtp180) REVERT: F 218 GLU cc_start: 0.8319 (pt0) cc_final: 0.8009 (pt0) REVERT: F 245 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7067 (p0) REVERT: C 145 ASP cc_start: 0.8460 (m-30) cc_final: 0.8108 (t0) REVERT: G 210 GLU cc_start: 0.8454 (tt0) cc_final: 0.8139 (tt0) REVERT: G 213 ARG cc_start: 0.8410 (mtp180) cc_final: 0.8006 (mtp180) REVERT: G 247 TYR cc_start: 0.8707 (m-80) cc_final: 0.8285 (m-80) REVERT: D 154 ARG cc_start: 0.8401 (ttp80) cc_final: 0.8112 (ttp-110) REVERT: D 285 ILE cc_start: 0.8179 (mm) cc_final: 0.7945 (mm) REVERT: D 303 ILE cc_start: 0.8040 (mt) cc_final: 0.7743 (mm) REVERT: D 327 ILE cc_start: 0.8277 (mm) cc_final: 0.7956 (mm) REVERT: H 218 GLU cc_start: 0.8295 (pt0) cc_final: 0.7983 (pt0) REVERT: H 245 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.6999 (p0) REVERT: H 250 MET cc_start: 0.9084 (mtm) cc_final: 0.8863 (mtp) outliers start: 14 outliers final: 10 residues processed: 237 average time/residue: 0.3396 time to fit residues: 110.2302 Evaluate side-chains 239 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 227 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU 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 245 ASP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 25 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 0.0270 chunk 77 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.148705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.105677 restraints weight = 30691.117| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.34 r_work: 0.2806 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 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 = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13400 Z= 0.100 Angle : 0.405 5.257 18152 Z= 0.217 Chirality : 0.046 0.137 2174 Planarity : 0.003 0.046 2360 Dihedral : 3.224 13.028 1942 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.45 % Allowed : 17.13 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1766 helix: 0.72 (0.19), residues: 846 sheet: 1.23 (0.28), residues: 304 loop : -0.33 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 123 HIS 0.003 0.000 HIS G 193 PHE 0.006 0.001 PHE G 251 TYR 0.007 0.001 TYR G 333 ARG 0.011 0.000 ARG E 241 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 600) hydrogen bonds : angle 4.10078 ( 1718) covalent geometry : bond 0.00246 (13400) covalent geometry : angle 0.40465 (18152) *********************** 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 249 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 1.562 Fit side-chains REVERT: A 138 GLU cc_start: 0.7303 (tt0) cc_final: 0.7056 (mt-10) REVERT: A 145 ASP cc_start: 0.8397 (m-30) cc_final: 0.8092 (t0) REVERT: E 116 ARG cc_start: 0.8089 (mtt90) cc_final: 0.6995 (mmm-85) REVERT: E 210 GLU cc_start: 0.8473 (tt0) cc_final: 0.8167 (tt0) REVERT: E 213 ARG cc_start: 0.8390 (mtp180) cc_final: 0.8042 (mtp180) REVERT: E 250 MET cc_start: 0.8817 (mtt) cc_final: 0.8532 (mtp) REVERT: B 154 ARG cc_start: 0.8386 (ttp80) cc_final: 0.8084 (ttp-110) REVERT: B 226 ASP cc_start: 0.8649 (m-30) cc_final: 0.8422 (m-30) REVERT: B 303 ILE cc_start: 0.8147 (mt) cc_final: 0.7854 (mm) REVERT: B 313 ARG cc_start: 0.7419 (mtp85) cc_final: 0.6963 (mtp180) REVERT: F 218 GLU cc_start: 0.8313 (pt0) cc_final: 0.8039 (pt0) REVERT: F 245 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7045 (p0) REVERT: C 145 ASP cc_start: 0.8489 (m-30) cc_final: 0.8150 (t0) REVERT: G 210 GLU cc_start: 0.8434 (tt0) cc_final: 0.8115 (tt0) REVERT: G 213 ARG cc_start: 0.8374 (mtp180) cc_final: 0.8022 (mtp180) REVERT: G 247 TYR cc_start: 0.8743 (m-80) cc_final: 0.8360 (m-80) REVERT: D 154 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8094 (ttp-110) REVERT: D 285 ILE cc_start: 0.8224 (mm) cc_final: 0.7961 (mm) REVERT: D 303 ILE cc_start: 0.8083 (mt) cc_final: 0.7796 (mm) REVERT: D 313 ARG cc_start: 0.7445 (mtp85) cc_final: 0.6996 (mtp180) REVERT: H 218 GLU cc_start: 0.8381 (pt0) cc_final: 0.8104 (pt0) REVERT: H 245 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7020 (p0) REVERT: H 250 MET cc_start: 0.9111 (mtm) cc_final: 0.8869 (mtp) outliers start: 18 outliers final: 13 residues processed: 237 average time/residue: 0.3150 time to fit residues: 101.3092 Evaluate side-chains 241 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 226 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU 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 245 ASP Chi-restraints excluded: chain F residue 264 MET 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 131 LEU Chi-restraints excluded: chain D residue 296 VAL 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 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 37 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 166 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 0.1980 chunk 74 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.149283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.103948 restraints weight = 33260.436| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.71 r_work: 0.2786 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2514 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= 0.095 Angle : 0.399 5.268 18152 Z= 0.214 Chirality : 0.046 0.136 2174 Planarity : 0.003 0.037 2360 Dihedral : 3.202 12.851 1942 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.31 % Allowed : 17.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1766 helix: 0.81 (0.19), residues: 846 sheet: 1.29 (0.28), residues: 304 loop : -0.30 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 123 HIS 0.003 0.000 HIS G 193 PHE 0.007 0.001 PHE G 251 TYR 0.007 0.001 TYR G 333 ARG 0.009 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.02954 ( 600) hydrogen bonds : angle 4.06941 ( 1718) covalent geometry : bond 0.00230 (13400) covalent geometry : angle 0.39934 (18152) ********************** 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 249 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 2.386 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7340 (tt0) cc_final: 0.7087 (mt-10) REVERT: A 145 ASP cc_start: 0.8404 (m-30) cc_final: 0.8043 (t0) REVERT: E 116 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7005 (mmm-85) REVERT: E 210 GLU cc_start: 0.8491 (tt0) cc_final: 0.8195 (tt0) REVERT: E 213 ARG cc_start: 0.8398 (mtp180) cc_final: 0.7982 (mtp180) REVERT: E 250 MET cc_start: 0.8808 (mtt) cc_final: 0.8511 (mtp) REVERT: B 154 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8095 (ttp-110) REVERT: B 226 ASP cc_start: 0.8651 (m-30) cc_final: 0.8427 (m-30) REVERT: B 303 ILE cc_start: 0.8114 (mt) cc_final: 0.7817 (mm) REVERT: B 313 ARG cc_start: 0.7392 (mtp85) cc_final: 0.6948 (mtp180) REVERT: F 218 GLU cc_start: 0.8349 (pt0) cc_final: 0.8053 (pt0) REVERT: F 245 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7077 (p0) REVERT: G 210 GLU cc_start: 0.8486 (tt0) cc_final: 0.8180 (tt0) REVERT: G 213 ARG cc_start: 0.8400 (mtp180) cc_final: 0.7980 (mtp180) REVERT: G 247 TYR cc_start: 0.8728 (m-80) cc_final: 0.8338 (m-80) REVERT: D 154 ARG cc_start: 0.8411 (ttp80) cc_final: 0.8094 (ttp-110) REVERT: D 285 ILE cc_start: 0.8227 (mm) cc_final: 0.7977 (mm) REVERT: D 303 ILE cc_start: 0.8090 (mt) cc_final: 0.7805 (mm) REVERT: D 313 ARG cc_start: 0.7427 (mtp85) cc_final: 0.6990 (mtp180) REVERT: H 218 GLU cc_start: 0.8344 (pt0) cc_final: 0.8048 (pt0) REVERT: H 245 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7075 (p0) REVERT: H 250 MET cc_start: 0.9113 (mtm) cc_final: 0.8881 (mtp) outliers start: 16 outliers final: 13 residues processed: 238 average time/residue: 0.4742 time to fit residues: 157.4531 Evaluate side-chains 244 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 229 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU 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 245 ASP Chi-restraints excluded: chain F residue 330 LEU 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 131 LEU 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 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 107 optimal weight: 0.0050 chunk 111 optimal weight: 0.0370 chunk 121 optimal weight: 0.9990 chunk 161 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 136 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.3272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.150575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.107369 restraints weight = 31977.431| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.77 r_work: 0.2833 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2660 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= 0.073 Angle : 0.379 5.097 18152 Z= 0.204 Chirality : 0.045 0.133 2174 Planarity : 0.003 0.037 2360 Dihedral : 3.062 11.229 1942 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.02 % Allowed : 17.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.20), residues: 1766 helix: 1.01 (0.19), residues: 846 sheet: 1.37 (0.28), residues: 304 loop : -0.23 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 123 HIS 0.002 0.000 HIS G 193 PHE 0.007 0.001 PHE E 251 TYR 0.008 0.001 TYR G 333 ARG 0.009 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.02571 ( 600) hydrogen bonds : angle 3.96888 ( 1718) covalent geometry : bond 0.00166 (13400) covalent geometry : angle 0.37926 (18152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7950.66 seconds wall clock time: 139 minutes 41.34 seconds (8381.34 seconds total)