Starting phenix.real_space_refine on Thu Jul 31 07:16:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uwn_20925/07_2025/6uwn_20925.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uwn_20925/07_2025/6uwn_20925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uwn_20925/07_2025/6uwn_20925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uwn_20925/07_2025/6uwn_20925.map" model { file = "/net/cci-nas-00/data/ceres_data/6uwn_20925/07_2025/6uwn_20925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uwn_20925/07_2025/6uwn_20925.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 24 9.91 5 S 56 5.16 5 C 8302 2.51 5 N 2374 2.21 5 O 2502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13258 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1662 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Conformer: "B" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 bond proxies already assigned to first conformer: 1660 Chain: "E" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1654 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1652 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1647 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 1662 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Conformer: "B" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 bond proxies already assigned to first conformer: 1660 Chain: "G" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1654 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1652 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "H" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1647 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 241 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 241 " occ=0.50 residue: pdb=" N AARG C 241 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 241 " occ=0.50 Time building chain proxies: 11.65, per 1000 atoms: 0.88 Number of scatterers: 13258 At special positions: 0 Unit cell: (138.03, 135.89, 66.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 24 19.99 S 56 16.00 O 2502 8.00 N 2374 7.00 C 8302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 2.4 seconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3268 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 16 sheets defined 43.7% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.581A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.666A pdb=" N THR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 230 through 241 Processing helix chain 'A' and resid 247 through 256 removed outlier: 3.655A pdb=" N LEU A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.531A pdb=" N VAL A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'E' and resid 124 through 134 removed outlier: 3.565A pdb=" N GLU E 133 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 155 Processing helix chain 'E' and resid 166 through 172 Processing helix chain 'E' and resid 187 through 202 Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.664A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.571A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.608A pdb=" N MET E 250 " --> pdb=" O GLY E 246 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 323 through 334 Processing helix chain 'B' and resid 124 through 131 removed outlier: 3.528A pdb=" N GLU B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 148 through 155 Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 187 through 202 removed outlier: 3.643A pdb=" N ILE B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.532A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.533A pdb=" N SER B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.664A pdb=" N LEU B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.645A pdb=" N ASP B 284 " --> pdb=" O VAL B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'F' and resid 124 through 133 removed outlier: 3.655A pdb=" N GLU F 133 " --> pdb=" O GLU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 147 No H-bonds generated for 'chain 'F' and resid 145 through 147' Processing helix chain 'F' and resid 148 through 155 Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.755A pdb=" N ALA F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 Processing helix chain 'F' and resid 216 through 223 Processing helix chain 'F' and resid 230 through 240 removed outlier: 3.505A pdb=" N ILE F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 removed outlier: 3.689A pdb=" N ASP F 254 " --> pdb=" O MET F 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU F 256 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.803A pdb=" N ASP F 284 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 289 Processing helix chain 'F' and resid 323 through 332 removed outlier: 3.507A pdb=" N ASN F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.894A pdb=" N GLU C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.530A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.594A pdb=" N THR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 230 through 242 Processing helix chain 'C' and resid 247 through 256 removed outlier: 3.509A pdb=" N VAL C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP C 254 " --> pdb=" O MET C 250 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 289 removed outlier: 3.535A pdb=" N VAL C 288 " --> pdb=" O ASP C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 334 Processing helix chain 'G' and resid 124 through 133 removed outlier: 3.531A pdb=" N GLU G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 155 Processing helix chain 'G' and resid 166 through 172 removed outlier: 3.501A pdb=" N LYS G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.643A pdb=" N GLY G 197 " --> pdb=" O HIS G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.557A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 241 removed outlier: 3.888A pdb=" N SER G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 256 removed outlier: 3.529A pdb=" N MET G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU G 256 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 289 Processing helix chain 'G' and resid 323 through 334 removed outlier: 3.879A pdb=" N GLU G 328 " --> pdb=" O PRO G 324 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN G 332 " --> pdb=" O GLU G 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 131 removed outlier: 3.519A pdb=" N GLU D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 148 through 155 Processing helix chain 'D' and resid 166 through 172 Processing helix chain 'D' and resid 187 through 202 removed outlier: 3.650A pdb=" N ILE D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.684A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.528A pdb=" N SER D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.664A pdb=" N LEU D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 284 removed outlier: 3.641A pdb=" N ASP D 284 " --> pdb=" O VAL D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'H' and resid 124 through 133 removed outlier: 3.664A pdb=" N GLU H 133 " --> pdb=" O GLU H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing helix chain 'H' and resid 148 through 155 Processing helix chain 'H' and resid 166 through 173 removed outlier: 3.761A pdb=" N ALA H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 Processing helix chain 'H' and resid 216 through 223 Processing helix chain 'H' and resid 230 through 241 removed outlier: 3.503A pdb=" N ILE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 256 removed outlier: 3.687A pdb=" N ASP H 254 " --> pdb=" O MET H 250 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU H 256 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.801A pdb=" N ASP H 284 " --> pdb=" O VAL H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 Processing helix chain 'H' and resid 323 through 332 removed outlier: 3.539A pdb=" N ASN H 332 " --> pdb=" O GLU H 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.792A pdb=" N VAL A 139 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL A 160 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 141 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 119 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 3.501A pdb=" N GLY A 295 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.540A pdb=" N ALA E 143 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL E 181 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLU E 210 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL E 183 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE E 229 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 263 through 268 removed outlier: 7.485A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU E 301 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.567A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 207 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE B 229 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA B 209 " --> pdb=" O ILE B 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.670A pdb=" N GLY B 322 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE B 317 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL B 296 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU B 319 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.504A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 263 through 268 removed outlier: 3.566A pdb=" N GLY F 322 " --> pdb=" O ARG F 263 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE F 317 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL F 296 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU F 319 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.781A pdb=" N VAL C 139 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL C 160 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL C 141 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C 119 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 263 through 268 removed outlier: 3.501A pdb=" N GLY C 295 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 158 through 161 removed outlier: 3.524A pdb=" N ALA G 143 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL G 181 " --> pdb=" O ILE G 208 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N GLU G 210 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL G 183 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE G 229 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 263 through 268 removed outlier: 7.467A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU G 301 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.559A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE D 207 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE D 229 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA D 209 " --> pdb=" O ILE D 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.667A pdb=" N GLY D 322 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE D 317 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL D 296 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU D 319 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.506A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 3.558A pdb=" N GLY H 322 " --> pdb=" O ARG H 263 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE H 317 " --> pdb=" O VAL H 296 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL H 296 " --> pdb=" O ILE H 317 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU H 319 " --> pdb=" O ILE H 294 " (cutoff:3.500A) 563 hydrogen bonds defined for protein. 1600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4531 1.34 - 1.45: 1220 1.45 - 1.57: 7561 1.57 - 1.69: 0 1.69 - 1.80: 88 Bond restraints: 13400 Sorted by residual: bond pdb=" CG LEU E 220 " pdb=" CD2 LEU E 220 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.72e+00 bond pdb=" CG1 ILE D 195 " pdb=" CD1 ILE D 195 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.33e+00 bond pdb=" CG1 ILE C 195 " pdb=" CD1 ILE C 195 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.21e+00 bond pdb=" CG LEU G 220 " pdb=" CD2 LEU G 220 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.18e+00 bond pdb=" CG LEU D 220 " pdb=" CD2 LEU D 220 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.16e+00 ... (remaining 13395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 17594 1.79 - 3.59: 507 3.59 - 5.38: 47 5.38 - 7.17: 1 7.17 - 8.96: 3 Bond angle restraints: 18152 Sorted by residual: angle pdb=" N ILE H 334 " pdb=" CA ILE H 334 " pdb=" C ILE H 334 " ideal model delta sigma weight residual 112.29 109.82 2.47 9.40e-01 1.13e+00 6.90e+00 angle pdb=" CA LEU E 275 " pdb=" CB LEU E 275 " pdb=" CG LEU E 275 " ideal model delta sigma weight residual 116.30 125.26 -8.96 3.50e+00 8.16e-02 6.56e+00 angle pdb=" N ILE F 334 " pdb=" CA ILE F 334 " pdb=" C ILE F 334 " ideal model delta sigma weight residual 112.29 109.88 2.41 9.40e-01 1.13e+00 6.55e+00 angle pdb=" CA LEU G 275 " pdb=" CB LEU G 275 " pdb=" CG LEU G 275 " ideal model delta sigma weight residual 116.30 125.23 -8.93 3.50e+00 8.16e-02 6.51e+00 angle pdb=" C ARG A 132 " pdb=" N GLU A 133 " pdb=" CA GLU A 133 " ideal model delta sigma weight residual 122.06 117.83 4.23 1.86e+00 2.89e-01 5.16e+00 ... (remaining 18147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 7465 18.04 - 36.07: 585 36.07 - 54.11: 98 54.11 - 72.15: 22 72.15 - 90.19: 10 Dihedral angle restraints: 8180 sinusoidal: 3108 harmonic: 5072 Sorted by residual: dihedral pdb=" CA GLU D 129 " pdb=" C GLU D 129 " pdb=" N CYS D 130 " pdb=" CA CYS D 130 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLU B 129 " pdb=" C GLU B 129 " pdb=" N CYS B 130 " pdb=" CA CYS B 130 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ASP C 169 " pdb=" CB ASP C 169 " pdb=" CG ASP C 169 " pdb=" OD1 ASP C 169 " ideal model delta sinusoidal sigma weight residual -30.00 -88.73 58.73 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 8177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1531 0.054 - 0.109: 520 0.109 - 0.163: 113 0.163 - 0.217: 8 0.217 - 0.272: 2 Chirality restraints: 2174 Sorted by residual: chirality pdb=" CB ILE D 293 " pdb=" CA ILE D 293 " pdb=" CG1 ILE D 293 " pdb=" CG2 ILE D 293 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE B 293 " pdb=" CA ILE B 293 " pdb=" CG1 ILE B 293 " pdb=" CG2 ILE B 293 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL D 205 " pdb=" CA VAL D 205 " pdb=" CG1 VAL D 205 " pdb=" CG2 VAL D 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2171 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 267 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO A 268 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 267 " -0.039 5.00e-02 4.00e+02 5.91e-02 5.58e+00 pdb=" N PRO C 268 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 268 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 268 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 267 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C VAL C 267 " 0.035 2.00e-02 2.50e+03 pdb=" O VAL C 267 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO C 268 " -0.012 2.00e-02 2.50e+03 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3815 2.81 - 3.33: 10954 3.33 - 3.85: 21131 3.85 - 4.38: 23886 4.38 - 4.90: 43557 Nonbonded interactions: 103343 Sorted by model distance: nonbonded pdb=" OE2 GLU G 212 " pdb=" O HOH G 501 " model vdw 2.285 3.040 nonbonded pdb=" OD1 ASP E 184 " pdb=" O HOH E 501 " model vdw 2.286 3.040 nonbonded pdb=" O ILE F 285 " pdb=" OG1 THR F 289 " model vdw 2.286 3.040 nonbonded pdb=" O ILE H 285 " pdb=" OG1 THR H 289 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASP G 184 " pdb=" O HOH G 501 " model vdw 2.289 3.040 ... (remaining 103338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 or (resid 135 and (name N or name CA o \ r name C or name O or name CB )) or resid 136 through 137 or (resid 138 and (nam \ e N or name CA or name C or name O or name CB )) or resid 139 through 143 or (re \ sid 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 170 or (resid 171 and (name N or name CA or name C or name \ O or name CB )) or resid 172 through 240 or resid 242 through 244 or (resid 245 \ and (name N or name CA or name C or name O or name CB )) or resid 246 through 2 \ 53 or (resid 254 and (name N or name CA or name C or name O or name CB )) or res \ id 255 through 262 or (resid 263 and (name N or name CA or name C or name O or n \ ame CB )) or resid 264 through 273 or (resid 274 and (name N or name CA or name \ C or name O or name CB )) or resid 275 through 283 or (resid 284 and (name N or \ name CA or name C or name O or name CB )) or resid 285 through 286 or (resid 287 \ and (name N or name CA or name C or name O or name CB )) or resid 288 through 2 \ 97 or (resid 298 and (name N or name CA or name C or name O or name CB )) or res \ id 299 through 312 or (resid 313 through 314 and (name N or name CA or name C or \ name O or name CB )) or resid 315 through 324 or (resid 325 and (name N or name \ CA or name C or name O or name CB )) or resid 326 through 327 or (resid 328 and \ (name N or name CA or name C or name O or name CB )) or resid 329 through 336 o \ r resid 401 through 402)) selection = (chain 'B' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 137 or (resid 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 throug \ h 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) or \ resid 148 or (resid 149 through 150 and (name N or name CA or name C or name O o \ r name CB )) or resid 151 through 153 or (resid 154 and (name N or name CA or na \ me C or name O or name CB )) or resid 155 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 240 or resid 2 \ 42 through 253 or (resid 254 and (name N or name CA or name C or name O or name \ CB )) or resid 255 through 270 or (resid 271 and (name N or name CA or name C or \ name O or name CB )) or resid 272 through 273 or (resid 274 and (name N or name \ CA or name C or name O or name CB )) or resid 275 or (resid 276 and (name N or \ name CA or name C or name O or name CB )) or resid 277 through 280 or (resid 281 \ through 284 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 85 through 297 or (resid 298 and (name N or name CA or name C or name O or name \ CB )) or resid 299 through 312 or (resid 313 through 314 and (name N or name CA \ or name C or name O or name CB )) or resid 315 through 336 or resid 401 through \ 402)) selection = (chain 'C' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 or (resid 135 and (name N or name CA o \ r name C or name O or name CB )) or resid 136 through 137 or (resid 138 and (nam \ e N or name CA or name C or name O or name CB )) or resid 139 through 143 or (re \ sid 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 170 or (resid 171 and (name N or name CA or name C or name \ O or name CB )) or resid 172 through 240 or resid 242 through 244 or (resid 245 \ and (name N or name CA or name C or name O or name CB )) or resid 246 through 2 \ 53 or (resid 254 and (name N or name CA or name C or name O or name CB )) or res \ id 255 through 262 or (resid 263 and (name N or name CA or name C or name O or n \ ame CB )) or resid 264 through 273 or (resid 274 and (name N or name CA or name \ C or name O or name CB )) or resid 275 through 283 or (resid 284 and (name N or \ name CA or name C or name O or name CB )) or resid 285 through 286 or (resid 287 \ and (name N or name CA or name C or name O or name CB )) or resid 288 through 2 \ 97 or (resid 298 and (name N or name CA or name C or name O or name CB )) or res \ id 299 through 312 or (resid 313 through 314 and (name N or name CA or name C or \ name O or name CB )) or resid 315 through 324 or (resid 325 and (name N or name \ CA or name C or name O or name CB )) or resid 326 through 327 or (resid 328 and \ (name N or name CA or name C or name O or name CB )) or resid 329 through 336 o \ r resid 401 through 402)) selection = (chain 'D' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 137 or (resid 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 throug \ h 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) or \ resid 148 or (resid 149 through 150 and (name N or name CA or name C or name O o \ r name CB )) or resid 151 through 153 or (resid 154 and (name N or name CA or na \ me C or name O or name CB )) or resid 155 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 240 or resid 2 \ 42 through 253 or (resid 254 and (name N or name CA or name C or name O or name \ CB )) or resid 255 through 270 or (resid 271 and (name N or name CA or name C or \ name O or name CB )) or resid 272 through 273 or (resid 274 and (name N or name \ CA or name C or name O or name CB )) or resid 275 or (resid 276 and (name N or \ name CA or name C or name O or name CB )) or resid 277 through 280 or (resid 281 \ through 284 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 85 through 297 or (resid 298 and (name N or name CA or name C or name O or name \ CB )) or resid 299 through 312 or (resid 313 through 314 and (name N or name CA \ or name C or name O or name CB )) or resid 315 through 336 or resid 401 through \ 402)) selection = (chain 'E' and (resid 115 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 148 or (resid 149 through 150 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 15 \ 3 or (resid 154 and (name N or name CA or name C or name O or name CB )) or resi \ d 155 through 170 or (resid 171 and (name N or name CA or name C or name O or na \ me CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C \ or name O or name CB )) or resid 204 through 217 or (resid 218 and (name N or n \ ame CA or name C or name O or name CB )) or resid 219 through 240 or resid 242 t \ hrough 243 or (resid 244 through 245 and (name N or name CA or name C or name O \ or name CB )) or resid 246 through 253 or (resid 254 and (name N or name CA or n \ ame C or name O or name CB )) or resid 255 through 262 or (resid 263 and (name N \ or name CA or name C or name O or name CB )) or resid 264 through 281 or (resid \ 282 through 284 and (name N or name CA or name C or name O or name CB )) or res \ id 285 through 300 or (resid 301 and (name N or name CA or name C or name O or n \ ame CB )) or resid 302 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 312 or (resid 313 through 314 and \ (name N or name CA or name C or name O or name CB )) or resid 315 through 324 o \ r (resid 325 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 26 through 336 or resid 401 through 402)) selection = (chain 'F' and (resid 115 through 143 or (resid 144 and (name N or name CA or na \ me C or name O or name CB )) or resid 145 or (resid 146 through 147 and (name N \ or name CA or name C or name O or name CB )) or resid 148 or (resid 149 through \ 150 and (name N or name CA or name C or name O or name CB )) or resid 151 throug \ h 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) or \ resid 155 through 217 or (resid 218 and (name N or name CA or name C or name O o \ r name CB )) or resid 219 through 240 or resid 242 through 243 or (resid 244 thr \ ough 245 and (name N or name CA or name C or name O or name CB )) or resid 246 t \ hrough 280 or (resid 281 through 284 and (name N or name CA or name C or name O \ or name CB )) or resid 285 through 286 or (resid 287 and (name N or name CA or n \ ame C or name O or name CB )) or resid 288 through 297 or (resid 298 and (name N \ or name CA or name C or name O or name CB )) or resid 299 or (resid 300 through \ 301 and (name N or name CA or name C or name O or name CB )) or resid 302 throu \ gh 307 or (resid 308 through 309 and (name N or name CA or name C or name O or n \ ame CB )) or resid 310 through 324 or (resid 325 and (name N or name CA or name \ C or name O or name CB )) or resid 326 through 327 or (resid 328 and (name N or \ name CA or name C or name O or name CB )) or resid 329 through 336 or resid 401 \ through 402)) selection = (chain 'G' and (resid 115 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 148 or (resid 149 through 150 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 15 \ 3 or (resid 154 and (name N or name CA or name C or name O or name CB )) or resi \ d 155 through 170 or (resid 171 and (name N or name CA or name C or name O or na \ me CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C \ or name O or name CB )) or resid 204 through 217 or (resid 218 and (name N or n \ ame CA or name C or name O or name CB )) or resid 219 through 240 or resid 242 t \ hrough 243 or (resid 244 through 245 and (name N or name CA or name C or name O \ or name CB )) or resid 246 through 253 or (resid 254 and (name N or name CA or n \ ame C or name O or name CB )) or resid 255 through 262 or (resid 263 and (name N \ or name CA or name C or name O or name CB )) or resid 264 through 281 or (resid \ 282 through 284 and (name N or name CA or name C or name O or name CB )) or res \ id 285 through 300 or (resid 301 and (name N or name CA or name C or name O or n \ ame CB )) or resid 302 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 312 or (resid 313 through 314 and \ (name N or name CA or name C or name O or name CB )) or resid 315 through 324 o \ r (resid 325 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 26 through 336 or resid 401 through 402)) selection = (chain 'H' and (resid 115 through 143 or (resid 144 and (name N or name CA or na \ me C or name O or name CB )) or resid 145 or (resid 146 through 147 and (name N \ or name CA or name C or name O or name CB )) or resid 148 or (resid 149 through \ 150 and (name N or name CA or name C or name O or name CB )) or resid 151 throug \ h 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) or \ resid 155 through 217 or (resid 218 and (name N or name CA or name C or name O o \ r name CB )) or resid 219 through 240 or resid 242 through 243 or (resid 244 thr \ ough 245 and (name N or name CA or name C or name O or name CB )) or resid 246 t \ hrough 280 or (resid 281 through 284 and (name N or name CA or name C or name O \ or name CB )) or resid 285 through 286 or (resid 287 and (name N or name CA or n \ ame C or name O or name CB )) or resid 288 through 297 or (resid 298 and (name N \ or name CA or name C or name O or name CB )) or resid 299 or (resid 300 through \ 301 and (name N or name CA or name C or name O or name CB )) or resid 302 throu \ gh 307 or (resid 308 through 309 and (name N or name CA or name C or name O or n \ ame CB )) or resid 310 through 324 or (resid 325 and (name N or name CA or name \ C or name O or name CB )) or resid 326 through 327 or (resid 328 and (name N or \ name CA or name C or name O or name CB )) or resid 329 through 336 or resid 401 \ through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.770 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 13400 Z= 0.305 Angle : 0.728 8.965 18152 Z= 0.425 Chirality : 0.055 0.272 2174 Planarity : 0.005 0.060 2360 Dihedral : 13.753 90.187 4912 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.15 % Allowed : 6.89 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.15), residues: 1766 helix: -4.24 (0.08), residues: 814 sheet: 0.25 (0.24), residues: 384 loop : -2.64 (0.19), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 123 HIS 0.009 0.001 HIS G 193 PHE 0.013 0.002 PHE A 232 TYR 0.020 0.002 TYR D 247 ARG 0.004 0.001 ARG H 166 Details of bonding type rmsd hydrogen bonds : bond 0.27641 ( 563) hydrogen bonds : angle 8.69561 ( 1600) covalent geometry : bond 0.00737 (13400) covalent geometry : angle 0.72821 (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 363 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 1.467 Fit side-chains REVERT: A 151 LYS cc_start: 0.8082 (ptpt) cc_final: 0.7625 (ttpt) REVERT: E 129 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8652 (mm-30) REVERT: E 190 GLU cc_start: 0.8501 (mp0) cc_final: 0.8121 (mt-10) REVERT: E 332 ASN cc_start: 0.8165 (m-40) cc_final: 0.7750 (t0) REVERT: B 226 ASP cc_start: 0.8346 (m-30) cc_final: 0.7758 (m-30) REVERT: B 310 TYR cc_start: 0.8518 (t80) cc_final: 0.7845 (t80) REVERT: F 125 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8476 (mm-30) REVERT: F 184 ASP cc_start: 0.8313 (t70) cc_final: 0.8079 (t0) REVERT: F 210 GLU cc_start: 0.8351 (tt0) cc_final: 0.7970 (tt0) REVERT: F 300 ASP cc_start: 0.7731 (t70) cc_final: 0.7320 (t70) REVERT: F 323 LYS cc_start: 0.8155 (mttm) cc_final: 0.7920 (mtpt) REVERT: C 151 LYS cc_start: 0.8013 (ptpt) cc_final: 0.7587 (ttpt) REVERT: G 210 GLU cc_start: 0.8411 (tt0) cc_final: 0.8077 (tt0) REVERT: G 239 MET cc_start: 0.8667 (mtt) cc_final: 0.8451 (mtt) REVERT: G 325 GLU cc_start: 0.8441 (tt0) cc_final: 0.8210 (tp30) REVERT: D 226 ASP cc_start: 0.8258 (m-30) cc_final: 0.7777 (m-30) REVERT: D 310 TYR cc_start: 0.8532 (t80) cc_final: 0.7877 (t80) REVERT: H 125 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8404 (mm-30) REVERT: H 184 ASP cc_start: 0.8302 (t70) cc_final: 0.8100 (t0) REVERT: H 210 GLU cc_start: 0.8337 (tt0) cc_final: 0.7993 (tt0) REVERT: H 300 ASP cc_start: 0.7683 (t70) cc_final: 0.7290 (t70) REVERT: H 323 LYS cc_start: 0.8173 (mttm) cc_final: 0.7936 (mtpt) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.3438 time to fit residues: 165.0831 Evaluate side-chains 283 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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: 2.9990 chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 137 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN B 227 GLN F 286 HIS C 219 GLN C 253 GLN D 227 GLN H 117 HIS H 286 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.172851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.132420 restraints weight = 41650.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.140303 restraints weight = 15673.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.145545 restraints weight = 7437.000| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13400 Z= 0.127 Angle : 0.474 4.644 18152 Z= 0.261 Chirality : 0.047 0.143 2174 Planarity : 0.004 0.041 2360 Dihedral : 3.935 18.224 1942 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.74 % Allowed : 11.97 % Favored : 86.28 % 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: -2.54 (0.17), residues: 1766 helix: -2.21 (0.15), residues: 822 sheet: 0.45 (0.26), residues: 336 loop : -1.90 (0.21), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 123 HIS 0.005 0.001 HIS G 193 PHE 0.007 0.001 PHE G 251 TYR 0.016 0.001 TYR E 333 ARG 0.007 0.000 ARG E 213 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 563) hydrogen bonds : angle 5.09566 ( 1600) covalent geometry : bond 0.00290 (13400) covalent geometry : angle 0.47391 (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 314 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 292 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8063 (ptpt) cc_final: 0.7597 (ttpt) REVERT: A 284 ASP cc_start: 0.8255 (t0) cc_final: 0.8001 (t0) REVERT: E 129 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8713 (mm-30) REVERT: E 190 GLU cc_start: 0.8360 (mp0) cc_final: 0.7935 (mt-10) REVERT: B 226 ASP cc_start: 0.8296 (m-30) cc_final: 0.7616 (m-30) REVERT: B 239 MET cc_start: 0.8849 (mtp) cc_final: 0.8393 (mtt) REVERT: B 303 ILE cc_start: 0.8585 (mp) cc_final: 0.8188 (tp) REVERT: B 310 TYR cc_start: 0.8544 (t80) cc_final: 0.7495 (t80) REVERT: F 184 ASP cc_start: 0.8378 (t70) cc_final: 0.7980 (t0) REVERT: F 210 GLU cc_start: 0.8388 (tt0) cc_final: 0.8027 (tt0) REVERT: F 300 ASP cc_start: 0.7565 (t70) cc_final: 0.7135 (t70) REVERT: C 151 LYS cc_start: 0.7898 (ptpt) cc_final: 0.7513 (ttpt) REVERT: C 284 ASP cc_start: 0.8254 (t0) cc_final: 0.7990 (t0) REVERT: D 226 ASP cc_start: 0.8253 (m-30) cc_final: 0.7625 (m-30) REVERT: D 239 MET cc_start: 0.8845 (mtp) cc_final: 0.8393 (mtt) REVERT: D 310 TYR cc_start: 0.8587 (t80) cc_final: 0.7551 (t80) REVERT: H 184 ASP cc_start: 0.8397 (t70) cc_final: 0.7997 (t0) REVERT: H 210 GLU cc_start: 0.8390 (tt0) cc_final: 0.8040 (tt0) REVERT: H 300 ASP cc_start: 0.7656 (t70) cc_final: 0.7242 (t70) outliers start: 22 outliers final: 13 residues processed: 303 average time/residue: 0.2739 time to fit residues: 116.4572 Evaluate side-chains 285 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 272 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 13 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 332 ASN H 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.170826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.130617 restraints weight = 42495.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.138523 restraints weight = 16341.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.143689 restraints weight = 7775.796| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13400 Z= 0.176 Angle : 0.487 4.540 18152 Z= 0.262 Chirality : 0.047 0.138 2174 Planarity : 0.004 0.040 2360 Dihedral : 3.725 17.419 1942 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.10 % Allowed : 14.66 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.45 (0.19), residues: 1766 helix: -1.05 (0.17), residues: 822 sheet: 0.46 (0.26), residues: 336 loop : -1.44 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 123 HIS 0.006 0.001 HIS G 193 PHE 0.007 0.001 PHE C 312 TYR 0.019 0.002 TYR A 333 ARG 0.006 0.000 ARG E 213 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 563) hydrogen bonds : angle 4.63510 ( 1600) covalent geometry : bond 0.00423 (13400) covalent geometry : angle 0.48708 (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 312 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 285 time to evaluate : 2.051 Fit side-chains REVERT: A 140 PHE cc_start: 0.8578 (m-80) cc_final: 0.8288 (m-80) REVERT: A 151 LYS cc_start: 0.8073 (ptpt) cc_final: 0.7696 (ttpt) REVERT: A 210 GLU cc_start: 0.7873 (tt0) cc_final: 0.7200 (tt0) REVERT: A 284 ASP cc_start: 0.8380 (t0) cc_final: 0.7868 (t0) REVERT: E 129 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8768 (mm-30) REVERT: E 190 GLU cc_start: 0.8275 (mp0) cc_final: 0.7955 (mt-10) REVERT: B 226 ASP cc_start: 0.8320 (m-30) cc_final: 0.7524 (m-30) REVERT: B 298 ARG cc_start: 0.6578 (ttp-110) cc_final: 0.6156 (mtp180) REVERT: B 303 ILE cc_start: 0.8633 (mp) cc_final: 0.8239 (tp) REVERT: F 153 LEU cc_start: 0.8456 (mt) cc_final: 0.8256 (mm) REVERT: F 300 ASP cc_start: 0.7647 (t70) cc_final: 0.7256 (t70) REVERT: F 323 LYS cc_start: 0.8267 (mttm) cc_final: 0.7908 (mtpt) REVERT: C 151 LYS cc_start: 0.7996 (ptpt) cc_final: 0.7608 (ttpt) REVERT: C 263 ARG cc_start: 0.7769 (mtt180) cc_final: 0.7565 (mtm-85) REVERT: C 284 ASP cc_start: 0.8400 (t0) cc_final: 0.7895 (t0) REVERT: G 145 ASP cc_start: 0.8656 (t70) cc_final: 0.8437 (t0) REVERT: D 226 ASP cc_start: 0.8277 (m-30) cc_final: 0.7550 (m-30) REVERT: D 298 ARG cc_start: 0.6582 (ttp-110) cc_final: 0.6165 (mtp180) REVERT: D 303 ILE cc_start: 0.8630 (mp) cc_final: 0.8233 (tp) REVERT: H 300 ASP cc_start: 0.7641 (t70) cc_final: 0.7248 (t70) REVERT: H 323 LYS cc_start: 0.8298 (mttm) cc_final: 0.7920 (mtpt) outliers start: 27 outliers final: 18 residues processed: 294 average time/residue: 0.2970 time to fit residues: 120.8038 Evaluate side-chains 298 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 280 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.0000 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 141 optimal weight: 0.0270 chunk 140 optimal weight: 0.5980 chunk 169 optimal weight: 0.0270 chunk 162 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 overall best weight: 0.2900 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.175025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.140253 restraints weight = 35107.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.145178 restraints weight = 16004.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.147207 restraints weight = 9946.566| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2455 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= 0.081 Angle : 0.409 4.914 18152 Z= 0.221 Chirality : 0.045 0.138 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.341 15.953 1942 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.45 % Allowed : 15.97 % Favored : 82.58 % 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: -0.78 (0.19), residues: 1766 helix: -0.40 (0.18), residues: 830 sheet: 0.62 (0.27), residues: 336 loop : -1.15 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 123 HIS 0.002 0.000 HIS G 193 PHE 0.006 0.001 PHE B 140 TYR 0.018 0.001 TYR E 333 ARG 0.007 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.02910 ( 563) hydrogen bonds : angle 4.27404 ( 1600) covalent geometry : bond 0.00178 (13400) covalent geometry : angle 0.40852 (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 315 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 297 time to evaluate : 1.697 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8471 (m-80) cc_final: 0.8251 (m-80) REVERT: A 151 LYS cc_start: 0.8097 (ptpt) cc_final: 0.7731 (ttpt) REVERT: A 284 ASP cc_start: 0.8278 (t0) cc_final: 0.8040 (t0) REVERT: A 333 TYR cc_start: 0.8388 (t80) cc_final: 0.8104 (t80) REVERT: E 190 GLU cc_start: 0.8177 (mp0) cc_final: 0.7768 (mt-10) REVERT: B 129 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7391 (tm-30) REVERT: B 226 ASP cc_start: 0.8312 (m-30) cc_final: 0.7519 (m-30) REVERT: B 298 ARG cc_start: 0.6595 (ttp-110) cc_final: 0.6227 (ttp-110) REVERT: B 303 ILE cc_start: 0.8600 (mp) cc_final: 0.8344 (tp) REVERT: F 266 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: F 300 ASP cc_start: 0.7541 (t70) cc_final: 0.7142 (t70) REVERT: F 323 LYS cc_start: 0.8308 (mttm) cc_final: 0.7954 (mtpt) REVERT: C 151 LYS cc_start: 0.7978 (ptpt) cc_final: 0.7627 (ttpt) REVERT: C 169 ASP cc_start: 0.8202 (m-30) cc_final: 0.7770 (m-30) REVERT: C 284 ASP cc_start: 0.8331 (t0) cc_final: 0.8085 (t0) REVERT: D 129 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7373 (tm-30) REVERT: D 226 ASP cc_start: 0.8305 (m-30) cc_final: 0.7534 (m-30) REVERT: D 298 ARG cc_start: 0.6641 (ttp-110) cc_final: 0.6284 (ttp-110) REVERT: D 303 ILE cc_start: 0.8588 (mp) cc_final: 0.8334 (tp) REVERT: H 266 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: H 300 ASP cc_start: 0.7549 (t70) cc_final: 0.7142 (t70) REVERT: H 323 LYS cc_start: 0.8264 (mttm) cc_final: 0.7905 (mtpt) outliers start: 18 outliers final: 13 residues processed: 306 average time/residue: 0.2692 time to fit residues: 115.9233 Evaluate side-chains 292 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 277 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 79 optimal weight: 3.9990 chunk 124 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.167836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.130298 restraints weight = 46007.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.135472 restraints weight = 14614.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.138841 restraints weight = 9107.353| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2580 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= 0.122 Angle : 0.439 5.383 18152 Z= 0.235 Chirality : 0.046 0.139 2174 Planarity : 0.003 0.041 2360 Dihedral : 3.322 15.784 1942 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.25 % Allowed : 15.82 % 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: -0.46 (0.20), residues: 1766 helix: -0.12 (0.19), residues: 830 sheet: 0.67 (0.26), residues: 336 loop : -0.97 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 123 HIS 0.003 0.001 HIS G 193 PHE 0.014 0.001 PHE C 140 TYR 0.020 0.001 TYR C 333 ARG 0.005 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 563) hydrogen bonds : angle 4.24399 ( 1600) covalent geometry : bond 0.00292 (13400) covalent geometry : angle 0.43939 (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 312 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 283 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8491 (m-80) cc_final: 0.8156 (m-80) REVERT: A 151 LYS cc_start: 0.8073 (ptpt) cc_final: 0.7737 (ttpt) REVERT: A 169 ASP cc_start: 0.8258 (m-30) cc_final: 0.7854 (m-30) REVERT: A 284 ASP cc_start: 0.8338 (t0) cc_final: 0.7825 (t0) REVERT: A 333 TYR cc_start: 0.8405 (t80) cc_final: 0.8140 (t80) REVERT: E 129 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8748 (mm-30) REVERT: E 190 GLU cc_start: 0.8288 (mp0) cc_final: 0.7773 (mt-10) REVERT: B 129 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7406 (tm-30) REVERT: B 169 ASP cc_start: 0.8635 (t0) cc_final: 0.8293 (t0) REVERT: B 226 ASP cc_start: 0.8294 (m-30) cc_final: 0.7544 (m-30) REVERT: B 239 MET cc_start: 0.8901 (mtp) cc_final: 0.8544 (mtt) REVERT: B 298 ARG cc_start: 0.6645 (ttp-110) cc_final: 0.6083 (ttp-110) REVERT: B 303 ILE cc_start: 0.8603 (mp) cc_final: 0.8342 (tp) REVERT: F 142 LEU cc_start: 0.8744 (tp) cc_final: 0.8491 (tt) REVERT: F 300 ASP cc_start: 0.7670 (t70) cc_final: 0.7285 (t70) REVERT: F 323 LYS cc_start: 0.8291 (mttm) cc_final: 0.7943 (mtpt) REVERT: C 151 LYS cc_start: 0.7988 (ptpt) cc_final: 0.7602 (ttpt) REVERT: C 169 ASP cc_start: 0.8286 (m-30) cc_final: 0.7833 (m-30) REVERT: C 284 ASP cc_start: 0.8352 (t0) cc_final: 0.7835 (t0) REVERT: D 129 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7408 (tm-30) REVERT: D 169 ASP cc_start: 0.8645 (t70) cc_final: 0.8308 (t0) REVERT: D 226 ASP cc_start: 0.8323 (m-30) cc_final: 0.7459 (m-30) REVERT: D 239 MET cc_start: 0.8903 (mtp) cc_final: 0.8555 (mtt) REVERT: D 298 ARG cc_start: 0.6676 (ttp-110) cc_final: 0.6115 (ttp-110) REVERT: D 303 ILE cc_start: 0.8590 (mp) cc_final: 0.8337 (tp) REVERT: H 142 LEU cc_start: 0.8741 (tp) cc_final: 0.8489 (tt) REVERT: H 266 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: H 300 ASP cc_start: 0.7679 (t70) cc_final: 0.7288 (t70) REVERT: H 323 LYS cc_start: 0.8267 (mttm) cc_final: 0.7912 (mtpt) outliers start: 29 outliers final: 18 residues processed: 295 average time/residue: 0.2585 time to fit residues: 109.5203 Evaluate side-chains 286 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 267 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 71 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.159708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.126491 restraints weight = 37313.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.129346 restraints weight = 28863.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.130936 restraints weight = 13829.102| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13400 Z= 0.132 Angle : 0.438 4.335 18152 Z= 0.235 Chirality : 0.046 0.139 2174 Planarity : 0.003 0.037 2360 Dihedral : 3.291 15.531 1942 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.32 % Allowed : 17.42 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.20), residues: 1766 helix: 0.07 (0.19), residues: 830 sheet: 0.71 (0.27), residues: 336 loop : -0.86 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 123 HIS 0.004 0.001 HIS G 193 PHE 0.006 0.001 PHE D 140 TYR 0.018 0.001 TYR E 333 ARG 0.006 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 563) hydrogen bonds : angle 4.18867 ( 1600) covalent geometry : bond 0.00321 (13400) covalent geometry : angle 0.43761 (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 305 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 275 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8528 (m-80) cc_final: 0.8311 (m-80) REVERT: A 151 LYS cc_start: 0.8081 (ptpt) cc_final: 0.7753 (ttpt) REVERT: A 169 ASP cc_start: 0.8215 (m-30) cc_final: 0.7867 (m-30) REVERT: A 263 ARG cc_start: 0.7500 (mtm-85) cc_final: 0.7299 (mtt180) REVERT: A 284 ASP cc_start: 0.8350 (t0) cc_final: 0.7884 (t0) REVERT: A 333 TYR cc_start: 0.8407 (t80) cc_final: 0.8199 (t80) REVERT: E 129 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8763 (mm-30) REVERT: B 169 ASP cc_start: 0.8611 (t0) cc_final: 0.8229 (t0) REVERT: B 226 ASP cc_start: 0.8310 (m-30) cc_final: 0.7474 (m-30) REVERT: B 239 MET cc_start: 0.8926 (mtp) cc_final: 0.8513 (mtt) REVERT: F 142 LEU cc_start: 0.8795 (tp) cc_final: 0.8510 (tt) REVERT: F 266 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: F 300 ASP cc_start: 0.7919 (t70) cc_final: 0.7496 (t70) REVERT: F 323 LYS cc_start: 0.8304 (mttm) cc_final: 0.7967 (mtpt) REVERT: C 151 LYS cc_start: 0.7972 (ptpt) cc_final: 0.7631 (ttpt) REVERT: C 169 ASP cc_start: 0.8239 (m-30) cc_final: 0.7843 (m-30) REVERT: C 284 ASP cc_start: 0.8357 (t0) cc_final: 0.7885 (t0) REVERT: D 169 ASP cc_start: 0.8646 (t70) cc_final: 0.8270 (t0) REVERT: D 184 ASP cc_start: 0.8694 (t70) cc_final: 0.8221 (t70) REVERT: D 210 GLU cc_start: 0.8289 (tt0) cc_final: 0.8030 (tt0) REVERT: D 226 ASP cc_start: 0.8292 (m-30) cc_final: 0.7469 (m-30) REVERT: D 239 MET cc_start: 0.8934 (mtp) cc_final: 0.8534 (mtt) REVERT: D 303 ILE cc_start: 0.8632 (mp) cc_final: 0.8427 (tp) REVERT: H 142 LEU cc_start: 0.8782 (tp) cc_final: 0.8513 (tt) REVERT: H 266 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: H 300 ASP cc_start: 0.7845 (t70) cc_final: 0.7429 (t70) REVERT: H 323 LYS cc_start: 0.8231 (mttm) cc_final: 0.7895 (mtpt) outliers start: 30 outliers final: 20 residues processed: 287 average time/residue: 0.2808 time to fit residues: 112.5733 Evaluate side-chains 286 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 264 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 150 optimal weight: 0.0370 chunk 118 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.159586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.124832 restraints weight = 30403.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.129062 restraints weight = 22343.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.129405 restraints weight = 15585.082| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2843 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= 0.102 Angle : 0.435 7.381 18152 Z= 0.230 Chirality : 0.046 0.139 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.189 14.999 1942 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.03 % Allowed : 18.07 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.20), residues: 1766 helix: 0.27 (0.19), residues: 830 sheet: 0.48 (0.27), residues: 320 loop : -0.82 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 123 HIS 0.003 0.000 HIS G 193 PHE 0.005 0.001 PHE B 140 TYR 0.019 0.001 TYR E 333 ARG 0.006 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.02851 ( 563) hydrogen bonds : angle 4.08967 ( 1600) covalent geometry : bond 0.00240 (13400) covalent geometry : angle 0.43549 (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 302 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8029 (ptpt) cc_final: 0.7772 (ttpt) REVERT: A 169 ASP cc_start: 0.8164 (m-30) cc_final: 0.7832 (m-30) REVERT: A 284 ASP cc_start: 0.8266 (t0) cc_final: 0.7857 (t0) REVERT: E 129 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8740 (mm-30) REVERT: B 169 ASP cc_start: 0.8651 (t0) cc_final: 0.8232 (t0) REVERT: B 226 ASP cc_start: 0.8296 (m-30) cc_final: 0.7482 (m-30) REVERT: B 239 MET cc_start: 0.8865 (mtp) cc_final: 0.8527 (mtt) REVERT: F 142 LEU cc_start: 0.8817 (tp) cc_final: 0.8551 (tt) REVERT: F 266 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: F 300 ASP cc_start: 0.7873 (t70) cc_final: 0.7457 (t70) REVERT: F 323 LYS cc_start: 0.8310 (mttm) cc_final: 0.8020 (mtpt) REVERT: C 151 LYS cc_start: 0.7978 (ptpt) cc_final: 0.7662 (ttpt) REVERT: C 169 ASP cc_start: 0.8188 (m-30) cc_final: 0.7863 (m-30) REVERT: C 284 ASP cc_start: 0.8305 (t0) cc_final: 0.7887 (t0) REVERT: D 129 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7425 (tm-30) REVERT: D 169 ASP cc_start: 0.8658 (t70) cc_final: 0.8295 (t0) REVERT: D 226 ASP cc_start: 0.8252 (m-30) cc_final: 0.7463 (m-30) REVERT: D 239 MET cc_start: 0.8869 (mtp) cc_final: 0.8548 (mtt) REVERT: H 142 LEU cc_start: 0.8784 (tp) cc_final: 0.8527 (tt) REVERT: H 266 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: H 300 ASP cc_start: 0.7755 (t70) cc_final: 0.7345 (t70) REVERT: H 323 LYS cc_start: 0.8272 (mttm) cc_final: 0.7953 (mtpt) outliers start: 26 outliers final: 17 residues processed: 290 average time/residue: 0.2834 time to fit residues: 115.4434 Evaluate side-chains 277 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 258 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 140 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 82 optimal weight: 0.0370 chunk 74 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 126 optimal weight: 0.0050 chunk 3 optimal weight: 0.0370 overall best weight: 0.2150 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.163678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.129565 restraints weight = 40431.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.134163 restraints weight = 30739.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.136522 restraints weight = 12706.481| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13400 Z= 0.078 Angle : 0.426 7.476 18152 Z= 0.224 Chirality : 0.046 0.161 2174 Planarity : 0.003 0.033 2360 Dihedral : 3.048 14.263 1942 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.60 % Allowed : 19.01 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1766 helix: 0.46 (0.19), residues: 830 sheet: 0.76 (0.26), residues: 336 loop : -0.70 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 123 HIS 0.002 0.000 HIS H 161 PHE 0.005 0.001 PHE D 140 TYR 0.023 0.001 TYR A 333 ARG 0.005 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.02562 ( 563) hydrogen bonds : angle 3.99484 ( 1600) covalent geometry : bond 0.00172 (13400) covalent geometry : angle 0.42597 (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 296 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 276 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8013 (ptpt) cc_final: 0.7673 (ttpt) REVERT: A 169 ASP cc_start: 0.8026 (m-30) cc_final: 0.7642 (m-30) REVERT: A 284 ASP cc_start: 0.8306 (t0) cc_final: 0.7826 (t0) REVERT: E 129 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8726 (mm-30) REVERT: E 210 GLU cc_start: 0.8494 (tt0) cc_final: 0.8092 (tt0) REVERT: E 215 GLU cc_start: 0.8159 (pm20) cc_final: 0.7932 (pt0) REVERT: B 163 ASP cc_start: 0.8265 (t70) cc_final: 0.7928 (t70) REVERT: B 169 ASP cc_start: 0.8636 (t0) cc_final: 0.8231 (t0) REVERT: B 226 ASP cc_start: 0.8269 (m-30) cc_final: 0.7472 (m-30) REVERT: B 239 MET cc_start: 0.8905 (mtp) cc_final: 0.8597 (mtt) REVERT: F 142 LEU cc_start: 0.8755 (tp) cc_final: 0.8513 (tt) REVERT: F 266 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: F 300 ASP cc_start: 0.7924 (t70) cc_final: 0.7525 (t70) REVERT: F 323 LYS cc_start: 0.8223 (mttm) cc_final: 0.7897 (mtpt) REVERT: C 151 LYS cc_start: 0.7939 (ptpt) cc_final: 0.7572 (ttpt) REVERT: C 263 ARG cc_start: 0.7579 (mtm-85) cc_final: 0.7318 (mtt180) REVERT: C 284 ASP cc_start: 0.8365 (t0) cc_final: 0.7875 (t0) REVERT: G 318 ILE cc_start: 0.8305 (mt) cc_final: 0.8102 (pt) REVERT: D 163 ASP cc_start: 0.8126 (t70) cc_final: 0.7818 (t0) REVERT: D 169 ASP cc_start: 0.8658 (t70) cc_final: 0.8311 (t0) REVERT: D 226 ASP cc_start: 0.8243 (m-30) cc_final: 0.7415 (m-30) REVERT: D 239 MET cc_start: 0.8909 (mtp) cc_final: 0.8609 (mtt) REVERT: H 142 LEU cc_start: 0.8741 (tp) cc_final: 0.8506 (tt) REVERT: H 266 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: H 300 ASP cc_start: 0.7932 (t70) cc_final: 0.7529 (t70) REVERT: H 323 LYS cc_start: 0.8120 (mttm) cc_final: 0.7836 (mtpt) outliers start: 20 outliers final: 15 residues processed: 285 average time/residue: 0.2849 time to fit residues: 112.7822 Evaluate side-chains 286 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 269 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 146 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.151685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.117832 restraints weight = 33759.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.120015 restraints weight = 28700.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.121366 restraints weight = 15727.423| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13400 Z= 0.120 Angle : 0.461 8.917 18152 Z= 0.241 Chirality : 0.047 0.202 2174 Planarity : 0.003 0.041 2360 Dihedral : 3.112 14.708 1942 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.74 % Allowed : 19.59 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.20), residues: 1766 helix: 0.45 (0.19), residues: 830 sheet: 0.53 (0.27), residues: 304 loop : -0.63 (0.24), residues: 632 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 0.007 0.001 PHE A 140 TYR 0.020 0.001 TYR A 333 ARG 0.010 0.000 ARG E 213 Details of bonding type rmsd hydrogen bonds : bond 0.02940 ( 563) hydrogen bonds : angle 4.05404 ( 1600) covalent geometry : bond 0.00292 (13400) covalent geometry : angle 0.46149 (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 287 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 264 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7969 (ptpt) cc_final: 0.7657 (ttpt) REVERT: A 169 ASP cc_start: 0.8129 (m-30) cc_final: 0.7797 (m-30) REVERT: A 210 GLU cc_start: 0.7880 (tt0) cc_final: 0.7306 (tt0) REVERT: A 284 ASP cc_start: 0.8325 (t0) cc_final: 0.7866 (t0) REVERT: E 215 GLU cc_start: 0.8235 (pm20) cc_final: 0.7928 (pt0) REVERT: E 266 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: B 129 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7377 (tm-30) REVERT: B 163 ASP cc_start: 0.8269 (t70) cc_final: 0.7942 (t70) REVERT: B 169 ASP cc_start: 0.8695 (t0) cc_final: 0.8325 (t0) REVERT: B 184 ASP cc_start: 0.8736 (t0) cc_final: 0.8327 (t70) REVERT: B 210 GLU cc_start: 0.8318 (tt0) cc_final: 0.8022 (tt0) REVERT: B 226 ASP cc_start: 0.8278 (m-30) cc_final: 0.7506 (m-30) REVERT: B 239 MET cc_start: 0.8883 (mtp) cc_final: 0.8555 (mtt) REVERT: F 142 LEU cc_start: 0.8815 (tp) cc_final: 0.8573 (tt) REVERT: F 266 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: F 300 ASP cc_start: 0.7901 (t70) cc_final: 0.7514 (t70) REVERT: F 323 LYS cc_start: 0.8252 (mttm) cc_final: 0.7940 (mtpt) REVERT: C 151 LYS cc_start: 0.7991 (ptpt) cc_final: 0.7649 (ttpt) REVERT: C 169 ASP cc_start: 0.8396 (m-30) cc_final: 0.8070 (m-30) REVERT: C 263 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.7275 (mtt180) REVERT: C 284 ASP cc_start: 0.8326 (t0) cc_final: 0.7867 (t0) REVERT: G 210 GLU cc_start: 0.8575 (tt0) cc_final: 0.8164 (tt0) REVERT: G 318 ILE cc_start: 0.8357 (mt) cc_final: 0.8076 (pt) REVERT: D 129 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7388 (tm-30) REVERT: D 163 ASP cc_start: 0.8237 (t70) cc_final: 0.7914 (t0) REVERT: D 169 ASP cc_start: 0.8682 (t70) cc_final: 0.8283 (t0) REVERT: D 184 ASP cc_start: 0.8663 (t70) cc_final: 0.8457 (t70) REVERT: D 226 ASP cc_start: 0.8239 (m-30) cc_final: 0.7474 (m-30) REVERT: D 239 MET cc_start: 0.8882 (mtp) cc_final: 0.8566 (mtt) REVERT: H 142 LEU cc_start: 0.8763 (tp) cc_final: 0.8528 (tt) REVERT: H 266 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: H 300 ASP cc_start: 0.7857 (t70) cc_final: 0.7477 (t70) REVERT: H 323 LYS cc_start: 0.8138 (mttm) cc_final: 0.7861 (mtpt) outliers start: 23 outliers final: 18 residues processed: 274 average time/residue: 0.2850 time to fit residues: 109.5380 Evaluate side-chains 278 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 257 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 46 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.161833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.127206 restraints weight = 31945.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.133133 restraints weight = 22679.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.133033 restraints weight = 13682.500| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3087 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= 0.114 Angle : 0.455 9.397 18152 Z= 0.238 Chirality : 0.046 0.155 2174 Planarity : 0.003 0.042 2360 Dihedral : 3.126 14.768 1942 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.81 % Allowed : 19.52 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.11 (0.20), residues: 1766 helix: 0.52 (0.19), residues: 822 sheet: 0.53 (0.28), residues: 304 loop : -0.60 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 123 HIS 0.003 0.000 HIS H 117 PHE 0.006 0.001 PHE H 251 TYR 0.022 0.001 TYR A 333 ARG 0.010 0.000 ARG E 213 Details of bonding type rmsd hydrogen bonds : bond 0.02933 ( 563) hydrogen bonds : angle 4.05191 ( 1600) covalent geometry : bond 0.00276 (13400) covalent geometry : angle 0.45513 (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 286 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7913 (ptpt) cc_final: 0.7665 (ttpt) REVERT: A 284 ASP cc_start: 0.8307 (t0) cc_final: 0.7882 (t0) REVERT: E 129 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8736 (mm-30) REVERT: E 215 GLU cc_start: 0.8242 (pm20) cc_final: 0.7928 (pt0) REVERT: B 163 ASP cc_start: 0.8288 (t70) cc_final: 0.7949 (t70) REVERT: B 169 ASP cc_start: 0.8719 (t0) cc_final: 0.8338 (t0) REVERT: B 184 ASP cc_start: 0.8700 (t0) cc_final: 0.8284 (t70) REVERT: B 210 GLU cc_start: 0.8342 (tt0) cc_final: 0.8038 (tt0) REVERT: B 226 ASP cc_start: 0.8295 (m-30) cc_final: 0.7510 (m-30) REVERT: B 239 MET cc_start: 0.8900 (mtp) cc_final: 0.8597 (mtt) REVERT: F 142 LEU cc_start: 0.8806 (tp) cc_final: 0.8539 (tt) REVERT: F 266 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: F 300 ASP cc_start: 0.7917 (t70) cc_final: 0.7546 (t70) REVERT: F 323 LYS cc_start: 0.8272 (mttm) cc_final: 0.7988 (mtpt) REVERT: C 151 LYS cc_start: 0.7882 (ptpt) cc_final: 0.7664 (ttpt) REVERT: C 169 ASP cc_start: 0.8368 (m-30) cc_final: 0.8014 (m-30) REVERT: C 263 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.7292 (mtt180) REVERT: C 284 ASP cc_start: 0.8359 (t0) cc_final: 0.7941 (t0) REVERT: C 294 ILE cc_start: 0.8806 (pt) cc_final: 0.8571 (mt) REVERT: G 318 ILE cc_start: 0.8367 (mt) cc_final: 0.8070 (pt) REVERT: D 129 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7430 (tm-30) REVERT: D 163 ASP cc_start: 0.8276 (t70) cc_final: 0.7949 (t0) REVERT: D 169 ASP cc_start: 0.8692 (t70) cc_final: 0.8276 (t0) REVERT: D 226 ASP cc_start: 0.8265 (m-30) cc_final: 0.7482 (m-30) REVERT: D 239 MET cc_start: 0.8889 (mtp) cc_final: 0.8589 (mtt) REVERT: H 142 LEU cc_start: 0.8769 (tp) cc_final: 0.8508 (tt) REVERT: H 266 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: H 300 ASP cc_start: 0.7865 (t70) cc_final: 0.7508 (t70) REVERT: H 323 LYS cc_start: 0.8169 (mttm) cc_final: 0.7899 (mtpt) outliers start: 24 outliers final: 19 residues processed: 274 average time/residue: 0.2713 time to fit residues: 104.8740 Evaluate side-chains 282 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 261 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 92 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.170674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134756 restraints weight = 35510.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.140359 restraints weight = 15873.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.141680 restraints weight = 9675.929| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13400 Z= 0.102 Angle : 0.453 9.527 18152 Z= 0.235 Chirality : 0.046 0.142 2174 Planarity : 0.003 0.043 2360 Dihedral : 3.105 14.532 1942 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.74 % Allowed : 19.96 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1766 helix: 0.58 (0.19), residues: 822 sheet: 0.54 (0.27), residues: 304 loop : -0.56 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 123 HIS 0.002 0.000 HIS G 193 PHE 0.006 0.001 PHE H 251 TYR 0.022 0.001 TYR A 333 ARG 0.010 0.000 ARG E 213 Details of bonding type rmsd hydrogen bonds : bond 0.02830 ( 563) hydrogen bonds : angle 4.04093 ( 1600) covalent geometry : bond 0.00244 (13400) covalent geometry : angle 0.45277 (18152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4753.80 seconds wall clock time: 82 minutes 36.58 seconds (4956.58 seconds total)