Starting phenix.real_space_refine on Sat Sep 12 05:51:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6v1x_21018/09_2026/6v1x_21018.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v1x_21018/09_2026/6v1x_21018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6v1x_21018/09_2026/6v1x_21018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v1x_21018/09_2026/6v1x_21018.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v1x_21018/09_2026/6v1x_21018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v1x_21018/09_2026/6v1x_21018.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6v1x_21018/09_2026/6v1x_21018.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6v1x_21018/09_2026/6v1x_21018.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 P 4 5.49 5 S 64 5.16 5 C 9304 2.51 5 N 2276 2.21 5 O 2348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13996 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3436 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'HIS:plan': 4, 'ASP:plan': 12, 'ASN:plan1': 3, 'GLU:plan': 10, 'GLN:plan1': 5, 'ARG:plan': 6, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 174 Chain: "B" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3436 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'HIS:plan': 4, 'ASP:plan': 12, 'ASN:plan1': 3, 'GLU:plan': 10, 'GLN:plan1': 5, 'ARG:plan': 6, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 174 Chain: "C" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3436 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'HIS:plan': 4, 'ASP:plan': 12, 'ASN:plan1': 3, 'GLU:plan': 10, 'GLN:plan1': 5, 'ARG:plan': 6, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 174 Chain: "D" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3436 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'HIS:plan': 4, 'ASP:plan': 12, 'ASN:plan1': 3, 'GLU:plan': 10, 'GLN:plan1': 5, 'ARG:plan': 6, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 174 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'QNJ': 1, 'QNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'QNJ': 1, 'QNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'QNJ': 1, 'QNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'QNJ': 1, 'QNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.15, per 1000 atoms: 0.23 Number of scatterers: 13996 At special positions: 0 Unit cell: (115.976, 115.976, 120.232, 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) S 64 16.00 P 4 15.00 O 2348 8.00 N 2276 7.00 C 9304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 623.1 milliseconds 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 8 sheets defined 63.5% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 56 through 83 removed outlier: 3.659A pdb=" N ARG A 60 " --> pdb=" O ASN A 56 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 91 through 109 removed outlier: 3.675A pdb=" N ILE A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 137 Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.572A pdb=" N ASP A 141 " --> pdb=" O TRP A 137 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.853A pdb=" N ASN A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.768A pdb=" N LEU A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.572A pdb=" N LEU A 172 " --> pdb=" O MET A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.827A pdb=" N SER A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 222 removed outlier: 3.542A pdb=" N ARG A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS A 198 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 259 removed outlier: 3.813A pdb=" N ARG A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 303 removed outlier: 3.957A pdb=" N ILE A 278 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 324 removed outlier: 3.661A pdb=" N ASN A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 343 removed outlier: 3.821A pdb=" N THR A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 354 removed outlier: 3.714A pdb=" N GLN A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 373 removed outlier: 3.765A pdb=" N PHE A 369 " --> pdb=" O ASN A 365 " (cutoff:3.500A) Proline residue: A 370 - end of helix Processing helix chain 'A' and resid 383 through 391 removed outlier: 4.172A pdb=" N GLN A 388 " --> pdb=" O ASN A 384 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 478 Processing helix chain 'A' and resid 484 through 498 removed outlier: 3.857A pdb=" N VAL A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 498 " --> pdb=" O PHE A 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 83 removed outlier: 3.658A pdb=" N ARG B 60 " --> pdb=" O ASN B 56 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) Proline residue: B 78 - end of helix Processing helix chain 'B' and resid 91 through 109 removed outlier: 3.676A pdb=" N ILE B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 137 Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.572A pdb=" N ASP B 141 " --> pdb=" O TRP B 137 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 156 removed outlier: 3.854A pdb=" N ASN B 156 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.768A pdb=" N LEU B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.571A pdb=" N LEU B 172 " --> pdb=" O MET B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.827A pdb=" N SER B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU B 186 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 222 removed outlier: 3.542A pdb=" N ARG B 197 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 259 removed outlier: 3.813A pdb=" N ARG B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 303 removed outlier: 3.957A pdb=" N ILE B 278 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 324 removed outlier: 3.662A pdb=" N ASN B 323 " --> pdb=" O PHE B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 343 removed outlier: 3.821A pdb=" N THR B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 removed outlier: 3.714A pdb=" N GLN B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 373 removed outlier: 3.764A pdb=" N PHE B 369 " --> pdb=" O ASN B 365 " (cutoff:3.500A) Proline residue: B 370 - end of helix Processing helix chain 'B' and resid 383 through 391 removed outlier: 4.172A pdb=" N GLN B 388 " --> pdb=" O ASN B 384 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER B 391 " --> pdb=" O PHE B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 478 Processing helix chain 'B' and resid 484 through 498 removed outlier: 3.857A pdb=" N VAL B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 498 " --> pdb=" O PHE B 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 83 removed outlier: 3.659A pdb=" N ARG C 60 " --> pdb=" O ASN C 56 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) Proline residue: C 78 - end of helix Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.675A pdb=" N ILE C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 137 Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.572A pdb=" N ASP C 141 " --> pdb=" O TRP C 137 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 156 removed outlier: 3.853A pdb=" N ASN C 156 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.768A pdb=" N LEU C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 174 removed outlier: 3.572A pdb=" N LEU C 172 " --> pdb=" O MET C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 188 removed outlier: 3.827A pdb=" N SER C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU C 186 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS C 187 " --> pdb=" O ALA C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 222 removed outlier: 3.542A pdb=" N ARG C 197 " --> pdb=" O TYR C 193 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS C 198 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 259 removed outlier: 3.813A pdb=" N ARG C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 303 removed outlier: 3.957A pdb=" N ILE C 278 " --> pdb=" O MET C 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 303 " --> pdb=" O VAL C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 324 removed outlier: 3.661A pdb=" N ASN C 323 " --> pdb=" O PHE C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 343 removed outlier: 3.821A pdb=" N THR C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 354 removed outlier: 3.714A pdb=" N GLN C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 373 removed outlier: 3.765A pdb=" N PHE C 369 " --> pdb=" O ASN C 365 " (cutoff:3.500A) Proline residue: C 370 - end of helix Processing helix chain 'C' and resid 383 through 391 removed outlier: 4.172A pdb=" N GLN C 388 " --> pdb=" O ASN C 384 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER C 391 " --> pdb=" O PHE C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 478 Processing helix chain 'C' and resid 484 through 498 removed outlier: 3.857A pdb=" N VAL C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG C 498 " --> pdb=" O PHE C 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 83 removed outlier: 3.659A pdb=" N ARG D 60 " --> pdb=" O ASN D 56 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 61 " --> pdb=" O PRO D 57 " (cutoff:3.500A) Proline residue: D 78 - end of helix Processing helix chain 'D' and resid 91 through 109 removed outlier: 3.675A pdb=" N ILE D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 137 Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.572A pdb=" N ASP D 141 " --> pdb=" O TRP D 137 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 156 removed outlier: 3.853A pdb=" N ASN D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 167 removed outlier: 3.768A pdb=" N LEU D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.572A pdb=" N LEU D 172 " --> pdb=" O MET D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 188 removed outlier: 3.827A pdb=" N SER D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU D 186 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 222 removed outlier: 3.542A pdb=" N ARG D 197 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 259 removed outlier: 3.813A pdb=" N ARG D 246 " --> pdb=" O SER D 242 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR D 257 " --> pdb=" O TRP D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 303 removed outlier: 3.957A pdb=" N ILE D 278 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 324 removed outlier: 3.661A pdb=" N ASN D 323 " --> pdb=" O PHE D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 343 removed outlier: 3.821A pdb=" N THR D 343 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 354 removed outlier: 3.714A pdb=" N GLN D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 373 removed outlier: 3.765A pdb=" N PHE D 369 " --> pdb=" O ASN D 365 " (cutoff:3.500A) Proline residue: D 370 - end of helix Processing helix chain 'D' and resid 383 through 391 removed outlier: 4.172A pdb=" N GLN D 388 " --> pdb=" O ASN D 384 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER D 391 " --> pdb=" O PHE D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 478 Processing helix chain 'D' and resid 484 through 498 removed outlier: 3.857A pdb=" N VAL D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG D 498 " --> pdb=" O PHE D 494 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 403 through 405 removed outlier: 6.451A pdb=" N VAL A 459 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 422 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA A 438 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 416 through 417 removed outlier: 3.596A pdb=" N ILE A 416 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 403 through 405 removed outlier: 6.451A pdb=" N VAL B 459 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B 422 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA B 438 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 416 through 417 removed outlier: 3.596A pdb=" N ILE B 416 " --> pdb=" O LEU B 468 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 403 through 405 removed outlier: 6.451A pdb=" N VAL C 459 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL C 422 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA C 438 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 416 through 417 removed outlier: 3.596A pdb=" N ILE C 416 " --> pdb=" O LEU C 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 403 through 405 removed outlier: 6.451A pdb=" N VAL D 459 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL D 422 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA D 438 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 416 through 417 removed outlier: 3.596A pdb=" N ILE D 416 " --> pdb=" O LEU D 468 " (cutoff:3.500A) 736 hydrogen bonds defined for protein. 2172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2024 1.29 - 1.42: 4252 1.42 - 1.55: 8002 1.55 - 1.68: 26 1.68 - 1.81: 104 Bond restraints: 14408 Sorted by residual: bond pdb=" C PRO B 150 " pdb=" N LEU B 151 " ideal model delta sigma weight residual 1.334 1.496 -0.162 1.43e-02 4.89e+03 1.29e+02 bond pdb=" C PRO C 150 " pdb=" N LEU C 151 " ideal model delta sigma weight residual 1.334 1.497 -0.163 1.46e-02 4.69e+03 1.24e+02 bond pdb=" C PRO D 150 " pdb=" N LEU D 151 " ideal model delta sigma weight residual 1.334 1.497 -0.163 1.46e-02 4.69e+03 1.24e+02 bond pdb=" C PRO A 150 " pdb=" N LEU A 151 " ideal model delta sigma weight residual 1.334 1.497 -0.163 1.46e-02 4.69e+03 1.24e+02 bond pdb=" O3 QNP C 602 " pdb=" P1 QNP C 602 " ideal model delta sigma weight residual 1.732 1.628 0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 14403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 18313 2.20 - 4.41: 1103 4.41 - 6.61: 221 6.61 - 8.82: 39 8.82 - 11.02: 20 Bond angle restraints: 19696 Sorted by residual: angle pdb=" C THR B 259 " pdb=" N THR B 260 " pdb=" CA THR B 260 " ideal model delta sigma weight residual 121.54 130.11 -8.57 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C THR A 259 " pdb=" N THR A 260 " pdb=" CA THR A 260 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C THR C 259 " pdb=" N THR C 260 " pdb=" CA THR C 260 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C THR D 259 " pdb=" N THR D 260 " pdb=" CA THR D 260 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C LYS B 127 " pdb=" N LYS B 128 " pdb=" CA LYS B 128 " ideal model delta sigma weight residual 121.54 129.82 -8.28 1.91e+00 2.74e-01 1.88e+01 ... (remaining 19691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 7691 15.59 - 31.18: 473 31.18 - 46.76: 88 46.76 - 62.35: 24 62.35 - 77.94: 8 Dihedral angle restraints: 8284 sinusoidal: 2992 harmonic: 5292 Sorted by residual: dihedral pdb=" CA SER B 125 " pdb=" C SER B 125 " pdb=" N PRO B 126 " pdb=" CA PRO B 126 " ideal model delta harmonic sigma weight residual -180.00 -152.77 -27.23 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER D 125 " pdb=" C SER D 125 " pdb=" N PRO D 126 " pdb=" CA PRO D 126 " ideal model delta harmonic sigma weight residual -180.00 -152.79 -27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA SER A 125 " pdb=" C SER A 125 " pdb=" N PRO A 126 " pdb=" CA PRO A 126 " ideal model delta harmonic sigma weight residual 180.00 -152.79 -27.21 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 8281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1889 0.084 - 0.167: 319 0.167 - 0.251: 36 0.251 - 0.334: 16 0.334 - 0.418: 4 Chirality restraints: 2264 Sorted by residual: chirality pdb=" C10 QNJ D 601 " pdb=" C1 QNJ D 601 " pdb=" C5 QNJ D 601 " pdb=" C9 QNJ D 601 " both_signs ideal model delta sigma weight residual False -2.91 -2.49 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" C10 QNJ C 601 " pdb=" C1 QNJ C 601 " pdb=" C5 QNJ C 601 " pdb=" C9 QNJ C 601 " both_signs ideal model delta sigma weight residual False -2.91 -2.49 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" C10 QNJ A 602 " pdb=" C1 QNJ A 602 " pdb=" C5 QNJ A 602 " pdb=" C9 QNJ A 602 " both_signs ideal model delta sigma weight residual False -2.91 -2.49 -0.42 2.00e-01 2.50e+01 4.36e+00 ... (remaining 2261 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 439 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C VAL B 439 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL B 439 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE B 440 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 439 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.77e+00 pdb=" C VAL C 439 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL C 439 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE C 440 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 439 " -0.015 2.00e-02 2.50e+03 3.13e-02 9.77e+00 pdb=" C VAL A 439 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL A 439 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE A 440 " -0.018 2.00e-02 2.50e+03 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3878 2.80 - 3.33: 12902 3.33 - 3.85: 21682 3.85 - 4.38: 23370 4.38 - 4.90: 41245 Nonbonded interactions: 103077 Sorted by model distance: nonbonded pdb=" O ALA B 358 " pdb=" OG SER B 361 " model vdw 2.279 3.040 nonbonded pdb=" O ALA C 358 " pdb=" OG SER C 361 " model vdw 2.280 3.040 nonbonded pdb=" O ALA D 358 " pdb=" OG SER D 361 " model vdw 2.280 3.040 nonbonded pdb=" O ALA A 358 " pdb=" OG SER A 361 " model vdw 2.280 3.040 nonbonded pdb=" O PHE A 191 " pdb=" NH2 ARG B 310 " model vdw 2.312 3.120 ... (remaining 103072 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and resid 50 through 498) selection = (chain 'B' and resid 50 through 498) selection = (chain 'C' and resid 50 through 498) selection = (chain 'D' and resid 50 through 498) } 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=1.00 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: 0.010 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.160 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 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 : 0.011 0.163 14408 Z= 0.541 Angle : 1.238 11.022 19696 Z= 0.662 Chirality : 0.069 0.418 2264 Planarity : 0.008 0.059 2416 Dihedral : 11.431 77.940 4852 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.50 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.16), residues: 1768 helix: -2.08 (0.12), residues: 1000 sheet: -2.22 (0.52), residues: 96 loop : -3.08 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 322 TYR 0.035 0.003 TYR A 223 PHE 0.025 0.003 PHE B 92 TRP 0.025 0.004 TRP B 75 HIS 0.014 0.003 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.01102 / 0.54 (14408) covalent geometry : angle 1.23756 / 0.66 (19696) hydrogen bonds : bond 0.14973 / 9.95 ( 736) hydrogen bonds : angle 5.83013 / 4.11 ( 2172) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8537 (mt0) cc_final: 0.8210 (mt0) REVERT: A 270 ASN cc_start: 0.8109 (t0) cc_final: 0.7808 (t0) REVERT: B 96 ASN cc_start: 0.9089 (m-40) cc_final: 0.8855 (m110) REVERT: B 149 GLN cc_start: 0.8598 (mt0) cc_final: 0.8049 (mt0) REVERT: B 270 ASN cc_start: 0.8039 (t0) cc_final: 0.7778 (t0) REVERT: C 105 ASP cc_start: 0.7856 (t0) cc_final: 0.7654 (t0) REVERT: C 149 GLN cc_start: 0.8538 (mt0) cc_final: 0.8218 (mt0) REVERT: C 270 ASN cc_start: 0.8114 (t0) cc_final: 0.7805 (t0) REVERT: D 149 GLN cc_start: 0.8539 (mt0) cc_final: 0.8219 (mt0) REVERT: D 270 ASN cc_start: 0.8110 (t0) cc_final: 0.7810 (t0) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.1388 time to fit residues: 66.5263 Evaluate side-chains 209 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 GLN A 284 ASN B 284 ASN C 99 ASN C 284 ASN D 284 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.195030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128371 restraints weight = 22441.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.131278 restraints weight = 13266.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132269 restraints weight = 8609.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132304 restraints weight = 8517.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.132555 restraints weight = 7780.947| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14408 Z= 0.141 Angle : 0.630 5.947 19696 Z= 0.336 Chirality : 0.042 0.154 2264 Planarity : 0.005 0.039 2416 Dihedral : 10.146 71.420 2120 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.24 % Favored : 92.53 % Rotamer: Outliers : 2.40 % Allowed : 8.98 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.19), residues: 1768 helix: 0.02 (0.15), residues: 1044 sheet: -2.25 (0.48), residues: 96 loop : -2.72 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 310 TYR 0.020 0.002 TYR D 376 PHE 0.030 0.001 PHE B 92 TRP 0.020 0.001 TRP A 253 HIS 0.003 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14408) covalent geometry : angle 0.62962 / 0.34 (19696) hydrogen bonds : bond 0.04941 / 3.24 ( 736) hydrogen bonds : angle 3.82372 / 2.72 ( 2172) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 0.571 Fit side-chains REVERT: A 105 ASP cc_start: 0.7729 (t0) cc_final: 0.7516 (t0) REVERT: A 195 TRP cc_start: 0.6520 (m100) cc_final: 0.6301 (m100) REVERT: A 314 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7572 (ttm-80) REVERT: B 105 ASP cc_start: 0.7969 (t0) cc_final: 0.7764 (t0) REVERT: B 314 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7566 (ttm-80) REVERT: C 105 ASP cc_start: 0.7822 (t0) cc_final: 0.7566 (t0) REVERT: C 195 TRP cc_start: 0.6512 (m100) cc_final: 0.6270 (m100) REVERT: C 314 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7562 (ttm-80) REVERT: D 105 ASP cc_start: 0.7734 (t0) cc_final: 0.7527 (t0) REVERT: D 195 TRP cc_start: 0.6510 (m100) cc_final: 0.6304 (m100) REVERT: D 314 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7585 (ttm-80) outliers start: 32 outliers final: 19 residues processed: 263 average time/residue: 0.0980 time to fit residues: 39.6146 Evaluate side-chains 222 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 397 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 59 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 170 optimal weight: 30.0000 chunk 62 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 127 optimal weight: 40.0000 chunk 10 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 168 optimal weight: 40.0000 chunk 14 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 GLN C 149 GLN D 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.194657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.140984 restraints weight = 22374.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.133971 restraints weight = 17443.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135486 restraints weight = 18363.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.134968 restraints weight = 13447.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136073 restraints weight = 11165.999| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14408 Z= 0.134 Angle : 0.580 5.741 19696 Z= 0.305 Chirality : 0.043 0.147 2264 Planarity : 0.004 0.039 2416 Dihedral : 9.083 76.568 2120 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.62 % Favored : 93.16 % Rotamer: Outliers : 2.40 % Allowed : 11.90 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1768 helix: 1.14 (0.16), residues: 1032 sheet: -1.96 (0.49), residues: 96 loop : -2.31 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 310 TYR 0.018 0.002 TYR C 133 PHE 0.024 0.001 PHE D 155 TRP 0.016 0.001 TRP B 137 HIS 0.003 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14408) covalent geometry : angle 0.57958 / 0.31 (19696) hydrogen bonds : bond 0.04799 / 3.13 ( 736) hydrogen bonds : angle 3.47067 / 2.47 ( 2172) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 0.460 Fit side-chains REVERT: A 105 ASP cc_start: 0.7975 (t70) cc_final: 0.7516 (t0) REVERT: A 314 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7682 (ttm-80) REVERT: B 105 ASP cc_start: 0.8060 (t70) cc_final: 0.7747 (t0) REVERT: B 314 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7606 (ttm-80) REVERT: C 314 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7658 (ttm-80) REVERT: D 105 ASP cc_start: 0.7981 (t70) cc_final: 0.7602 (t0) REVERT: D 314 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7691 (ttm-80) outliers start: 32 outliers final: 17 residues processed: 240 average time/residue: 0.1069 time to fit residues: 38.4568 Evaluate side-chains 220 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 397 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 46 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS B 118 HIS B 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.192122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134011 restraints weight = 22277.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.126231 restraints weight = 16799.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127371 restraints weight = 14368.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128384 restraints weight = 10353.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128610 restraints weight = 9256.754| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14408 Z= 0.207 Angle : 0.629 6.557 19696 Z= 0.331 Chirality : 0.045 0.151 2264 Planarity : 0.004 0.042 2416 Dihedral : 9.318 76.915 2120 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.90 % Favored : 92.87 % Rotamer: Outliers : 3.82 % Allowed : 11.15 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.21), residues: 1768 helix: 1.13 (0.16), residues: 1052 sheet: -2.14 (0.48), residues: 96 loop : -2.42 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 310 TYR 0.031 0.002 TYR C 133 PHE 0.021 0.001 PHE B 155 TRP 0.014 0.001 TRP B 137 HIS 0.006 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (14408) covalent geometry : angle 0.62889 / 0.33 (19696) hydrogen bonds : bond 0.05799 / 3.75 ( 736) hydrogen bonds : angle 3.67821 / 2.61 ( 2172) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 0.510 Fit side-chains REVERT: A 95 ASP cc_start: 0.8500 (m-30) cc_final: 0.8286 (m-30) REVERT: A 105 ASP cc_start: 0.8267 (t70) cc_final: 0.7946 (t0) REVERT: B 105 ASP cc_start: 0.8325 (t70) cc_final: 0.8069 (t0) REVERT: C 95 ASP cc_start: 0.8430 (m-30) cc_final: 0.8220 (m-30) REVERT: D 95 ASP cc_start: 0.8461 (m-30) cc_final: 0.8254 (m-30) outliers start: 51 outliers final: 34 residues processed: 238 average time/residue: 0.1184 time to fit residues: 41.3995 Evaluate side-chains 236 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 397 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 137 optimal weight: 0.4980 chunk 123 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 38 optimal weight: 50.0000 chunk 131 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN C 348 GLN D 149 GLN D 348 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.195326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138918 restraints weight = 21939.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136955 restraints weight = 14367.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.136997 restraints weight = 12113.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137191 restraints weight = 8803.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.137439 restraints weight = 7899.977| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14408 Z= 0.127 Angle : 0.535 5.465 19696 Z= 0.282 Chirality : 0.043 0.146 2264 Planarity : 0.004 0.038 2416 Dihedral : 9.148 79.554 2120 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.33 % Favored : 93.44 % Rotamer: Outliers : 3.07 % Allowed : 13.02 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1768 helix: 1.57 (0.17), residues: 1040 sheet: -1.91 (0.50), residues: 96 loop : -1.98 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 322 TYR 0.013 0.001 TYR C 133 PHE 0.017 0.001 PHE B 92 TRP 0.014 0.001 TRP B 137 HIS 0.003 0.001 HIS D 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (14408) covalent geometry : angle 0.53517 / 0.28 (19696) hydrogen bonds : bond 0.04421 / 2.88 ( 736) hydrogen bonds : angle 3.35860 / 2.37 ( 2172) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.488 Fit side-chains REVERT: A 105 ASP cc_start: 0.8338 (t70) cc_final: 0.7945 (t0) REVERT: D 105 ASP cc_start: 0.8043 (t0) cc_final: 0.7791 (t0) outliers start: 41 outliers final: 30 residues processed: 231 average time/residue: 0.0901 time to fit residues: 33.4173 Evaluate side-chains 228 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 397 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 128 optimal weight: 30.0000 chunk 114 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 166 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS D 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.196800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141036 restraints weight = 21969.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.137292 restraints weight = 14296.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.138007 restraints weight = 12072.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.138408 restraints weight = 8933.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.138641 restraints weight = 8224.771| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14408 Z= 0.123 Angle : 0.524 5.483 19696 Z= 0.276 Chirality : 0.042 0.141 2264 Planarity : 0.004 0.038 2416 Dihedral : 8.888 76.239 2120 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.96 % Favored : 92.82 % Rotamer: Outliers : 3.07 % Allowed : 14.07 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.21), residues: 1768 helix: 1.70 (0.17), residues: 1040 sheet: -2.18 (0.45), residues: 116 loop : -1.69 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 322 TYR 0.012 0.001 TYR C 252 PHE 0.016 0.001 PHE B 92 TRP 0.012 0.001 TRP B 137 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14408) covalent geometry : angle 0.52385 / 0.28 (19696) hydrogen bonds : bond 0.04414 / 2.88 ( 736) hydrogen bonds : angle 3.34943 / 2.36 ( 2172) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.508 Fit side-chains REVERT: A 397 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: B 141 ASP cc_start: 0.8802 (t0) cc_final: 0.8465 (t0) REVERT: B 397 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: C 397 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7748 (m-80) REVERT: D 105 ASP cc_start: 0.8028 (t0) cc_final: 0.7743 (t0) outliers start: 41 outliers final: 35 residues processed: 230 average time/residue: 0.0869 time to fit residues: 32.9730 Evaluate side-chains 237 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 397 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 91 optimal weight: 0.0020 chunk 116 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 149 GLN C 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.197256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140971 restraints weight = 21543.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.137293 restraints weight = 14661.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.137890 restraints weight = 11962.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138262 restraints weight = 9123.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.138561 restraints weight = 8274.798| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14408 Z= 0.117 Angle : 0.513 6.295 19696 Z= 0.269 Chirality : 0.042 0.140 2264 Planarity : 0.004 0.038 2416 Dihedral : 8.764 76.311 2120 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.45 % Favored : 93.33 % Rotamer: Outliers : 3.29 % Allowed : 14.07 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1768 helix: 1.79 (0.17), residues: 1044 sheet: -1.56 (0.52), residues: 96 loop : -1.71 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 322 TYR 0.010 0.001 TYR A 252 PHE 0.015 0.001 PHE B 92 TRP 0.013 0.001 TRP B 137 HIS 0.003 0.001 HIS C 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (14408) covalent geometry : angle 0.51321 / 0.27 (19696) hydrogen bonds : bond 0.04225 / 2.77 ( 736) hydrogen bonds : angle 3.28211 / 2.30 ( 2172) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.420 Fit side-chains REVERT: A 324 GLN cc_start: 0.8824 (mp10) cc_final: 0.8387 (mp10) REVERT: A 327 HIS cc_start: 0.6866 (m-70) cc_final: 0.6665 (m-70) REVERT: A 397 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: B 141 ASP cc_start: 0.8812 (t0) cc_final: 0.8453 (t0) REVERT: B 324 GLN cc_start: 0.8858 (mp10) cc_final: 0.8411 (mp10) REVERT: B 397 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: C 324 GLN cc_start: 0.8793 (mp10) cc_final: 0.8348 (mp10) REVERT: C 397 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: D 105 ASP cc_start: 0.8103 (t0) cc_final: 0.7839 (t0) REVERT: D 324 GLN cc_start: 0.8825 (mp10) cc_final: 0.8379 (mp10) REVERT: D 327 HIS cc_start: 0.6839 (m-70) cc_final: 0.6638 (m-70) outliers start: 44 outliers final: 34 residues processed: 236 average time/residue: 0.0836 time to fit residues: 32.3839 Evaluate side-chains 244 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 397 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 73 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 105 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 77 optimal weight: 50.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.198477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145341 restraints weight = 21490.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144594 restraints weight = 15877.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144609 restraints weight = 11558.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144455 restraints weight = 9133.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.144955 restraints weight = 7911.957| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14408 Z= 0.112 Angle : 0.510 6.915 19696 Z= 0.267 Chirality : 0.042 0.175 2264 Planarity : 0.004 0.038 2416 Dihedral : 8.628 75.838 2120 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.28 % Favored : 93.50 % Rotamer: Outliers : 3.37 % Allowed : 14.22 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.21), residues: 1768 helix: 1.91 (0.17), residues: 1040 sheet: -1.46 (0.53), residues: 96 loop : -1.53 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 322 TYR 0.010 0.001 TYR C 252 PHE 0.020 0.001 PHE B 155 TRP 0.010 0.001 TRP B 137 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14408) covalent geometry : angle 0.50989 / 0.27 (19696) hydrogen bonds : bond 0.04140 / 2.72 ( 736) hydrogen bonds : angle 3.28984 / 2.31 ( 2172) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 1.489 Fit side-chains REVERT: A 80 GLN cc_start: 0.8931 (pt0) cc_final: 0.8694 (pp30) REVERT: A 324 GLN cc_start: 0.8806 (mp10) cc_final: 0.8366 (mp10) REVERT: A 397 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: B 149 GLN cc_start: 0.8736 (mt0) cc_final: 0.8451 (mt0) REVERT: B 324 GLN cc_start: 0.8812 (mp10) cc_final: 0.8395 (mp10) REVERT: B 397 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: C 80 GLN cc_start: 0.8953 (pt0) cc_final: 0.8711 (pp30) REVERT: C 101 PHE cc_start: 0.8560 (m-80) cc_final: 0.8355 (m-80) REVERT: C 324 GLN cc_start: 0.8770 (mp10) cc_final: 0.8333 (mp10) REVERT: C 397 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7869 (m-80) REVERT: D 80 GLN cc_start: 0.8930 (pt0) cc_final: 0.8701 (pp30) REVERT: D 105 ASP cc_start: 0.8124 (t0) cc_final: 0.7889 (t0) REVERT: D 324 GLN cc_start: 0.8809 (mp10) cc_final: 0.8408 (mp10) outliers start: 45 outliers final: 31 residues processed: 238 average time/residue: 0.0946 time to fit residues: 36.6384 Evaluate side-chains 239 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 397 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 152 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 126 optimal weight: 50.0000 chunk 157 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 42 optimal weight: 10.0000 chunk 110 optimal weight: 0.6980 chunk 96 optimal weight: 0.0030 chunk 116 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.197220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.140851 restraints weight = 21832.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.134162 restraints weight = 15204.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.134940 restraints weight = 14816.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.136910 restraints weight = 9853.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136712 restraints weight = 8733.118| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14408 Z= 0.108 Angle : 0.503 7.965 19696 Z= 0.262 Chirality : 0.041 0.200 2264 Planarity : 0.003 0.037 2416 Dihedral : 8.492 75.988 2120 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.11 % Favored : 93.67 % Rotamer: Outliers : 2.84 % Allowed : 14.37 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1768 helix: 1.96 (0.16), residues: 1048 sheet: -1.39 (0.54), residues: 96 loop : -1.49 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 322 TYR 0.010 0.001 TYR C 86 PHE 0.021 0.001 PHE B 92 TRP 0.009 0.001 TRP B 230 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (14408) covalent geometry : angle 0.50306 / 0.26 (19696) hydrogen bonds : bond 0.03960 / 2.60 ( 736) hydrogen bonds : angle 3.19540 / 2.23 ( 2172) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.527 Fit side-chains REVERT: A 324 GLN cc_start: 0.8793 (mp10) cc_final: 0.8399 (mp10) REVERT: A 397 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: B 149 GLN cc_start: 0.8691 (mt0) cc_final: 0.8272 (mm-40) REVERT: B 324 GLN cc_start: 0.8834 (mp10) cc_final: 0.8400 (mp10) REVERT: B 397 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: C 324 GLN cc_start: 0.8786 (mp10) cc_final: 0.8338 (mp10) REVERT: C 397 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: D 105 ASP cc_start: 0.8069 (t0) cc_final: 0.7811 (t0) REVERT: D 149 GLN cc_start: 0.8845 (mt0) cc_final: 0.8376 (mm-40) REVERT: D 324 GLN cc_start: 0.8778 (mp10) cc_final: 0.8436 (mp10) outliers start: 38 outliers final: 26 residues processed: 236 average time/residue: 0.0864 time to fit residues: 33.0571 Evaluate side-chains 230 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 397 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 151 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 97 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 76 optimal weight: 40.0000 chunk 9 optimal weight: 5.9990 chunk 170 optimal weight: 40.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.198375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138633 restraints weight = 21611.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.131302 restraints weight = 14887.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.132571 restraints weight = 15257.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.134590 restraints weight = 10260.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134443 restraints weight = 8884.522| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14408 Z= 0.124 Angle : 0.517 8.048 19696 Z= 0.270 Chirality : 0.042 0.192 2264 Planarity : 0.004 0.038 2416 Dihedral : 8.549 75.410 2120 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.39 % Favored : 93.38 % Rotamer: Outliers : 2.62 % Allowed : 14.82 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1768 helix: 1.97 (0.16), residues: 1044 sheet: -1.35 (0.54), residues: 96 loop : -1.49 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 322 TYR 0.012 0.001 TYR A 252 PHE 0.023 0.001 PHE B 92 TRP 0.010 0.001 TRP B 137 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (14408) covalent geometry : angle 0.51663 / 0.27 (19696) hydrogen bonds : bond 0.04314 / 2.81 ( 736) hydrogen bonds : angle 3.19314 / 2.24 ( 2172) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.479 Fit side-chains REVERT: A 324 GLN cc_start: 0.8813 (mp10) cc_final: 0.8324 (mp10) REVERT: A 397 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7530 (m-80) REVERT: B 324 GLN cc_start: 0.8851 (mp10) cc_final: 0.8366 (mp10) REVERT: B 397 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7581 (m-80) REVERT: C 324 GLN cc_start: 0.8812 (mp10) cc_final: 0.8353 (mp10) REVERT: C 397 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: D 105 ASP cc_start: 0.8152 (t0) cc_final: 0.7891 (t0) REVERT: D 324 GLN cc_start: 0.8832 (mp10) cc_final: 0.8357 (mp10) outliers start: 35 outliers final: 28 residues processed: 227 average time/residue: 0.0854 time to fit residues: 31.8953 Evaluate side-chains 229 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 397 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 152 optimal weight: 0.0770 chunk 27 optimal weight: 0.0670 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 168 optimal weight: 50.0000 chunk 7 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.8878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.195042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136499 restraints weight = 21765.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130886 restraints weight = 15848.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.132257 restraints weight = 18569.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.132257 restraints weight = 12996.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.135226 restraints weight = 9942.626| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14408 Z= 0.136 Angle : 0.527 8.023 19696 Z= 0.275 Chirality : 0.042 0.207 2264 Planarity : 0.004 0.039 2416 Dihedral : 8.667 74.505 2120 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.17 % Favored : 93.61 % Rotamer: Outliers : 2.77 % Allowed : 15.42 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.21), residues: 1768 helix: 1.92 (0.16), residues: 1048 sheet: -1.26 (0.55), residues: 96 loop : -1.42 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 322 TYR 0.017 0.001 TYR A 86 PHE 0.023 0.001 PHE B 92 TRP 0.008 0.001 TRP D 137 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (14408) covalent geometry : angle 0.52656 / 0.27 (19696) hydrogen bonds : bond 0.04592 / 3.00 ( 736) hydrogen bonds : angle 3.23078 / 2.27 ( 2172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2328.08 seconds wall clock time: 40 minutes 50.78 seconds (2450.78 seconds total)