Starting phenix.real_space_refine on Mon Sep 14 03:21:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6v1y_21019/09_2026/6v1y_21019.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v1y_21019/09_2026/6v1y_21019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6v1y_21019/09_2026/6v1y_21019.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6v1y_21019/09_2026/6v1y_21019.cif" model { file = "/net/cci-nas-00/data/ceres_data/6v1y_21019/09_2026/6v1y_21019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v1y_21019/09_2026/6v1y_21019.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v1y_21019/09_2026/6v1y_21019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v1y_21019/09_2026/6v1y_21019.map" } resolution = 3.8 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 120 5.16 5 C 18520 2.51 5 N 4552 2.21 5 O 4696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s 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: 27896 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 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': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 180 Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 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': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 180 Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 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': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 180 Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 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': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 180 Chain: "M" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 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': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 180 Chain: "N" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 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': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 180 Chain: "O" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 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': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 180 Chain: "P" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 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': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 180 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} Chain: "M" 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: "N" 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: "O" 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: "P" 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: 5.76, per 1000 atoms: 0.21 Number of scatterers: 27896 At special positions: 0 Unit cell: (115.976, 115.976, 226.632, 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 120 16.00 P 8 15.00 O 4696 8.00 N 4552 7.00 C 18520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 941.6 milliseconds 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6864 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 16 sheets defined 63.5% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 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 helix chain 'M' and resid 56 through 83 removed outlier: 3.659A pdb=" N ARG M 60 " --> pdb=" O ASN M 56 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA M 61 " --> pdb=" O PRO M 57 " (cutoff:3.500A) Proline residue: M 78 - end of helix Processing helix chain 'M' and resid 91 through 109 removed outlier: 3.675A pdb=" N ILE M 107 " --> pdb=" O ALA M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 137 Processing helix chain 'M' and resid 137 through 146 removed outlier: 3.572A pdb=" N ASP M 141 " --> pdb=" O TRP M 137 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA M 146 " --> pdb=" O VAL M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 148 through 156 removed outlier: 3.853A pdb=" N ASN M 156 " --> pdb=" O SER M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 167 removed outlier: 3.768A pdb=" N LEU M 167 " --> pdb=" O GLY M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 174 removed outlier: 3.572A pdb=" N LEU M 172 " --> pdb=" O MET M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 188 removed outlier: 3.827A pdb=" N SER M 179 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU M 186 " --> pdb=" O PHE M 182 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS M 187 " --> pdb=" O ALA M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 222 removed outlier: 3.542A pdb=" N ARG M 197 " --> pdb=" O TYR M 193 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N CYS M 198 " --> pdb=" O PHE M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 259 removed outlier: 3.813A pdb=" N ARG M 246 " --> pdb=" O SER M 242 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR M 257 " --> pdb=" O TRP M 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 303 removed outlier: 3.957A pdb=" N ILE M 278 " --> pdb=" O MET M 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE M 279 " --> pdb=" O LEU M 275 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR M 303 " --> pdb=" O VAL M 299 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 324 removed outlier: 3.661A pdb=" N ASN M 323 " --> pdb=" O PHE M 319 " (cutoff:3.500A) Processing helix chain 'M' and resid 327 through 343 removed outlier: 3.821A pdb=" N THR M 343 " --> pdb=" O LEU M 339 " (cutoff:3.500A) Processing helix chain 'M' and resid 344 through 354 removed outlier: 3.714A pdb=" N GLN M 348 " --> pdb=" O GLU M 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 373 removed outlier: 3.765A pdb=" N PHE M 369 " --> pdb=" O ASN M 365 " (cutoff:3.500A) Proline residue: M 370 - end of helix Processing helix chain 'M' and resid 383 through 391 removed outlier: 4.172A pdb=" N GLN M 388 " --> pdb=" O ASN M 384 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER M 391 " --> pdb=" O PHE M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 471 through 478 Processing helix chain 'M' and resid 484 through 498 removed outlier: 3.857A pdb=" N VAL M 488 " --> pdb=" O ASP M 484 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG M 498 " --> pdb=" O PHE M 494 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 83 removed outlier: 3.657A pdb=" N ARG N 60 " --> pdb=" O ASN N 56 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA N 61 " --> pdb=" O PRO N 57 " (cutoff:3.500A) Proline residue: N 78 - end of helix Processing helix chain 'N' and resid 91 through 109 removed outlier: 3.676A pdb=" N ILE N 107 " --> pdb=" O ALA N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 137 Processing helix chain 'N' and resid 137 through 146 removed outlier: 3.573A pdb=" N ASP N 141 " --> pdb=" O TRP N 137 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA N 146 " --> pdb=" O VAL N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 156 removed outlier: 3.853A pdb=" N ASN N 156 " --> pdb=" O SER N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 167 removed outlier: 3.768A pdb=" N LEU N 167 " --> pdb=" O GLY N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 174 removed outlier: 3.571A pdb=" N LEU N 172 " --> pdb=" O MET N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 188 removed outlier: 3.827A pdb=" N SER N 179 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU N 186 " --> pdb=" O PHE N 182 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS N 187 " --> pdb=" O ALA N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 222 removed outlier: 3.542A pdb=" N ARG N 197 " --> pdb=" O TYR N 193 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS N 198 " --> pdb=" O PHE N 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 242 through 259 removed outlier: 3.813A pdb=" N ARG N 246 " --> pdb=" O SER N 242 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR N 257 " --> pdb=" O TRP N 253 " (cutoff:3.500A) Processing helix chain 'N' and resid 270 through 303 removed outlier: 3.957A pdb=" N ILE N 278 " --> pdb=" O MET N 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE N 279 " --> pdb=" O LEU N 275 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR N 303 " --> pdb=" O VAL N 299 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 324 removed outlier: 3.662A pdb=" N ASN N 323 " --> pdb=" O PHE N 319 " (cutoff:3.500A) Processing helix chain 'N' and resid 327 through 343 removed outlier: 3.821A pdb=" N THR N 343 " --> pdb=" O LEU N 339 " (cutoff:3.500A) Processing helix chain 'N' and resid 344 through 354 removed outlier: 3.713A pdb=" N GLN N 348 " --> pdb=" O GLU N 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 373 removed outlier: 3.764A pdb=" N PHE N 369 " --> pdb=" O ASN N 365 " (cutoff:3.500A) Proline residue: N 370 - end of helix Processing helix chain 'N' and resid 383 through 391 removed outlier: 4.172A pdb=" N GLN N 388 " --> pdb=" O ASN N 384 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER N 391 " --> pdb=" O PHE N 387 " (cutoff:3.500A) Processing helix chain 'N' and resid 471 through 478 Processing helix chain 'N' and resid 484 through 498 removed outlier: 3.857A pdb=" N VAL N 488 " --> pdb=" O ASP N 484 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG N 498 " --> pdb=" O PHE N 494 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 83 removed outlier: 3.659A pdb=" N ARG O 60 " --> pdb=" O ASN O 56 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA O 61 " --> pdb=" O PRO O 57 " (cutoff:3.500A) Proline residue: O 78 - end of helix Processing helix chain 'O' and resid 91 through 109 removed outlier: 3.675A pdb=" N ILE O 107 " --> pdb=" O ALA O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 137 Processing helix chain 'O' and resid 137 through 146 removed outlier: 3.572A pdb=" N ASP O 141 " --> pdb=" O TRP O 137 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA O 146 " --> pdb=" O VAL O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 156 removed outlier: 3.853A pdb=" N ASN O 156 " --> pdb=" O SER O 152 " (cutoff:3.500A) Processing helix chain 'O' and resid 162 through 167 removed outlier: 3.768A pdb=" N LEU O 167 " --> pdb=" O GLY O 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 174 removed outlier: 3.571A pdb=" N LEU O 172 " --> pdb=" O MET O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 175 through 188 removed outlier: 3.827A pdb=" N SER O 179 " --> pdb=" O LEU O 175 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU O 186 " --> pdb=" O PHE O 182 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS O 187 " --> pdb=" O ALA O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 222 removed outlier: 3.542A pdb=" N ARG O 197 " --> pdb=" O TYR O 193 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS O 198 " --> pdb=" O PHE O 194 " (cutoff:3.500A) Processing helix chain 'O' and resid 242 through 259 removed outlier: 3.812A pdb=" N ARG O 246 " --> pdb=" O SER O 242 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR O 257 " --> pdb=" O TRP O 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 303 removed outlier: 3.957A pdb=" N ILE O 278 " --> pdb=" O MET O 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE O 279 " --> pdb=" O LEU O 275 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR O 303 " --> pdb=" O VAL O 299 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 324 removed outlier: 3.661A pdb=" N ASN O 323 " --> pdb=" O PHE O 319 " (cutoff:3.500A) Processing helix chain 'O' and resid 327 through 343 removed outlier: 3.820A pdb=" N THR O 343 " --> pdb=" O LEU O 339 " (cutoff:3.500A) Processing helix chain 'O' and resid 344 through 354 removed outlier: 3.714A pdb=" N GLN O 348 " --> pdb=" O GLU O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 373 removed outlier: 3.765A pdb=" N PHE O 369 " --> pdb=" O ASN O 365 " (cutoff:3.500A) Proline residue: O 370 - end of helix Processing helix chain 'O' and resid 383 through 391 removed outlier: 4.172A pdb=" N GLN O 388 " --> pdb=" O ASN O 384 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER O 391 " --> pdb=" O PHE O 387 " (cutoff:3.500A) Processing helix chain 'O' and resid 471 through 478 Processing helix chain 'O' and resid 484 through 498 removed outlier: 3.856A pdb=" N VAL O 488 " --> pdb=" O ASP O 484 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG O 498 " --> pdb=" O PHE O 494 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 83 removed outlier: 3.659A pdb=" N ARG P 60 " --> pdb=" O ASN P 56 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA P 61 " --> pdb=" O PRO P 57 " (cutoff:3.500A) Proline residue: P 78 - end of helix Processing helix chain 'P' and resid 91 through 109 removed outlier: 3.675A pdb=" N ILE P 107 " --> pdb=" O ALA P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 137 Processing helix chain 'P' and resid 137 through 146 removed outlier: 3.572A pdb=" N ASP P 141 " --> pdb=" O TRP P 137 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA P 146 " --> pdb=" O VAL P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 148 through 156 removed outlier: 3.854A pdb=" N ASN P 156 " --> pdb=" O SER P 152 " (cutoff:3.500A) Processing helix chain 'P' and resid 162 through 167 removed outlier: 3.768A pdb=" N LEU P 167 " --> pdb=" O GLY P 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 174 removed outlier: 3.572A pdb=" N LEU P 172 " --> pdb=" O MET P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 188 removed outlier: 3.827A pdb=" N SER P 179 " --> pdb=" O LEU P 175 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 222 removed outlier: 3.542A pdb=" N ARG P 197 " --> pdb=" O TYR P 193 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N CYS P 198 " --> pdb=" O PHE P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 259 removed outlier: 3.813A pdb=" N ARG P 246 " --> pdb=" O SER P 242 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR P 257 " --> pdb=" O TRP P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 303 removed outlier: 3.956A pdb=" N ILE P 278 " --> pdb=" O MET P 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE P 279 " --> pdb=" O LEU P 275 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR P 303 " --> pdb=" O VAL P 299 " (cutoff:3.500A) Processing helix chain 'P' and resid 304 through 324 removed outlier: 3.661A pdb=" N ASN P 323 " --> pdb=" O PHE P 319 " (cutoff:3.500A) Processing helix chain 'P' and resid 327 through 343 removed outlier: 3.821A pdb=" N THR P 343 " --> pdb=" O LEU P 339 " (cutoff:3.500A) Processing helix chain 'P' and resid 344 through 354 removed outlier: 3.715A pdb=" N GLN P 348 " --> pdb=" O GLU P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 358 through 373 removed outlier: 3.766A pdb=" N PHE P 369 " --> pdb=" O ASN P 365 " (cutoff:3.500A) Proline residue: P 370 - end of helix Processing helix chain 'P' and resid 383 through 391 removed outlier: 4.172A pdb=" N GLN P 388 " --> pdb=" O ASN P 384 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER P 391 " --> pdb=" O PHE P 387 " (cutoff:3.500A) Processing helix chain 'P' and resid 471 through 478 Processing helix chain 'P' and resid 484 through 498 removed outlier: 3.856A pdb=" N VAL P 488 " --> pdb=" O ASP P 484 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG P 498 " --> pdb=" O PHE P 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) Processing sheet with id=AA9, first strand: chain 'M' and resid 403 through 405 removed outlier: 6.451A pdb=" N VAL M 459 " --> pdb=" O ILE M 404 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL M 422 " --> pdb=" O ALA M 438 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA M 438 " --> pdb=" O VAL M 422 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 416 through 417 removed outlier: 3.597A pdb=" N ILE M 416 " --> pdb=" O LEU M 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 403 through 405 removed outlier: 6.451A pdb=" N VAL N 459 " --> pdb=" O ILE N 404 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL N 422 " --> pdb=" O ALA N 438 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA N 438 " --> pdb=" O VAL N 422 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 416 through 417 removed outlier: 3.596A pdb=" N ILE N 416 " --> pdb=" O LEU N 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 403 through 405 removed outlier: 6.451A pdb=" N VAL O 459 " --> pdb=" O ILE O 404 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL O 422 " --> pdb=" O ALA O 438 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA O 438 " --> pdb=" O VAL O 422 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 416 through 417 removed outlier: 3.597A pdb=" N ILE O 416 " --> pdb=" O LEU O 468 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 403 through 405 removed outlier: 6.451A pdb=" N VAL P 459 " --> pdb=" O ILE P 404 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL P 422 " --> pdb=" O ALA P 438 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA P 438 " --> pdb=" O VAL P 422 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 416 through 417 removed outlier: 3.596A pdb=" N ILE P 416 " --> pdb=" O LEU P 468 " (cutoff:3.500A) 1472 hydrogen bonds defined for protein. 4344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.59 Time building geometry restraints manager: 2.82 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: 4048 1.29 - 1.42: 8455 1.42 - 1.55: 15953 1.55 - 1.67: 64 1.67 - 1.80: 192 Bond restraints: 28712 Sorted by residual: bond pdb=" C PRO O 150 " pdb=" N LEU O 151 " ideal model delta sigma weight residual 1.334 1.497 -0.162 1.43e-02 4.89e+03 1.29e+02 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 N 150 " pdb=" N LEU N 151 " ideal model delta sigma weight residual 1.334 1.496 -0.162 1.43e-02 4.89e+03 1.28e+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 ... (remaining 28707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 36502 2.20 - 4.41: 2203 4.41 - 6.61: 440 6.61 - 8.82: 79 8.82 - 11.02: 40 Bond angle restraints: 39264 Sorted by residual: angle pdb=" C THR N 259 " pdb=" N THR N 260 " pdb=" CA THR N 260 " ideal model delta sigma weight residual 121.54 130.11 -8.57 1.91e+00 2.74e-01 2.02e+01 angle pdb=" C THR O 259 " pdb=" N THR O 260 " pdb=" CA THR O 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 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 P 259 " pdb=" N THR P 260 " pdb=" CA THR P 260 " ideal model delta sigma weight residual 121.54 130.10 -8.56 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 ... (remaining 39259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 15335 15.59 - 31.18: 937 31.18 - 46.76: 176 46.76 - 62.35: 48 62.35 - 77.94: 16 Dihedral angle restraints: 16512 sinusoidal: 5928 harmonic: 10584 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 N 125 " pdb=" C SER N 125 " pdb=" N PRO N 126 " pdb=" CA PRO N 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 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 ... (remaining 16509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3767 0.084 - 0.168: 642 0.168 - 0.253: 71 0.253 - 0.337: 32 0.337 - 0.421: 8 Chirality restraints: 4520 Sorted by residual: chirality pdb=" C10 QNJ O 601 " pdb=" C1 QNJ O 601 " pdb=" C5 QNJ O 601 " pdb=" C9 QNJ O 601 " both_signs ideal model delta sigma weight residual False -2.91 -2.49 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" C10 QNJ N 602 " pdb=" C1 QNJ N 602 " pdb=" C5 QNJ N 602 " pdb=" C9 QNJ N 602 " both_signs ideal model delta sigma weight residual False -2.91 -2.49 -0.42 2.00e-01 2.50e+01 4.38e+00 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 ... (remaining 4517 not shown) Planarity restraints: 4824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL O 439 " -0.015 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C VAL O 439 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL O 439 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE O 440 " -0.019 2.00e-02 2.50e+03 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 P 439 " -0.015 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C VAL P 439 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL P 439 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE P 440 " -0.018 2.00e-02 2.50e+03 ... (remaining 4821 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7689 2.80 - 3.33: 25765 3.33 - 3.85: 43301 3.85 - 4.38: 46624 4.38 - 4.90: 82285 Nonbonded interactions: 205664 Sorted by model distance: nonbonded pdb=" O ALA N 358 " pdb=" OG SER N 361 " model vdw 2.278 3.040 nonbonded pdb=" O ALA B 358 " pdb=" OG SER B 361 " model vdw 2.279 3.040 nonbonded pdb=" O ALA O 358 " pdb=" OG SER O 361 " model vdw 2.280 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 ... (remaining 205659 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) selection = (chain 'M' and resid 50 through 498) selection = (chain 'N' and resid 50 through 498) selection = (chain 'O' and resid 50 through 498) selection = (chain 'P' 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: 2.590 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: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.010 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 28712 Z= 0.542 Angle : 1.238 11.023 39264 Z= 0.663 Chirality : 0.069 0.421 4520 Planarity : 0.008 0.060 4824 Dihedral : 11.440 77.940 9648 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.50 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: -3.80 (0.12), residues: 3536 helix: -2.08 (0.09), residues: 2000 sheet: -2.22 (0.36), residues: 192 loop : -3.08 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 322 TYR 0.035 0.003 TYR A 223 PHE 0.025 0.003 PHE M 92 TRP 0.026 0.004 TRP O 75 HIS 0.014 0.003 HIS P 301 Details of bonding type rmsd/Z covalent geometry : bond 0.01104 / 0.54 (28712) covalent geometry : angle 1.23844 / 0.66 (39264) hydrogen bonds : bond 0.14972 / 9.74 ( 1472) hydrogen bonds : angle 5.82986 / 4.09 ( 4344) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 743 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 TRP cc_start: 0.8428 (t-100) cc_final: 0.8071 (t60) REVERT: A 301 HIS cc_start: 0.7388 (t70) cc_final: 0.7178 (t-90) REVERT: B 58 ARG cc_start: 0.5432 (tpt170) cc_final: 0.5195 (tmt170) REVERT: B 173 TRP cc_start: 0.8454 (t-100) cc_final: 0.8021 (t60) REVERT: C 173 TRP cc_start: 0.8425 (t-100) cc_final: 0.8065 (t60) REVERT: C 301 HIS cc_start: 0.7418 (t70) cc_final: 0.7175 (t-90) REVERT: D 173 TRP cc_start: 0.8431 (t-100) cc_final: 0.8067 (t60) REVERT: D 301 HIS cc_start: 0.7410 (t70) cc_final: 0.7169 (t-90) REVERT: M 58 ARG cc_start: 0.6097 (tpt170) cc_final: 0.5476 (tmt170) REVERT: M 95 ASP cc_start: 0.8222 (m-30) cc_final: 0.7870 (t0) REVERT: M 302 TRP cc_start: 0.7894 (t-100) cc_final: 0.7679 (t60) REVERT: N 58 ARG cc_start: 0.6078 (tpt170) cc_final: 0.5467 (tmt170) REVERT: N 96 ASN cc_start: 0.8428 (m-40) cc_final: 0.8110 (m110) REVERT: N 302 TRP cc_start: 0.7943 (t-100) cc_final: 0.7719 (t60) REVERT: N 476 MET cc_start: 0.7270 (mmm) cc_final: 0.7028 (mmm) REVERT: O 58 ARG cc_start: 0.6082 (tpt170) cc_final: 0.5430 (tmt170) REVERT: O 95 ASP cc_start: 0.8227 (m-30) cc_final: 0.7946 (t0) REVERT: O 133 TYR cc_start: 0.8290 (t80) cc_final: 0.8083 (t80) REVERT: O 302 TRP cc_start: 0.7912 (t-100) cc_final: 0.7705 (t60) REVERT: P 58 ARG cc_start: 0.6072 (tpt170) cc_final: 0.5458 (tmt170) REVERT: P 95 ASP cc_start: 0.8230 (m-30) cc_final: 0.7879 (t0) REVERT: P 302 TRP cc_start: 0.7903 (t-100) cc_final: 0.7703 (t60) outliers start: 0 outliers final: 0 residues processed: 743 average time/residue: 0.1831 time to fit residues: 212.7188 Evaluate side-chains 441 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 ASN A 99 ASN A 149 GLN B 56 ASN B 99 ASN B 332 GLN C 56 ASN C 99 ASN D 56 ASN D 99 ASN D 149 GLN M 56 ASN M 332 GLN N 56 ASN N 332 GLN O 56 ASN ** O 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 332 GLN P 56 ASN P 332 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.122697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099358 restraints weight = 58652.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.102013 restraints weight = 33261.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.103668 restraints weight = 23309.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.104550 restraints weight = 18772.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.105357 restraints weight = 16586.169| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28712 Z= 0.146 Angle : 0.652 6.796 39264 Z= 0.346 Chirality : 0.043 0.159 4520 Planarity : 0.005 0.041 4824 Dihedral : 10.346 71.422 4240 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.30 % Favored : 92.48 % Rotamer: Outliers : 3.74 % Allowed : 10.08 % Favored : 86.18 % 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: -1.62 (0.14), residues: 3536 helix: -0.03 (0.11), residues: 2088 sheet: -2.49 (0.33), residues: 192 loop : -2.58 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 314 TYR 0.030 0.002 TYR P 376 PHE 0.017 0.001 PHE B 148 TRP 0.019 0.002 TRP A 253 HIS 0.004 0.001 HIS N 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (28712) covalent geometry : angle 0.65187 / 0.35 (39264) hydrogen bonds : bond 0.05072 / 3.30 ( 1472) hydrogen bonds : angle 3.93713 / 2.80 ( 4344) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 498 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.7316 (mmm) cc_final: 0.6850 (mmt) REVERT: A 105 ASP cc_start: 0.7759 (t0) cc_final: 0.7413 (t70) REVERT: A 143 CYS cc_start: 0.8277 (m) cc_final: 0.7997 (m) REVERT: A 148 PHE cc_start: 0.7147 (m-10) cc_final: 0.6887 (m-80) REVERT: A 295 MET cc_start: 0.8358 (mmt) cc_final: 0.8071 (mmt) REVERT: B 58 ARG cc_start: 0.5428 (tpt170) cc_final: 0.5078 (tmt170) REVERT: B 64 MET cc_start: 0.7332 (mmm) cc_final: 0.6936 (mmt) REVERT: B 105 ASP cc_start: 0.7808 (t0) cc_final: 0.7439 (t0) REVERT: B 148 PHE cc_start: 0.7334 (m-10) cc_final: 0.7086 (m-80) REVERT: B 295 MET cc_start: 0.8351 (mmt) cc_final: 0.8093 (mmt) REVERT: B 397 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: B 415 TYR cc_start: 0.6913 (m-10) cc_final: 0.6548 (m-10) REVERT: C 64 MET cc_start: 0.7326 (mmm) cc_final: 0.6849 (mmt) REVERT: C 105 ASP cc_start: 0.7747 (t0) cc_final: 0.7407 (t70) REVERT: C 143 CYS cc_start: 0.8286 (m) cc_final: 0.7993 (m) REVERT: C 148 PHE cc_start: 0.7151 (m-10) cc_final: 0.6885 (m-80) REVERT: C 295 MET cc_start: 0.8362 (mmt) cc_final: 0.8070 (mmt) REVERT: D 64 MET cc_start: 0.7324 (mmm) cc_final: 0.6845 (mmt) REVERT: D 105 ASP cc_start: 0.7742 (t0) cc_final: 0.7403 (t70) REVERT: D 143 CYS cc_start: 0.8269 (m) cc_final: 0.7983 (m) REVERT: D 148 PHE cc_start: 0.7135 (m-10) cc_final: 0.6880 (m-80) REVERT: D 295 MET cc_start: 0.8364 (mmt) cc_final: 0.8065 (mmt) REVERT: M 58 ARG cc_start: 0.6539 (tpt170) cc_final: 0.5585 (ttt-90) REVERT: M 96 ASN cc_start: 0.8537 (m-40) cc_final: 0.8232 (m110) REVERT: M 149 GLN cc_start: 0.8234 (pt0) cc_final: 0.7719 (mm-40) REVERT: M 153 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7892 (pp) REVERT: M 173 TRP cc_start: 0.8604 (t-100) cc_final: 0.8355 (t-100) REVERT: M 479 MET cc_start: 0.7107 (ppp) cc_final: 0.6695 (mmm) REVERT: N 58 ARG cc_start: 0.6469 (tpt170) cc_final: 0.5564 (ttt-90) REVERT: N 96 ASN cc_start: 0.8584 (m-40) cc_final: 0.8235 (m110) REVERT: N 149 GLN cc_start: 0.8366 (pt0) cc_final: 0.7716 (mm110) REVERT: N 173 TRP cc_start: 0.8631 (t-100) cc_final: 0.8385 (t-100) REVERT: O 58 ARG cc_start: 0.6411 (tpt170) cc_final: 0.5498 (ttt-90) REVERT: O 96 ASN cc_start: 0.8573 (m-40) cc_final: 0.8264 (m110) REVERT: O 153 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7848 (pp) REVERT: O 173 TRP cc_start: 0.8604 (t-100) cc_final: 0.8378 (t-100) REVERT: P 58 ARG cc_start: 0.6503 (tpt170) cc_final: 0.5555 (ttt-90) REVERT: P 96 ASN cc_start: 0.8549 (m-40) cc_final: 0.8192 (m110) REVERT: P 149 GLN cc_start: 0.8248 (pt0) cc_final: 0.7748 (mm-40) REVERT: P 153 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7886 (pp) REVERT: P 173 TRP cc_start: 0.8609 (t-100) cc_final: 0.8362 (t-100) outliers start: 99 outliers final: 50 residues processed: 563 average time/residue: 0.1604 time to fit residues: 149.9446 Evaluate side-chains 473 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 419 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 327 HIS Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 381 VAL Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 327 HIS Chi-restraints excluded: chain N residue 381 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain O residue 109 THR Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 153 LEU Chi-restraints excluded: chain O residue 327 HIS Chi-restraints excluded: chain O residue 381 VAL Chi-restraints excluded: chain P residue 80 GLN Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 327 HIS Chi-restraints excluded: chain P residue 381 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 275 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 192 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 302 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 455 GLN N 455 GLN ** O 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.118680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.094750 restraints weight = 59161.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097587 restraints weight = 31549.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099356 restraints weight = 21541.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100472 restraints weight = 17130.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.100912 restraints weight = 14947.737| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28712 Z= 0.168 Angle : 0.641 7.675 39264 Z= 0.337 Chirality : 0.043 0.149 4520 Planarity : 0.004 0.046 4824 Dihedral : 9.706 75.969 4240 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.75 % Favored : 92.02 % Rotamer: Outliers : 3.85 % Allowed : 12.80 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3536 helix: 0.77 (0.11), residues: 2104 sheet: -2.41 (0.34), residues: 192 loop : -2.20 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 165 TYR 0.026 0.002 TYR P 376 PHE 0.014 0.001 PHE N 92 TRP 0.015 0.002 TRP B 173 HIS 0.005 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (28712) covalent geometry : angle 0.64145 / 0.34 (39264) hydrogen bonds : bond 0.05136 / 3.32 ( 1472) hydrogen bonds : angle 3.65516 / 2.61 ( 4344) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 473 time to evaluate : 0.996 Fit side-chains REVERT: A 143 CYS cc_start: 0.8345 (m) cc_final: 0.8108 (m) REVERT: A 148 PHE cc_start: 0.7427 (m-10) cc_final: 0.7023 (m-10) REVERT: A 215 PHE cc_start: 0.8574 (t80) cc_final: 0.8280 (t80) REVERT: A 295 MET cc_start: 0.8400 (mmt) cc_final: 0.8143 (mmt) REVERT: A 327 HIS cc_start: 0.6013 (OUTLIER) cc_final: 0.5666 (t70) REVERT: A 342 LYS cc_start: 0.7955 (mptt) cc_final: 0.7688 (mptt) REVERT: B 58 ARG cc_start: 0.5555 (tpt170) cc_final: 0.5105 (tmt170) REVERT: B 148 PHE cc_start: 0.7429 (m-10) cc_final: 0.6934 (m-10) REVERT: B 295 MET cc_start: 0.8422 (mmt) cc_final: 0.8168 (mmt) REVERT: B 333 MET cc_start: 0.8919 (mtm) cc_final: 0.8719 (mtp) REVERT: B 397 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8478 (m-80) REVERT: B 415 TYR cc_start: 0.7019 (m-10) cc_final: 0.6508 (m-10) REVERT: C 143 CYS cc_start: 0.8352 (m) cc_final: 0.8114 (m) REVERT: C 148 PHE cc_start: 0.7415 (m-10) cc_final: 0.7008 (m-10) REVERT: C 215 PHE cc_start: 0.8566 (t80) cc_final: 0.8274 (t80) REVERT: C 295 MET cc_start: 0.8400 (mmt) cc_final: 0.8147 (mmt) REVERT: C 327 HIS cc_start: 0.5996 (OUTLIER) cc_final: 0.5675 (t70) REVERT: C 342 LYS cc_start: 0.7946 (mptt) cc_final: 0.7684 (mptt) REVERT: D 143 CYS cc_start: 0.8345 (m) cc_final: 0.8109 (m) REVERT: D 148 PHE cc_start: 0.7419 (m-10) cc_final: 0.7019 (m-10) REVERT: D 215 PHE cc_start: 0.8569 (t80) cc_final: 0.8273 (t80) REVERT: D 295 MET cc_start: 0.8400 (mmt) cc_final: 0.8138 (mmt) REVERT: D 324 GLN cc_start: 0.9031 (mp10) cc_final: 0.8593 (mp10) REVERT: D 327 HIS cc_start: 0.5966 (OUTLIER) cc_final: 0.5650 (t70) REVERT: D 342 LYS cc_start: 0.7951 (mptt) cc_final: 0.7684 (mptt) REVERT: M 58 ARG cc_start: 0.6688 (tpt170) cc_final: 0.5490 (tmt170) REVERT: M 96 ASN cc_start: 0.8720 (m-40) cc_final: 0.8409 (m110) REVERT: M 149 GLN cc_start: 0.8307 (pt0) cc_final: 0.7827 (mm-40) REVERT: M 311 ASP cc_start: 0.8201 (t0) cc_final: 0.7936 (t0) REVERT: M 479 MET cc_start: 0.7027 (ppp) cc_final: 0.6579 (mmm) REVERT: N 58 ARG cc_start: 0.6677 (tpt170) cc_final: 0.5496 (tmt170) REVERT: N 96 ASN cc_start: 0.8652 (m-40) cc_final: 0.8352 (m110) REVERT: N 149 GLN cc_start: 0.8352 (pt0) cc_final: 0.7560 (mm110) REVERT: N 153 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7772 (pp) REVERT: O 58 ARG cc_start: 0.6585 (tpt170) cc_final: 0.5435 (tmt170) REVERT: O 96 ASN cc_start: 0.8760 (m-40) cc_final: 0.8424 (m110) REVERT: O 270 ASN cc_start: 0.8366 (t0) cc_final: 0.8092 (m-40) REVERT: O 311 ASP cc_start: 0.8212 (t0) cc_final: 0.7931 (t0) REVERT: P 58 ARG cc_start: 0.6644 (tpt170) cc_final: 0.5469 (tmt170) REVERT: P 96 ASN cc_start: 0.8682 (m-40) cc_final: 0.8365 (m110) REVERT: P 149 GLN cc_start: 0.8243 (pt0) cc_final: 0.7843 (mm-40) REVERT: P 270 ASN cc_start: 0.8327 (t0) cc_final: 0.8105 (m-40) outliers start: 102 outliers final: 78 residues processed: 540 average time/residue: 0.1749 time to fit residues: 153.5623 Evaluate side-chains 493 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 410 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 299 VAL Chi-restraints excluded: chain M residue 327 HIS Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 381 VAL Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 296 THR Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 327 HIS Chi-restraints excluded: chain N residue 381 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 296 THR Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 327 HIS Chi-restraints excluded: chain O residue 339 LEU Chi-restraints excluded: chain O residue 376 TYR Chi-restraints excluded: chain O residue 381 VAL Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain P residue 80 GLN Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 296 THR Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 327 HIS Chi-restraints excluded: chain P residue 339 LEU Chi-restraints excluded: chain P residue 376 TYR Chi-restraints excluded: chain P residue 381 VAL Chi-restraints excluded: chain P residue 473 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 212 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 51 optimal weight: 0.0040 chunk 296 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 215 optimal weight: 0.0980 chunk 207 optimal weight: 1.9990 chunk 272 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 285 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 270 ASN M 349 GLN N 270 ASN N 284 ASN O 149 GLN O 349 GLN P 349 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.122120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098896 restraints weight = 58838.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.101829 restraints weight = 30724.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.103674 restraints weight = 20568.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.104814 restraints weight = 16168.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.105287 restraints weight = 14044.319| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 28712 Z= 0.110 Angle : 0.564 10.069 39264 Z= 0.293 Chirality : 0.041 0.160 4520 Planarity : 0.004 0.041 4824 Dihedral : 8.939 78.655 4240 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.73 % Favored : 93.04 % Rotamer: Outliers : 2.72 % Allowed : 15.45 % Favored : 81.84 % 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: -0.00 (0.15), residues: 3536 helix: 1.33 (0.11), residues: 2104 sheet: -2.25 (0.34), residues: 192 loop : -2.01 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 314 TYR 0.024 0.001 TYR B 376 PHE 0.012 0.001 PHE P 138 TRP 0.019 0.001 TRP O 75 HIS 0.004 0.001 HIS N 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (28712) covalent geometry : angle 0.56405 / 0.29 (39264) hydrogen bonds : bond 0.03844 / 2.49 ( 1472) hydrogen bonds : angle 3.27239 / 2.34 ( 4344) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 473 time to evaluate : 1.095 Fit side-chains REVERT: A 143 CYS cc_start: 0.8275 (m) cc_final: 0.7944 (m) REVERT: A 148 PHE cc_start: 0.7490 (m-80) cc_final: 0.7136 (m-80) REVERT: A 327 HIS cc_start: 0.5889 (OUTLIER) cc_final: 0.5551 (t70) REVERT: A 331 ASP cc_start: 0.8211 (m-30) cc_final: 0.7923 (m-30) REVERT: A 397 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8294 (m-80) REVERT: B 58 ARG cc_start: 0.5251 (tpt170) cc_final: 0.4732 (tmt170) REVERT: B 148 PHE cc_start: 0.7439 (m-80) cc_final: 0.7097 (m-80) REVERT: B 397 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.8322 (m-80) REVERT: B 415 TYR cc_start: 0.6882 (m-10) cc_final: 0.6385 (m-10) REVERT: B 476 MET cc_start: 0.7737 (mmm) cc_final: 0.7447 (mmm) REVERT: C 143 CYS cc_start: 0.8278 (m) cc_final: 0.7950 (m) REVERT: C 148 PHE cc_start: 0.7498 (m-80) cc_final: 0.7148 (m-80) REVERT: C 277 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8738 (m-30) REVERT: C 327 HIS cc_start: 0.5893 (OUTLIER) cc_final: 0.5549 (t70) REVERT: C 331 ASP cc_start: 0.8201 (m-30) cc_final: 0.7913 (m-30) REVERT: C 397 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8289 (m-80) REVERT: D 143 CYS cc_start: 0.8266 (m) cc_final: 0.7936 (m) REVERT: D 148 PHE cc_start: 0.7480 (m-80) cc_final: 0.7138 (m-80) REVERT: D 277 ASP cc_start: 0.8965 (OUTLIER) cc_final: 0.8745 (m-30) REVERT: D 327 HIS cc_start: 0.5930 (OUTLIER) cc_final: 0.5517 (t70) REVERT: D 331 ASP cc_start: 0.8255 (m-30) cc_final: 0.7993 (m-30) REVERT: D 397 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: M 58 ARG cc_start: 0.6647 (tpt170) cc_final: 0.5467 (tmt170) REVERT: M 75 TRP cc_start: 0.7892 (t60) cc_final: 0.7386 (t60) REVERT: M 96 ASN cc_start: 0.8623 (m-40) cc_final: 0.8307 (m110) REVERT: M 149 GLN cc_start: 0.8307 (pt0) cc_final: 0.7795 (mm-40) REVERT: M 153 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7966 (pp) REVERT: M 295 MET cc_start: 0.8321 (mmt) cc_final: 0.8099 (mmt) REVERT: M 311 ASP cc_start: 0.8152 (t0) cc_final: 0.7817 (t0) REVERT: M 479 MET cc_start: 0.7021 (ppp) cc_final: 0.6608 (mmm) REVERT: N 58 ARG cc_start: 0.6648 (tpt170) cc_final: 0.5479 (tmt170) REVERT: N 75 TRP cc_start: 0.7992 (t60) cc_final: 0.7424 (t60) REVERT: N 96 ASN cc_start: 0.8590 (m-40) cc_final: 0.8329 (m110) REVERT: N 149 GLN cc_start: 0.8295 (pt0) cc_final: 0.7646 (mm110) REVERT: N 153 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7794 (pp) REVERT: N 295 MET cc_start: 0.8315 (mmt) cc_final: 0.8113 (mmt) REVERT: O 58 ARG cc_start: 0.6671 (tpt170) cc_final: 0.5498 (tmt170) REVERT: O 75 TRP cc_start: 0.7914 (t60) cc_final: 0.7407 (t60) REVERT: O 96 ASN cc_start: 0.8735 (m-40) cc_final: 0.8442 (m110) REVERT: O 295 MET cc_start: 0.8310 (mmt) cc_final: 0.8103 (mmt) REVERT: O 311 ASP cc_start: 0.8162 (t0) cc_final: 0.7803 (t0) REVERT: P 58 ARG cc_start: 0.6634 (tpt170) cc_final: 0.5463 (tmt170) REVERT: P 75 TRP cc_start: 0.7925 (t60) cc_final: 0.7384 (t60) REVERT: P 96 ASN cc_start: 0.8573 (m-40) cc_final: 0.8258 (m110) REVERT: P 149 GLN cc_start: 0.8338 (pt0) cc_final: 0.7850 (mm-40) REVERT: P 153 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8037 (pp) REVERT: P 295 MET cc_start: 0.8317 (mmt) cc_final: 0.8113 (mmt) outliers start: 72 outliers final: 39 residues processed: 517 average time/residue: 0.1716 time to fit residues: 145.7901 Evaluate side-chains 475 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 424 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 327 HIS Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 381 VAL Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 327 HIS Chi-restraints excluded: chain N residue 339 LEU Chi-restraints excluded: chain N residue 381 VAL Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 327 HIS Chi-restraints excluded: chain O residue 381 VAL Chi-restraints excluded: chain P residue 80 GLN Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 327 HIS Chi-restraints excluded: chain P residue 381 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 239 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 250 optimal weight: 0.7980 chunk 344 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 319 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 225 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN C 330 GLN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 210 HIS O 270 ASN P 270 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.120211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096729 restraints weight = 58513.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099566 restraints weight = 30934.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.101406 restraints weight = 20914.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.102420 restraints weight = 16590.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.103172 restraints weight = 14527.835| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 28712 Z= 0.120 Angle : 0.565 6.815 39264 Z= 0.296 Chirality : 0.042 0.144 4520 Planarity : 0.004 0.035 4824 Dihedral : 8.916 77.932 4240 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.67 % Favored : 93.10 % Rotamer: Outliers : 2.79 % Allowed : 15.45 % Favored : 81.76 % 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: 0.22 (0.15), residues: 3536 helix: 1.49 (0.11), residues: 2104 sheet: -2.13 (0.36), residues: 192 loop : -1.88 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 177 TYR 0.026 0.001 TYR D 376 PHE 0.010 0.001 PHE O 92 TRP 0.014 0.001 TRP B 173 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (28712) covalent geometry : angle 0.56476 / 0.30 (39264) hydrogen bonds : bond 0.04175 / 2.71 ( 1472) hydrogen bonds : angle 3.20467 / 2.30 ( 4344) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 449 time to evaluate : 0.936 Fit side-chains REVERT: A 148 PHE cc_start: 0.7383 (m-80) cc_final: 0.7041 (m-10) REVERT: A 284 ASN cc_start: 0.8604 (t0) cc_final: 0.8013 (t0) REVERT: A 327 HIS cc_start: 0.5869 (OUTLIER) cc_final: 0.5510 (t70) REVERT: A 331 ASP cc_start: 0.8241 (m-30) cc_final: 0.7792 (m-30) REVERT: A 397 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: B 58 ARG cc_start: 0.5269 (tpt170) cc_final: 0.4811 (tmt170) REVERT: B 148 PHE cc_start: 0.7366 (m-80) cc_final: 0.6984 (m-10) REVERT: B 169 MET cc_start: 0.8132 (tpp) cc_final: 0.7658 (mmm) REVERT: B 284 ASN cc_start: 0.8674 (m-40) cc_final: 0.8174 (t0) REVERT: B 415 TYR cc_start: 0.6869 (m-10) cc_final: 0.6307 (m-10) REVERT: C 148 PHE cc_start: 0.7398 (m-80) cc_final: 0.7069 (m-10) REVERT: C 327 HIS cc_start: 0.6000 (OUTLIER) cc_final: 0.5653 (t70) REVERT: C 331 ASP cc_start: 0.8238 (m-30) cc_final: 0.7792 (m-30) REVERT: C 397 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: D 148 PHE cc_start: 0.7376 (m-80) cc_final: 0.7039 (m-10) REVERT: D 327 HIS cc_start: 0.5825 (OUTLIER) cc_final: 0.5372 (t70) REVERT: D 331 ASP cc_start: 0.8241 (m-30) cc_final: 0.7859 (m-30) REVERT: D 342 LYS cc_start: 0.7780 (mptt) cc_final: 0.7579 (mptt) REVERT: D 397 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: M 58 ARG cc_start: 0.6652 (tpt170) cc_final: 0.5459 (tmt170) REVERT: M 75 TRP cc_start: 0.7823 (t60) cc_final: 0.7355 (t60) REVERT: M 149 GLN cc_start: 0.8466 (pt0) cc_final: 0.7945 (mm-40) REVERT: M 153 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8036 (pp) REVERT: M 257 THR cc_start: 0.9536 (OUTLIER) cc_final: 0.9294 (m) REVERT: M 311 ASP cc_start: 0.7996 (t0) cc_final: 0.7717 (t0) REVERT: M 479 MET cc_start: 0.6908 (ppp) cc_final: 0.6704 (mmm) REVERT: N 58 ARG cc_start: 0.6675 (tpt170) cc_final: 0.5500 (tmt170) REVERT: N 75 TRP cc_start: 0.7962 (t60) cc_final: 0.7446 (t60) REVERT: N 141 ASP cc_start: 0.8100 (m-30) cc_final: 0.7865 (m-30) REVERT: N 149 GLN cc_start: 0.8352 (pt0) cc_final: 0.7747 (mm110) REVERT: N 257 THR cc_start: 0.9515 (OUTLIER) cc_final: 0.9285 (m) REVERT: O 58 ARG cc_start: 0.6632 (tpt170) cc_final: 0.5465 (tmt170) REVERT: O 75 TRP cc_start: 0.7853 (t60) cc_final: 0.7369 (t60) REVERT: O 96 ASN cc_start: 0.8597 (m-40) cc_final: 0.8389 (m110) REVERT: O 311 ASP cc_start: 0.8013 (t0) cc_final: 0.7729 (t0) REVERT: P 58 ARG cc_start: 0.6635 (tpt170) cc_final: 0.5472 (tmt170) REVERT: P 75 TRP cc_start: 0.7838 (t60) cc_final: 0.7356 (t60) REVERT: P 96 ASN cc_start: 0.8527 (m-40) cc_final: 0.8269 (m110) REVERT: P 149 GLN cc_start: 0.8429 (pt0) cc_final: 0.7952 (mm-40) REVERT: P 153 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8025 (pp) REVERT: P 257 THR cc_start: 0.9590 (OUTLIER) cc_final: 0.9305 (m) outliers start: 74 outliers final: 52 residues processed: 496 average time/residue: 0.1666 time to fit residues: 137.1946 Evaluate side-chains 490 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 427 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 257 THR Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 327 HIS Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 381 VAL Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 257 THR Chi-restraints excluded: chain N residue 284 ASN Chi-restraints excluded: chain N residue 296 THR Chi-restraints excluded: chain N residue 327 HIS Chi-restraints excluded: chain N residue 381 VAL Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 296 THR Chi-restraints excluded: chain O residue 327 HIS Chi-restraints excluded: chain O residue 376 TYR Chi-restraints excluded: chain O residue 381 VAL Chi-restraints excluded: chain P residue 80 GLN Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 296 THR Chi-restraints excluded: chain P residue 327 HIS Chi-restraints excluded: chain P residue 376 TYR Chi-restraints excluded: chain P residue 381 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 271 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 279 optimal weight: 0.9980 chunk 273 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 295 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 216 optimal weight: 0.0020 chunk 109 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN C 330 GLN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 210 HIS O 210 HIS P 210 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.120565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097245 restraints weight = 58469.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100117 restraints weight = 30621.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.101943 restraints weight = 20669.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103032 restraints weight = 16368.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103411 restraints weight = 14263.577| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 28712 Z= 0.116 Angle : 0.557 6.969 39264 Z= 0.292 Chirality : 0.042 0.155 4520 Planarity : 0.003 0.035 4824 Dihedral : 8.799 77.748 4240 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.45 % Favored : 93.33 % Rotamer: Outliers : 3.25 % Allowed : 16.01 % Favored : 80.74 % 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: 0.30 (0.15), residues: 3536 helix: 1.54 (0.11), residues: 2152 sheet: -2.15 (0.36), residues: 192 loop : -1.96 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.023 0.001 TYR C 376 PHE 0.010 0.001 PHE P 138 TRP 0.016 0.001 TRP N 173 HIS 0.002 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (28712) covalent geometry : angle 0.55743 / 0.29 (39264) hydrogen bonds : bond 0.03960 / 2.57 ( 1472) hydrogen bonds : angle 3.12364 / 2.23 ( 4344) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 461 time to evaluate : 1.107 Fit side-chains REVERT: A 148 PHE cc_start: 0.7407 (m-80) cc_final: 0.7125 (m-80) REVERT: A 169 MET cc_start: 0.8199 (tpp) cc_final: 0.7776 (mmm) REVERT: A 215 PHE cc_start: 0.8396 (t80) cc_final: 0.8188 (t80) REVERT: A 327 HIS cc_start: 0.5901 (OUTLIER) cc_final: 0.5506 (t70) REVERT: A 331 ASP cc_start: 0.8203 (m-30) cc_final: 0.7736 (m-30) REVERT: A 397 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: A 476 MET cc_start: 0.7343 (mmm) cc_final: 0.6927 (mmp) REVERT: B 58 ARG cc_start: 0.5224 (tpt170) cc_final: 0.4754 (tmt170) REVERT: B 148 PHE cc_start: 0.7398 (m-80) cc_final: 0.7144 (m-10) REVERT: B 169 MET cc_start: 0.8280 (tpp) cc_final: 0.7860 (mmm) REVERT: B 284 ASN cc_start: 0.8693 (m-40) cc_final: 0.8466 (t0) REVERT: B 415 TYR cc_start: 0.6813 (m-10) cc_final: 0.6308 (m-10) REVERT: C 148 PHE cc_start: 0.7408 (m-80) cc_final: 0.7032 (m-10) REVERT: C 169 MET cc_start: 0.8325 (tpp) cc_final: 0.7915 (mmm) REVERT: C 215 PHE cc_start: 0.8376 (t80) cc_final: 0.8133 (t80) REVERT: C 284 ASN cc_start: 0.8710 (t0) cc_final: 0.8171 (t0) REVERT: C 327 HIS cc_start: 0.5916 (OUTLIER) cc_final: 0.5514 (t70) REVERT: C 331 ASP cc_start: 0.8198 (m-30) cc_final: 0.7730 (m-30) REVERT: C 476 MET cc_start: 0.7338 (mmm) cc_final: 0.6923 (mmp) REVERT: D 148 PHE cc_start: 0.7394 (m-80) cc_final: 0.7122 (m-80) REVERT: D 169 MET cc_start: 0.8219 (tpp) cc_final: 0.7810 (mmm) REVERT: D 215 PHE cc_start: 0.8381 (t80) cc_final: 0.8165 (t80) REVERT: D 327 HIS cc_start: 0.5826 (OUTLIER) cc_final: 0.5369 (t70) REVERT: D 331 ASP cc_start: 0.8261 (m-30) cc_final: 0.7844 (m-30) REVERT: D 476 MET cc_start: 0.7337 (mmm) cc_final: 0.6928 (mmp) REVERT: M 75 TRP cc_start: 0.7831 (t60) cc_final: 0.7360 (t60) REVERT: M 149 GLN cc_start: 0.8427 (pt0) cc_final: 0.7853 (mm-40) REVERT: M 153 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8024 (pp) REVERT: M 257 THR cc_start: 0.9554 (OUTLIER) cc_final: 0.9290 (m) REVERT: M 311 ASP cc_start: 0.7995 (t0) cc_final: 0.7701 (t0) REVERT: M 479 MET cc_start: 0.6905 (ppp) cc_final: 0.6702 (mmm) REVERT: N 75 TRP cc_start: 0.7901 (t60) cc_final: 0.7376 (t60) REVERT: N 149 GLN cc_start: 0.8341 (pt0) cc_final: 0.7738 (mm110) REVERT: N 257 THR cc_start: 0.9525 (OUTLIER) cc_final: 0.9289 (m) REVERT: N 397 TYR cc_start: 0.7826 (OUTLIER) cc_final: 0.7240 (t80) REVERT: O 75 TRP cc_start: 0.7912 (t60) cc_final: 0.7336 (t60) REVERT: O 257 THR cc_start: 0.9531 (OUTLIER) cc_final: 0.9301 (m) REVERT: O 311 ASP cc_start: 0.8013 (t0) cc_final: 0.7699 (t0) REVERT: P 75 TRP cc_start: 0.7891 (t60) cc_final: 0.7328 (t60) REVERT: P 96 ASN cc_start: 0.8592 (m-40) cc_final: 0.8361 (m110) REVERT: P 149 GLN cc_start: 0.8447 (pt0) cc_final: 0.7858 (mm-40) REVERT: P 153 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8006 (pp) REVERT: P 257 THR cc_start: 0.9570 (OUTLIER) cc_final: 0.9317 (m) outliers start: 86 outliers final: 59 residues processed: 516 average time/residue: 0.1678 time to fit residues: 143.9833 Evaluate side-chains 493 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 423 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 257 THR Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 327 HIS Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 381 VAL Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 257 THR Chi-restraints excluded: chain N residue 284 ASN Chi-restraints excluded: chain N residue 296 THR Chi-restraints excluded: chain N residue 327 HIS Chi-restraints excluded: chain N residue 339 LEU Chi-restraints excluded: chain N residue 381 VAL Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 257 THR Chi-restraints excluded: chain O residue 296 THR Chi-restraints excluded: chain O residue 327 HIS Chi-restraints excluded: chain O residue 339 LEU Chi-restraints excluded: chain O residue 376 TYR Chi-restraints excluded: chain O residue 381 VAL Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain P residue 80 GLN Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 296 THR Chi-restraints excluded: chain P residue 327 HIS Chi-restraints excluded: chain P residue 339 LEU Chi-restraints excluded: chain P residue 376 TYR Chi-restraints excluded: chain P residue 381 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 168 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 292 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 250 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 210 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.121573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098764 restraints weight = 58149.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.101513 restraints weight = 31618.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103265 restraints weight = 21659.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104287 restraints weight = 17244.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.104773 restraints weight = 15160.245| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 28712 Z= 0.107 Angle : 0.552 7.075 39264 Z= 0.287 Chirality : 0.041 0.167 4520 Planarity : 0.003 0.036 4824 Dihedral : 8.625 78.658 4240 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.31 % Favored : 93.47 % Rotamer: Outliers : 3.21 % Allowed : 16.84 % Favored : 79.95 % 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: 0.48 (0.15), residues: 3536 helix: 1.69 (0.11), residues: 2152 sheet: -2.07 (0.37), residues: 192 loop : -1.89 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 177 TYR 0.023 0.001 TYR C 376 PHE 0.017 0.001 PHE A 378 TRP 0.021 0.001 TRP N 173 HIS 0.002 0.001 HIS P 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (28712) covalent geometry : angle 0.55229 / 0.29 (39264) hydrogen bonds : bond 0.03701 / 2.41 ( 1472) hydrogen bonds : angle 3.05015 / 2.18 ( 4344) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 438 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.9149 (mm) cc_final: 0.8859 (pp) REVERT: A 148 PHE cc_start: 0.7450 (m-80) cc_final: 0.7198 (m-10) REVERT: A 169 MET cc_start: 0.8101 (tpp) cc_final: 0.7778 (mmm) REVERT: A 327 HIS cc_start: 0.5853 (OUTLIER) cc_final: 0.5353 (t70) REVERT: A 331 ASP cc_start: 0.8219 (m-30) cc_final: 0.7844 (m-30) REVERT: A 479 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6380 (mmt) REVERT: B 58 ARG cc_start: 0.5304 (tpt170) cc_final: 0.4886 (tmt170) REVERT: B 148 PHE cc_start: 0.7444 (m-80) cc_final: 0.7183 (m-10) REVERT: B 169 MET cc_start: 0.8168 (tpp) cc_final: 0.7823 (mmm) REVERT: B 342 LYS cc_start: 0.7855 (mptt) cc_final: 0.7644 (mptt) REVERT: B 415 TYR cc_start: 0.6837 (m-10) cc_final: 0.6222 (m-10) REVERT: B 476 MET cc_start: 0.7395 (mmm) cc_final: 0.6809 (mmp) REVERT: C 69 LEU cc_start: 0.9148 (mm) cc_final: 0.8840 (pp) REVERT: C 148 PHE cc_start: 0.7458 (m-80) cc_final: 0.7204 (m-10) REVERT: C 169 MET cc_start: 0.8229 (tpp) cc_final: 0.7868 (mmm) REVERT: C 327 HIS cc_start: 0.5848 (OUTLIER) cc_final: 0.5386 (t70) REVERT: C 331 ASP cc_start: 0.8221 (m-30) cc_final: 0.7865 (m-30) REVERT: C 479 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6383 (mmt) REVERT: D 69 LEU cc_start: 0.9147 (mm) cc_final: 0.8865 (pp) REVERT: D 148 PHE cc_start: 0.7443 (m-80) cc_final: 0.7202 (m-10) REVERT: D 169 MET cc_start: 0.8110 (tpp) cc_final: 0.7791 (mmm) REVERT: D 327 HIS cc_start: 0.5805 (OUTLIER) cc_final: 0.5339 (t70) REVERT: D 331 ASP cc_start: 0.8302 (m-30) cc_final: 0.7840 (m-30) REVERT: D 479 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6395 (mmt) REVERT: M 75 TRP cc_start: 0.7855 (t60) cc_final: 0.7356 (t60) REVERT: M 149 GLN cc_start: 0.8497 (pt0) cc_final: 0.7960 (mm-40) REVERT: M 153 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8061 (pp) REVERT: M 295 MET cc_start: 0.8299 (mmt) cc_final: 0.8083 (mmt) REVERT: M 311 ASP cc_start: 0.8023 (t0) cc_final: 0.7729 (t0) REVERT: M 479 MET cc_start: 0.6906 (ppp) cc_final: 0.6674 (mmm) REVERT: N 75 TRP cc_start: 0.7934 (t60) cc_final: 0.7336 (t60) REVERT: N 149 GLN cc_start: 0.8295 (pt0) cc_final: 0.7733 (mm110) REVERT: N 295 MET cc_start: 0.8292 (mmt) cc_final: 0.8081 (mmt) REVERT: N 397 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7346 (t80) REVERT: O 75 TRP cc_start: 0.7905 (t60) cc_final: 0.7362 (t60) REVERT: O 295 MET cc_start: 0.8290 (mmt) cc_final: 0.8053 (mmt) REVERT: O 311 ASP cc_start: 0.8049 (t0) cc_final: 0.7768 (t0) REVERT: P 75 TRP cc_start: 0.7905 (t60) cc_final: 0.7339 (t60) REVERT: P 96 ASN cc_start: 0.8595 (m-40) cc_final: 0.8384 (m110) REVERT: P 149 GLN cc_start: 0.8473 (pt0) cc_final: 0.7906 (mm-40) REVERT: P 153 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8027 (pp) REVERT: P 295 MET cc_start: 0.8297 (mmt) cc_final: 0.8087 (mmt) outliers start: 85 outliers final: 59 residues processed: 494 average time/residue: 0.1600 time to fit residues: 132.5235 Evaluate side-chains 495 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 427 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 349 GLN Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 327 HIS Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 381 VAL Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 284 ASN Chi-restraints excluded: chain N residue 327 HIS Chi-restraints excluded: chain N residue 339 LEU Chi-restraints excluded: chain N residue 381 VAL Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain O residue 91 ILE Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 327 HIS Chi-restraints excluded: chain O residue 376 TYR Chi-restraints excluded: chain O residue 381 VAL Chi-restraints excluded: chain P residue 80 GLN Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 327 HIS Chi-restraints excluded: chain P residue 376 TYR Chi-restraints excluded: chain P residue 381 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 223 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 71 optimal weight: 0.0270 chunk 302 optimal weight: 0.0570 chunk 6 optimal weight: 0.0670 chunk 170 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 284 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.125299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102474 restraints weight = 58407.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.105434 restraints weight = 30612.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107341 restraints weight = 20532.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108301 restraints weight = 16093.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.109145 restraints weight = 14085.839| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 28712 Z= 0.099 Angle : 0.542 7.854 39264 Z= 0.280 Chirality : 0.040 0.158 4520 Planarity : 0.003 0.036 4824 Dihedral : 8.306 81.462 4240 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.88 % Favored : 93.89 % Rotamer: Outliers : 2.27 % Allowed : 17.67 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 3536 helix: 1.93 (0.12), residues: 2104 sheet: -1.79 (0.38), residues: 192 loop : -1.67 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 177 TYR 0.022 0.001 TYR C 376 PHE 0.012 0.001 PHE A 378 TRP 0.024 0.001 TRP N 173 HIS 0.003 0.001 HIS P 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (28712) covalent geometry : angle 0.54220 / 0.28 (39264) hydrogen bonds : bond 0.03076 / 2.00 ( 1472) hydrogen bonds : angle 2.92609 / 2.09 ( 4344) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 472 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 PHE cc_start: 0.7390 (m-80) cc_final: 0.7129 (m-10) REVERT: A 169 MET cc_start: 0.8033 (tpp) cc_final: 0.7537 (mmp) REVERT: A 327 HIS cc_start: 0.5786 (OUTLIER) cc_final: 0.5278 (t70) REVERT: A 331 ASP cc_start: 0.8235 (m-30) cc_final: 0.7758 (m-30) REVERT: A 479 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6408 (mmt) REVERT: B 58 ARG cc_start: 0.5306 (tpt170) cc_final: 0.4854 (tmt170) REVERT: B 148 PHE cc_start: 0.7362 (m-80) cc_final: 0.7108 (m-10) REVERT: B 169 MET cc_start: 0.7984 (tpp) cc_final: 0.7526 (mmp) REVERT: B 327 HIS cc_start: 0.5466 (OUTLIER) cc_final: 0.5161 (t70) REVERT: B 415 TYR cc_start: 0.6795 (m-10) cc_final: 0.6221 (m-10) REVERT: B 476 MET cc_start: 0.7455 (mmm) cc_final: 0.6857 (mmp) REVERT: B 479 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6055 (mmt) REVERT: C 148 PHE cc_start: 0.7387 (m-80) cc_final: 0.7114 (m-10) REVERT: C 169 MET cc_start: 0.8163 (tpp) cc_final: 0.7523 (mmp) REVERT: C 327 HIS cc_start: 0.5898 (OUTLIER) cc_final: 0.5223 (t70) REVERT: C 331 ASP cc_start: 0.8294 (m-30) cc_final: 0.7784 (m-30) REVERT: C 479 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6409 (mmt) REVERT: D 148 PHE cc_start: 0.7384 (m-80) cc_final: 0.7128 (m-10) REVERT: D 169 MET cc_start: 0.8047 (tpp) cc_final: 0.7548 (mmp) REVERT: D 327 HIS cc_start: 0.5700 (OUTLIER) cc_final: 0.5205 (t70) REVERT: D 331 ASP cc_start: 0.8253 (m-30) cc_final: 0.7714 (m-30) REVERT: D 479 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6412 (mmt) REVERT: M 75 TRP cc_start: 0.7707 (t60) cc_final: 0.7220 (t60) REVERT: M 149 GLN cc_start: 0.8481 (pt0) cc_final: 0.7971 (mm-40) REVERT: M 153 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8017 (pp) REVERT: M 311 ASP cc_start: 0.7946 (t0) cc_final: 0.7690 (t0) REVERT: M 479 MET cc_start: 0.6860 (ppp) cc_final: 0.6639 (mmm) REVERT: N 75 TRP cc_start: 0.7764 (t60) cc_final: 0.7339 (t60) REVERT: N 149 GLN cc_start: 0.8330 (pt0) cc_final: 0.7746 (mm110) REVERT: O 69 LEU cc_start: 0.9293 (mm) cc_final: 0.9060 (tp) REVERT: O 75 TRP cc_start: 0.7660 (t60) cc_final: 0.7307 (t60) REVERT: O 311 ASP cc_start: 0.7956 (t0) cc_final: 0.7695 (t0) REVERT: P 75 TRP cc_start: 0.7734 (t60) cc_final: 0.7334 (t60) REVERT: P 149 GLN cc_start: 0.8499 (pt0) cc_final: 0.7947 (mm-40) REVERT: P 153 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8049 (pp) outliers start: 60 outliers final: 47 residues processed: 503 average time/residue: 0.1641 time to fit residues: 139.9591 Evaluate side-chains 482 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 425 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 349 GLN Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 327 HIS Chi-restraints excluded: chain M residue 381 VAL Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 284 ASN Chi-restraints excluded: chain N residue 321 SER Chi-restraints excluded: chain N residue 327 HIS Chi-restraints excluded: chain N residue 339 LEU Chi-restraints excluded: chain N residue 381 VAL Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 327 HIS Chi-restraints excluded: chain O residue 376 TYR Chi-restraints excluded: chain O residue 381 VAL Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 327 HIS Chi-restraints excluded: chain P residue 376 TYR Chi-restraints excluded: chain P residue 381 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 103 optimal weight: 0.6980 chunk 284 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 323 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 215 optimal weight: 0.0670 chunk 278 optimal weight: 1.9990 chunk 334 optimal weight: 3.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN B 149 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 GLN M 210 HIS N 332 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.122476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.099178 restraints weight = 58315.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102050 restraints weight = 30721.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.103896 restraints weight = 20728.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105049 restraints weight = 16320.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105596 restraints weight = 14196.911| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 28712 Z= 0.113 Angle : 0.570 8.916 39264 Z= 0.293 Chirality : 0.042 0.180 4520 Planarity : 0.003 0.037 4824 Dihedral : 8.393 79.494 4240 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.39 % Favored : 93.38 % Rotamer: Outliers : 2.64 % Allowed : 18.09 % Favored : 79.27 % 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: 0.77 (0.15), residues: 3536 helix: 1.89 (0.11), residues: 2112 sheet: -1.69 (0.38), residues: 192 loop : -1.63 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 177 TYR 0.022 0.001 TYR A 376 PHE 0.022 0.001 PHE O 444 TRP 0.023 0.001 TRP N 173 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (28712) covalent geometry : angle 0.56959 / 0.29 (39264) hydrogen bonds : bond 0.03671 / 2.38 ( 1472) hydrogen bonds : angle 2.99519 / 2.14 ( 4344) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 432 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 PHE cc_start: 0.7432 (m-80) cc_final: 0.6998 (m-10) REVERT: A 169 MET cc_start: 0.8062 (tpp) cc_final: 0.7544 (mmp) REVERT: A 327 HIS cc_start: 0.5867 (OUTLIER) cc_final: 0.5334 (t70) REVERT: A 331 ASP cc_start: 0.8221 (m-30) cc_final: 0.7812 (m-30) REVERT: A 479 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6356 (mmt) REVERT: B 58 ARG cc_start: 0.5416 (tpt170) cc_final: 0.4938 (tmt170) REVERT: B 148 PHE cc_start: 0.7405 (m-80) cc_final: 0.7137 (m-10) REVERT: B 169 MET cc_start: 0.8128 (tpp) cc_final: 0.7869 (mmm) REVERT: B 397 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8117 (m-80) REVERT: B 415 TYR cc_start: 0.6874 (m-10) cc_final: 0.6355 (m-10) REVERT: B 476 MET cc_start: 0.7460 (mmm) cc_final: 0.6910 (mmp) REVERT: B 479 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6078 (mmt) REVERT: C 148 PHE cc_start: 0.7430 (m-80) cc_final: 0.6980 (m-10) REVERT: C 169 MET cc_start: 0.8140 (tpp) cc_final: 0.7413 (mmp) REVERT: C 327 HIS cc_start: 0.5907 (OUTLIER) cc_final: 0.5090 (t70) REVERT: C 331 ASP cc_start: 0.8291 (m-30) cc_final: 0.7708 (m-30) REVERT: C 397 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8284 (m-80) REVERT: C 479 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6358 (mmt) REVERT: D 86 TYR cc_start: 0.5639 (OUTLIER) cc_final: 0.5437 (t80) REVERT: D 148 PHE cc_start: 0.7421 (m-80) cc_final: 0.6994 (m-10) REVERT: D 169 MET cc_start: 0.8079 (tpp) cc_final: 0.7555 (mmp) REVERT: D 397 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: D 479 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6366 (mmt) REVERT: M 69 LEU cc_start: 0.9451 (tp) cc_final: 0.9196 (tp) REVERT: M 75 TRP cc_start: 0.7855 (t60) cc_final: 0.7360 (t60) REVERT: M 149 GLN cc_start: 0.8465 (pt0) cc_final: 0.7931 (mm-40) REVERT: M 153 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8108 (pp) REVERT: M 257 THR cc_start: 0.9535 (OUTLIER) cc_final: 0.9274 (m) REVERT: M 295 MET cc_start: 0.8280 (mmt) cc_final: 0.8067 (mmt) REVERT: N 69 LEU cc_start: 0.9412 (tp) cc_final: 0.9148 (tp) REVERT: N 75 TRP cc_start: 0.7905 (t60) cc_final: 0.7328 (t60) REVERT: N 149 GLN cc_start: 0.8346 (pt0) cc_final: 0.7735 (mm110) REVERT: N 295 MET cc_start: 0.8291 (mmt) cc_final: 0.8079 (mmt) REVERT: O 75 TRP cc_start: 0.7885 (t60) cc_final: 0.7371 (t60) REVERT: P 69 LEU cc_start: 0.9448 (tp) cc_final: 0.9196 (tp) REVERT: P 75 TRP cc_start: 0.7877 (t60) cc_final: 0.7336 (t60) REVERT: P 149 GLN cc_start: 0.8477 (pt0) cc_final: 0.7951 (mm-40) REVERT: P 153 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8104 (pp) REVERT: P 295 MET cc_start: 0.8296 (mmt) cc_final: 0.8093 (mmt) outliers start: 70 outliers final: 50 residues processed: 475 average time/residue: 0.1630 time to fit residues: 131.2249 Evaluate side-chains 481 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 418 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 349 GLN Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 257 THR Chi-restraints excluded: chain M residue 327 HIS Chi-restraints excluded: chain M residue 381 VAL Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 284 ASN Chi-restraints excluded: chain N residue 327 HIS Chi-restraints excluded: chain N residue 339 LEU Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 327 HIS Chi-restraints excluded: chain O residue 339 LEU Chi-restraints excluded: chain O residue 376 TYR Chi-restraints excluded: chain O residue 381 VAL Chi-restraints excluded: chain P residue 80 GLN Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 327 HIS Chi-restraints excluded: chain P residue 339 LEU Chi-restraints excluded: chain P residue 376 TYR Chi-restraints excluded: chain P residue 381 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 270 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 291 optimal weight: 0.3980 chunk 329 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 271 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 GLN M 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.122946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099627 restraints weight = 58282.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102555 restraints weight = 30709.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.104404 restraints weight = 20705.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.105541 restraints weight = 16326.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106005 restraints weight = 14174.759| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 28712 Z= 0.108 Angle : 0.571 8.568 39264 Z= 0.294 Chirality : 0.042 0.305 4520 Planarity : 0.003 0.038 4824 Dihedral : 8.299 79.584 4240 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.56 % Favored : 93.21 % Rotamer: Outliers : 2.64 % Allowed : 18.16 % Favored : 79.19 % 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: 0.79 (0.15), residues: 3536 helix: 1.90 (0.11), residues: 2112 sheet: -1.58 (0.38), residues: 192 loop : -1.64 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 177 TYR 0.022 0.001 TYR C 376 PHE 0.021 0.001 PHE O 444 TRP 0.026 0.001 TRP P 173 HIS 0.002 0.001 HIS P 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (28712) covalent geometry : angle 0.57077 / 0.29 (39264) hydrogen bonds : bond 0.03527 / 2.28 ( 1472) hydrogen bonds : angle 2.97686 / 2.12 ( 4344) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 429 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 PHE cc_start: 0.7430 (m-80) cc_final: 0.7181 (m-10) REVERT: A 169 MET cc_start: 0.8005 (tpp) cc_final: 0.7509 (mmp) REVERT: A 327 HIS cc_start: 0.5845 (OUTLIER) cc_final: 0.4981 (t70) REVERT: A 331 ASP cc_start: 0.8336 (m-30) cc_final: 0.7759 (m-30) REVERT: A 397 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.8248 (m-80) REVERT: A 479 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6269 (mmt) REVERT: B 58 ARG cc_start: 0.5509 (tpt170) cc_final: 0.4958 (tmt170) REVERT: B 148 PHE cc_start: 0.7405 (m-80) cc_final: 0.7140 (m-10) REVERT: B 169 MET cc_start: 0.8084 (tpp) cc_final: 0.7619 (mmp) REVERT: B 397 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.8106 (m-80) REVERT: B 415 TYR cc_start: 0.6957 (m-10) cc_final: 0.6327 (m-10) REVERT: B 476 MET cc_start: 0.7497 (mmm) cc_final: 0.6933 (mmp) REVERT: B 479 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6093 (mmt) REVERT: C 148 PHE cc_start: 0.7420 (m-80) cc_final: 0.7152 (m-10) REVERT: C 169 MET cc_start: 0.8090 (tpp) cc_final: 0.7401 (mmp) REVERT: C 327 HIS cc_start: 0.5884 (OUTLIER) cc_final: 0.5024 (t70) REVERT: C 331 ASP cc_start: 0.8331 (m-30) cc_final: 0.7698 (m-30) REVERT: C 397 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8221 (m-80) REVERT: C 479 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6271 (mmt) REVERT: D 148 PHE cc_start: 0.7425 (m-80) cc_final: 0.7169 (m-10) REVERT: D 169 MET cc_start: 0.8020 (tpp) cc_final: 0.7517 (mmp) REVERT: D 327 HIS cc_start: 0.5582 (OUTLIER) cc_final: 0.4935 (t70) REVERT: D 331 ASP cc_start: 0.8230 (m-30) cc_final: 0.7611 (m-30) REVERT: D 397 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: D 479 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6280 (mmt) REVERT: M 69 LEU cc_start: 0.9435 (tp) cc_final: 0.9186 (tp) REVERT: M 75 TRP cc_start: 0.7879 (t60) cc_final: 0.7354 (t60) REVERT: M 149 GLN cc_start: 0.8489 (pt0) cc_final: 0.7946 (mm-40) REVERT: M 153 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8046 (pp) REVERT: M 295 MET cc_start: 0.8286 (mmt) cc_final: 0.8082 (mmt) REVERT: N 69 LEU cc_start: 0.9397 (tp) cc_final: 0.9133 (tp) REVERT: N 75 TRP cc_start: 0.7966 (t60) cc_final: 0.7390 (t60) REVERT: N 149 GLN cc_start: 0.8345 (pt0) cc_final: 0.7725 (mm110) REVERT: O 69 LEU cc_start: 0.9411 (tp) cc_final: 0.9158 (tp) REVERT: O 75 TRP cc_start: 0.7932 (t60) cc_final: 0.7338 (t60) REVERT: O 295 MET cc_start: 0.8288 (mmt) cc_final: 0.8036 (mmt) REVERT: P 69 LEU cc_start: 0.9426 (tp) cc_final: 0.9172 (tp) REVERT: P 75 TRP cc_start: 0.7952 (t60) cc_final: 0.7315 (t60) REVERT: P 149 GLN cc_start: 0.8501 (pt0) cc_final: 0.7911 (mm-40) REVERT: P 153 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8091 (pp) REVERT: P 258 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9120 (tp) outliers start: 70 outliers final: 50 residues processed: 472 average time/residue: 0.1598 time to fit residues: 127.6403 Evaluate side-chains 485 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 421 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 349 GLN Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 327 HIS Chi-restraints excluded: chain M residue 381 VAL Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 284 ASN Chi-restraints excluded: chain N residue 339 LEU Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 327 HIS Chi-restraints excluded: chain O residue 339 LEU Chi-restraints excluded: chain O residue 376 TYR Chi-restraints excluded: chain O residue 381 VAL Chi-restraints excluded: chain P residue 80 GLN Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 258 LEU Chi-restraints excluded: chain P residue 327 HIS Chi-restraints excluded: chain P residue 339 LEU Chi-restraints excluded: chain P residue 376 TYR Chi-restraints excluded: chain P residue 381 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 341 optimal weight: 0.7980 chunk 186 optimal weight: 9.9990 chunk 201 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 228 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 HIS ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 GLN M 210 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.122648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099423 restraints weight = 57974.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.102329 restraints weight = 30575.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104178 restraints weight = 20584.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.105295 restraints weight = 16293.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105989 restraints weight = 14149.994| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 28712 Z= 0.109 Angle : 0.573 8.473 39264 Z= 0.295 Chirality : 0.042 0.319 4520 Planarity : 0.003 0.038 4824 Dihedral : 8.247 79.458 4240 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.42 % Favored : 93.35 % Rotamer: Outliers : 2.45 % Allowed : 18.54 % Favored : 79.00 % 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 (0.15), residues: 3536 helix: 1.97 (0.11), residues: 2104 sheet: -1.52 (0.37), residues: 192 loop : -1.71 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.028 0.001 TYR A 86 PHE 0.021 0.001 PHE O 444 TRP 0.025 0.001 TRP M 173 HIS 0.005 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (28712) covalent geometry : angle 0.57303 / 0.30 (39264) hydrogen bonds : bond 0.03559 / 2.30 ( 1472) hydrogen bonds : angle 2.97712 / 2.12 ( 4344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4805.67 seconds wall clock time: 83 minutes 40.53 seconds (5020.53 seconds total)