Starting phenix.real_space_refine on Thu Jul 31 00:14:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cnm_7537/07_2025/6cnm_7537.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cnm_7537/07_2025/6cnm_7537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cnm_7537/07_2025/6cnm_7537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cnm_7537/07_2025/6cnm_7537.map" model { file = "/net/cci-nas-00/data/ceres_data/6cnm_7537/07_2025/6cnm_7537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cnm_7537/07_2025/6cnm_7537.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 5 8.98 5 P 4 5.49 5 S 80 5.16 5 C 8096 2.51 5 N 2212 2.21 5 O 2144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12541 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2694 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2694 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2694 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 99 Chain: "D" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2694 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 99 Chain: "E" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 363 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 65} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "F" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 363 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 65} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "G" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 363 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 65} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "H" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 363 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 65} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 82 Unusual residues: {' K': 5, 'LMT': 2, 'POV': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'LMT': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'LMT': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'LMT': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 8.39, per 1000 atoms: 0.67 Number of scatterers: 12541 At special positions: 0 Unit cell: (132.87, 132.87, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 5 19.00 S 80 16.00 P 4 15.00 O 2144 8.00 N 2212 7.00 C 8096 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.7 seconds 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3160 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 78.6% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 10 through 49 removed outlier: 4.880A pdb=" N ARG A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 91 removed outlier: 3.801A pdb=" N PHE A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 78 " --> pdb=" O CYS A 74 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 115 removed outlier: 3.807A pdb=" N VAL A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 removed outlier: 4.609A pdb=" N LEU A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 162 removed outlier: 4.033A pdb=" N TYR A 161 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 170 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.880A pdb=" N ILE A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 205 through 227 removed outlier: 3.947A pdb=" N THR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 249 removed outlier: 4.750A pdb=" N TRP A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 261 through 289 removed outlier: 3.712A pdb=" N ILE A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 331 removed outlier: 3.517A pdb=" N GLN A 306 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 367 removed outlier: 3.966A pdb=" N ARG A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG A 339 " --> pdb=" O HIS A 335 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N HIS A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 386 removed outlier: 3.588A pdb=" N TYR A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 383 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 49 removed outlier: 4.873A pdb=" N ARG B 14 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 21 " --> pdb=" O ARG B 17 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.795A pdb=" N PHE B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 78 " --> pdb=" O CYS B 74 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 115 removed outlier: 3.789A pdb=" N VAL B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 155 removed outlier: 4.623A pdb=" N LEU B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 removed outlier: 4.034A pdb=" N TYR B 161 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.888A pdb=" N ILE B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 205 through 227 removed outlier: 3.946A pdb=" N THR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 249 removed outlier: 4.749A pdb=" N TRP B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) Proline residue: B 245 - end of helix Processing helix chain 'B' and resid 261 through 289 removed outlier: 3.711A pdb=" N ILE B 265 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 271 " --> pdb=" O CYS B 267 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 331 removed outlier: 3.516A pdb=" N GLN B 306 " --> pdb=" O MET B 302 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 315 " --> pdb=" O MET B 311 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 367 removed outlier: 3.971A pdb=" N ARG B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG B 339 " --> pdb=" O HIS B 335 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N HIS B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 386 removed outlier: 3.590A pdb=" N TYR B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 383 " --> pdb=" O TYR B 379 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER B 386 " --> pdb=" O GLN B 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 49 removed outlier: 4.875A pdb=" N ARG C 14 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 19 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 91 removed outlier: 3.802A pdb=" N PHE C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 78 " --> pdb=" O CYS C 74 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 115 removed outlier: 3.788A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 removed outlier: 4.611A pdb=" N LEU C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 152 " --> pdb=" O GLY C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 162 removed outlier: 4.033A pdb=" N TYR C 161 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 Processing helix chain 'C' and resid 177 through 186 removed outlier: 3.886A pdb=" N ILE C 182 " --> pdb=" O SER C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 205 through 227 removed outlier: 3.946A pdb=" N THR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 249 removed outlier: 4.750A pdb=" N TRP C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Proline residue: C 245 - end of helix Processing helix chain 'C' and resid 261 through 289 removed outlier: 3.711A pdb=" N ILE C 265 " --> pdb=" O MET C 261 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY C 271 " --> pdb=" O CYS C 267 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 331 removed outlier: 3.515A pdb=" N GLN C 306 " --> pdb=" O MET C 302 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 315 " --> pdb=" O MET C 311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 367 removed outlier: 3.968A pdb=" N ARG C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG C 339 " --> pdb=" O HIS C 335 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N HIS C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 361 " --> pdb=" O LYS C 357 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 362 " --> pdb=" O HIS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 386 removed outlier: 3.588A pdb=" N TYR C 379 " --> pdb=" O HIS C 375 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 383 " --> pdb=" O TYR C 379 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER C 386 " --> pdb=" O GLN C 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 49 removed outlier: 4.891A pdb=" N ARG D 14 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 19 " --> pdb=" O ARG D 15 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D 21 " --> pdb=" O ARG D 17 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 39 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 3.802A pdb=" N PHE D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 78 " --> pdb=" O CYS D 74 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 115 removed outlier: 3.835A pdb=" N VAL D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 4.608A pdb=" N LEU D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 162 removed outlier: 4.032A pdb=" N TYR D 161 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 170 Processing helix chain 'D' and resid 177 through 186 removed outlier: 3.880A pdb=" N ILE D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 205 through 227 removed outlier: 3.947A pdb=" N THR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 removed outlier: 4.767A pdb=" N TRP D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) Proline residue: D 245 - end of helix Processing helix chain 'D' and resid 261 through 289 removed outlier: 3.711A pdb=" N ILE D 265 " --> pdb=" O MET D 261 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY D 271 " --> pdb=" O CYS D 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET D 273 " --> pdb=" O CYS D 269 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 331 removed outlier: 3.518A pdb=" N GLN D 306 " --> pdb=" O MET D 302 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS D 309 " --> pdb=" O ILE D 305 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 315 " --> pdb=" O MET D 311 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU D 321 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 367 removed outlier: 3.967A pdb=" N ARG D 338 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG D 339 " --> pdb=" O HIS D 335 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 361 " --> pdb=" O LYS D 357 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D 362 " --> pdb=" O HIS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 386 removed outlier: 3.581A pdb=" N TYR D 379 " --> pdb=" O HIS D 375 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN D 383 " --> pdb=" O TYR D 379 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER D 386 " --> pdb=" O GLN D 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 92 removed outlier: 3.555A pdb=" N VAL E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 removed outlier: 4.163A pdb=" N MET E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 138 through 146 removed outlier: 3.780A pdb=" N GLN E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 92 removed outlier: 3.555A pdb=" N VAL F 91 " --> pdb=" O GLU F 87 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 110 removed outlier: 4.164A pdb=" N MET F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 138 through 146 removed outlier: 3.780A pdb=" N GLN F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 92 removed outlier: 3.555A pdb=" N VAL G 91 " --> pdb=" O GLU G 87 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 removed outlier: 4.164A pdb=" N MET G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 138 through 146 removed outlier: 3.779A pdb=" N GLN G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 92 removed outlier: 3.555A pdb=" N VAL H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 110 removed outlier: 4.163A pdb=" N MET H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 138 through 146 removed outlier: 3.780A pdb=" N GLN H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=B, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=C, first strand: chain 'G' and resid 99 through 101 Processing sheet with id=D, first strand: chain 'H' and resid 99 through 101 836 hydrogen bonds defined for protein. 2472 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3947 1.34 - 1.46: 2547 1.46 - 1.58: 6138 1.58 - 1.70: 8 1.70 - 1.82: 128 Bond restraints: 12768 Sorted by residual: bond pdb=" C31 POV B1101 " pdb=" O31 POV B1101 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C31 POV D1101 " pdb=" O31 POV D1101 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C31 POV A1101 " pdb=" O31 POV A1101 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C31 POV C1101 " pdb=" O31 POV C1101 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C21 POV A1101 " pdb=" O21 POV A1101 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.87e+01 ... (remaining 12763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 16413 2.17 - 4.33: 716 4.33 - 6.50: 143 6.50 - 8.67: 28 8.67 - 10.83: 28 Bond angle restraints: 17328 Sorted by residual: angle pdb=" C LEU B 249 " pdb=" N THR B 250 " pdb=" CA THR B 250 " ideal model delta sigma weight residual 122.07 128.25 -6.18 1.43e+00 4.89e-01 1.87e+01 angle pdb=" C LEU D 249 " pdb=" N THR D 250 " pdb=" CA THR D 250 " ideal model delta sigma weight residual 122.07 128.25 -6.18 1.43e+00 4.89e-01 1.87e+01 angle pdb=" C LEU A 249 " pdb=" N THR A 250 " pdb=" CA THR A 250 " ideal model delta sigma weight residual 122.07 128.24 -6.17 1.43e+00 4.89e-01 1.86e+01 angle pdb=" C LEU C 249 " pdb=" N THR C 250 " pdb=" CA THR C 250 " ideal model delta sigma weight residual 122.07 128.23 -6.16 1.43e+00 4.89e-01 1.86e+01 angle pdb=" CA PRO A 164 " pdb=" N PRO A 164 " pdb=" CD PRO A 164 " ideal model delta sigma weight residual 112.00 107.28 4.72 1.40e+00 5.10e-01 1.14e+01 ... (remaining 17323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.52: 7293 18.52 - 37.03: 283 37.03 - 55.55: 44 55.55 - 74.06: 60 74.06 - 92.58: 32 Dihedral angle restraints: 7712 sinusoidal: 2836 harmonic: 4876 Sorted by residual: dihedral pdb=" CA LEU D 19 " pdb=" C LEU D 19 " pdb=" N GLU D 20 " pdb=" CA GLU D 20 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEU A 19 " pdb=" C LEU A 19 " pdb=" N GLU A 20 " pdb=" CA GLU A 20 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LEU B 19 " pdb=" C LEU B 19 " pdb=" N GLU B 20 " pdb=" CA GLU B 20 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 7709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1455 0.052 - 0.103: 526 0.103 - 0.155: 81 0.155 - 0.206: 18 0.206 - 0.258: 20 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CB VAL A 163 " pdb=" CA VAL A 163 " pdb=" CG1 VAL A 163 " pdb=" CG2 VAL A 163 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL B 163 " pdb=" CA VAL B 163 " pdb=" CG1 VAL B 163 " pdb=" CG2 VAL B 163 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL D 163 " pdb=" CA VAL D 163 " pdb=" CG1 VAL D 163 " pdb=" CG2 VAL D 163 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 2097 not shown) Planarity restraints: 2108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 157 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C LEU C 157 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU C 157 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU C 158 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 157 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C LEU D 157 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU D 157 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU D 158 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 157 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C LEU B 157 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU B 157 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 158 " -0.011 2.00e-02 2.50e+03 ... (remaining 2105 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.89: 4460 2.89 - 3.45: 13819 3.45 - 4.02: 21110 4.02 - 4.58: 31494 4.58 - 5.14: 42558 Nonbonded interactions: 113441 Sorted by model distance: nonbonded pdb=" OH TYR A 253 " pdb=" OG1 THR B 247 " model vdw 2.331 3.040 nonbonded pdb=" OH TYR B 253 " pdb=" OG1 THR C 247 " model vdw 2.332 3.040 nonbonded pdb=" OH TYR C 253 " pdb=" OG1 THR D 247 " model vdw 2.332 3.040 nonbonded pdb=" OG1 THR A 247 " pdb=" OH TYR D 253 " model vdw 2.332 3.040 nonbonded pdb=" O LEU B 356 " pdb=" NZ LYS B 360 " model vdw 2.429 3.120 ... (remaining 113436 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 10 through 386) selection = (chain 'B' and resid 10 through 386) selection = (chain 'C' and resid 10 through 386) selection = (chain 'D' and resid 10 through 386) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 31.030 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.010 0.128 12772 Z= 0.432 Angle : 1.114 10.833 17328 Z= 0.572 Chirality : 0.057 0.258 2100 Planarity : 0.006 0.042 2108 Dihedral : 14.653 92.579 4552 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.15), residues: 1676 helix: -2.82 (0.10), residues: 1292 sheet: None (None), residues: 0 loop : -1.92 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 221 HIS 0.012 0.002 HIS B 297 PHE 0.029 0.003 PHE B 291 TYR 0.027 0.005 TYR B 307 ARG 0.014 0.001 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.13056 ( 836) hydrogen bonds : angle 6.11072 ( 2472) covalent geometry : bond 0.00976 (12768) covalent geometry : angle 1.11404 (17328) Misc. bond : bond 0.00058 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2528 time to fit residues: 93.9384 Evaluate side-chains 171 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 364 GLN B 320 GLN B 364 GLN C 320 GLN C 364 GLN D 364 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.096327 restraints weight = 21118.379| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.01 r_work: 0.2986 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12772 Z= 0.113 Angle : 0.531 8.153 17328 Z= 0.266 Chirality : 0.037 0.119 2100 Planarity : 0.003 0.031 2108 Dihedral : 9.129 64.974 2232 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.19), residues: 1676 helix: -0.85 (0.13), residues: 1296 sheet: None (None), residues: 0 loop : -1.18 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 221 HIS 0.004 0.001 HIS D 297 PHE 0.009 0.001 PHE C 291 TYR 0.018 0.002 TYR A 326 ARG 0.003 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 836) hydrogen bonds : angle 3.68935 ( 2472) covalent geometry : bond 0.00246 (12768) covalent geometry : angle 0.53053 (17328) Misc. bond : bond 0.00042 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8703 (ttp) cc_final: 0.8355 (ttm) REVERT: A 306 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7544 (tm-30) REVERT: A 310 GLU cc_start: 0.8729 (mp0) cc_final: 0.8278 (mp0) REVERT: A 348 ILE cc_start: 0.8825 (pt) cc_final: 0.8607 (mt) REVERT: A 356 LEU cc_start: 0.8612 (tp) cc_final: 0.8143 (mt) REVERT: B 46 MET cc_start: 0.8685 (ttp) cc_final: 0.8343 (ttm) REVERT: B 306 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7542 (tm-30) REVERT: B 310 GLU cc_start: 0.8735 (mp0) cc_final: 0.8283 (mp0) REVERT: B 348 ILE cc_start: 0.8816 (pt) cc_final: 0.8596 (mt) REVERT: C 46 MET cc_start: 0.8712 (ttp) cc_final: 0.8363 (ttm) REVERT: C 306 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7536 (tm-30) REVERT: C 310 GLU cc_start: 0.8713 (mp0) cc_final: 0.8253 (mp0) REVERT: C 348 ILE cc_start: 0.8816 (pt) cc_final: 0.8597 (mt) REVERT: C 356 LEU cc_start: 0.8622 (tp) cc_final: 0.8303 (mm) REVERT: D 46 MET cc_start: 0.8689 (ttp) cc_final: 0.8325 (ttm) REVERT: D 156 MET cc_start: 0.9121 (mmm) cc_final: 0.8416 (mtp) REVERT: D 306 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7440 (tm-30) REVERT: D 310 GLU cc_start: 0.8731 (mp0) cc_final: 0.8287 (mp0) REVERT: D 348 ILE cc_start: 0.8821 (pt) cc_final: 0.8606 (mt) REVERT: D 356 LEU cc_start: 0.8593 (tp) cc_final: 0.8290 (mm) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2055 time to fit residues: 70.7545 Evaluate side-chains 183 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 55 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 92 optimal weight: 0.0050 chunk 69 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS B 340 HIS C 340 HIS D 340 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.092176 restraints weight = 21446.738| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.98 r_work: 0.2901 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12772 Z= 0.204 Angle : 0.568 7.409 17328 Z= 0.291 Chirality : 0.040 0.127 2100 Planarity : 0.003 0.031 2108 Dihedral : 8.446 60.729 2232 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.88 % Allowed : 11.28 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1676 helix: -0.12 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -0.86 (0.39), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 28 HIS 0.004 0.001 HIS D 340 PHE 0.018 0.002 PHE B 291 TYR 0.015 0.002 TYR F 138 ARG 0.005 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 836) hydrogen bonds : angle 3.69905 ( 2472) covalent geometry : bond 0.00492 (12768) covalent geometry : angle 0.56842 (17328) Misc. bond : bond 0.00018 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.9108 (mtp) cc_final: 0.8907 (mtp) REVERT: A 310 GLU cc_start: 0.8717 (mp0) cc_final: 0.8240 (mp0) REVERT: A 348 ILE cc_start: 0.8845 (pt) cc_final: 0.8562 (mt) REVERT: B 310 GLU cc_start: 0.8727 (mp0) cc_final: 0.8252 (mp0) REVERT: B 348 ILE cc_start: 0.8841 (pt) cc_final: 0.8559 (mt) REVERT: B 356 LEU cc_start: 0.8602 (tp) cc_final: 0.8284 (mm) REVERT: C 156 MET cc_start: 0.9101 (mtp) cc_final: 0.8901 (mtp) REVERT: C 310 GLU cc_start: 0.8691 (mp0) cc_final: 0.8225 (mp0) REVERT: C 348 ILE cc_start: 0.8833 (pt) cc_final: 0.8553 (mt) REVERT: C 356 LEU cc_start: 0.8629 (tp) cc_final: 0.8301 (mm) REVERT: D 310 GLU cc_start: 0.8715 (mp0) cc_final: 0.8412 (mp0) outliers start: 20 outliers final: 20 residues processed: 181 average time/residue: 0.1769 time to fit residues: 51.9692 Evaluate side-chains 178 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 159 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.134590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.094605 restraints weight = 21165.416| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.03 r_work: 0.2930 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12772 Z= 0.103 Angle : 0.454 8.633 17328 Z= 0.233 Chirality : 0.036 0.138 2100 Planarity : 0.002 0.027 2108 Dihedral : 7.294 59.191 2232 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.03 % Allowed : 13.25 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1676 helix: 0.56 (0.14), residues: 1304 sheet: None (None), residues: 0 loop : -0.90 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 221 HIS 0.002 0.001 HIS C 236 PHE 0.009 0.001 PHE D 291 TYR 0.014 0.001 TYR D 326 ARG 0.004 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 836) hydrogen bonds : angle 3.21998 ( 2472) covalent geometry : bond 0.00231 (12768) covalent geometry : angle 0.45438 (17328) Misc. bond : bond 0.00010 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LEU cc_start: 0.9016 (mt) cc_final: 0.8809 (mt) REVERT: A 288 LYS cc_start: 0.8563 (mmtt) cc_final: 0.8338 (mtmt) REVERT: A 310 GLU cc_start: 0.8750 (mp0) cc_final: 0.8456 (mp0) REVERT: A 348 ILE cc_start: 0.8804 (pt) cc_final: 0.8571 (mt) REVERT: B 310 GLU cc_start: 0.8735 (mp0) cc_final: 0.8440 (mp0) REVERT: B 348 ILE cc_start: 0.8801 (pt) cc_final: 0.8554 (mt) REVERT: B 356 LEU cc_start: 0.8594 (tp) cc_final: 0.8276 (mm) REVERT: C 215 LEU cc_start: 0.9026 (mt) cc_final: 0.8819 (mt) REVERT: C 288 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8339 (mtmt) REVERT: C 310 GLU cc_start: 0.8731 (mp0) cc_final: 0.8440 (mp0) REVERT: C 348 ILE cc_start: 0.8797 (pt) cc_final: 0.8566 (mt) REVERT: C 356 LEU cc_start: 0.8576 (tp) cc_final: 0.8260 (mm) REVERT: D 215 LEU cc_start: 0.9018 (mt) cc_final: 0.8809 (mt) REVERT: D 288 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8336 (mtmt) REVERT: D 310 GLU cc_start: 0.8719 (mp0) cc_final: 0.8461 (mp0) REVERT: D 348 ILE cc_start: 0.8851 (pt) cc_final: 0.8572 (mt) outliers start: 11 outliers final: 11 residues processed: 188 average time/residue: 0.1844 time to fit residues: 54.9920 Evaluate side-chains 189 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 89 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 66 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.135211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.095022 restraints weight = 21114.643| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.16 r_work: 0.2951 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12772 Z= 0.098 Angle : 0.436 6.932 17328 Z= 0.225 Chirality : 0.036 0.117 2100 Planarity : 0.002 0.026 2108 Dihedral : 6.869 59.494 2232 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.79 % Allowed : 12.78 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.21), residues: 1676 helix: 1.04 (0.14), residues: 1304 sheet: None (None), residues: 0 loop : -0.85 (0.36), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 323 HIS 0.002 0.001 HIS A 236 PHE 0.010 0.001 PHE A 291 TYR 0.017 0.002 TYR C 326 ARG 0.003 0.000 ARG D 287 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 836) hydrogen bonds : angle 3.08841 ( 2472) covalent geometry : bond 0.00220 (12768) covalent geometry : angle 0.43629 (17328) Misc. bond : bond 0.00017 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLU cc_start: 0.8717 (mp0) cc_final: 0.8259 (mp0) REVERT: B 288 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8364 (mtmt) REVERT: B 323 TRP cc_start: 0.8130 (t60) cc_final: 0.7908 (t-100) REVERT: C 310 GLU cc_start: 0.8726 (mp0) cc_final: 0.8426 (mp0) REVERT: D 310 GLU cc_start: 0.8708 (mp0) cc_final: 0.8445 (mp0) outliers start: 19 outliers final: 17 residues processed: 193 average time/residue: 0.1946 time to fit residues: 59.1925 Evaluate side-chains 189 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 356 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 134 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 320 GLN ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 GLN ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.135201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.096344 restraints weight = 21507.093| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.18 r_work: 0.2918 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12772 Z= 0.096 Angle : 0.434 6.903 17328 Z= 0.222 Chirality : 0.036 0.159 2100 Planarity : 0.002 0.025 2108 Dihedral : 6.788 59.530 2232 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.79 % Allowed : 12.59 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1676 helix: 1.37 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.83 (0.36), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 323 HIS 0.002 0.001 HIS C 236 PHE 0.009 0.001 PHE B 291 TYR 0.017 0.002 TYR A 326 ARG 0.003 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.03095 ( 836) hydrogen bonds : angle 3.02190 ( 2472) covalent geometry : bond 0.00216 (12768) covalent geometry : angle 0.43374 (17328) Misc. bond : bond 0.00016 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7958 (m) REVERT: A 310 GLU cc_start: 0.8765 (mp0) cc_final: 0.8282 (mp0) REVERT: A 323 TRP cc_start: 0.8121 (t60) cc_final: 0.7875 (t60) REVERT: B 323 TRP cc_start: 0.8163 (t60) cc_final: 0.7895 (t60) REVERT: C 310 GLU cc_start: 0.8770 (mp0) cc_final: 0.8279 (mp0) REVERT: C 323 TRP cc_start: 0.8121 (t60) cc_final: 0.7874 (t60) REVERT: D 63 CYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7897 (m) REVERT: D 306 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8118 (tm-30) REVERT: D 323 TRP cc_start: 0.8157 (t60) cc_final: 0.7914 (t60) outliers start: 19 outliers final: 16 residues processed: 186 average time/residue: 0.1693 time to fit residues: 51.0606 Evaluate side-chains 186 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 356 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 8 optimal weight: 0.0670 chunk 50 optimal weight: 6.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 GLN ** D 340 HIS ** 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 = 0.3750 r_free = 0.3750 target = 0.136118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.095738 restraints weight = 21224.651| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.07 r_work: 0.2963 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12772 Z= 0.088 Angle : 0.431 9.011 17328 Z= 0.218 Chirality : 0.036 0.159 2100 Planarity : 0.002 0.025 2108 Dihedral : 6.639 59.398 2232 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.60 % Allowed : 12.88 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.21), residues: 1676 helix: 1.66 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.70 (0.36), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 221 HIS 0.002 0.001 HIS B 328 PHE 0.008 0.001 PHE B 291 TYR 0.017 0.002 TYR D 326 ARG 0.003 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 836) hydrogen bonds : angle 2.94995 ( 2472) covalent geometry : bond 0.00191 (12768) covalent geometry : angle 0.43081 (17328) Misc. bond : bond 0.00011 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLU cc_start: 0.8727 (mp0) cc_final: 0.8259 (mp0) REVERT: A 323 TRP cc_start: 0.8017 (t60) cc_final: 0.7787 (t60) REVERT: B 323 TRP cc_start: 0.8116 (t60) cc_final: 0.7869 (t60) REVERT: C 310 GLU cc_start: 0.8716 (mp0) cc_final: 0.8242 (mp0) REVERT: C 323 TRP cc_start: 0.8061 (t60) cc_final: 0.7821 (t60) REVERT: D 306 GLN cc_start: 0.8592 (tm-30) cc_final: 0.7954 (tm-30) REVERT: D 323 TRP cc_start: 0.8061 (t60) cc_final: 0.7832 (t60) outliers start: 17 outliers final: 15 residues processed: 186 average time/residue: 0.1781 time to fit residues: 53.9470 Evaluate side-chains 182 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 356 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 85 optimal weight: 30.0000 chunk 40 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN B 320 GLN C 107 GLN D 107 GLN D 320 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.093932 restraints weight = 21261.567| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.06 r_work: 0.2933 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12772 Z= 0.124 Angle : 0.466 6.983 17328 Z= 0.236 Chirality : 0.037 0.156 2100 Planarity : 0.002 0.025 2108 Dihedral : 6.884 59.931 2232 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.88 % Allowed : 12.97 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.21), residues: 1676 helix: 1.68 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -0.47 (0.37), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 221 HIS 0.003 0.001 HIS C 328 PHE 0.013 0.001 PHE B 291 TYR 0.017 0.002 TYR D 326 ARG 0.002 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 836) hydrogen bonds : angle 3.11118 ( 2472) covalent geometry : bond 0.00292 (12768) covalent geometry : angle 0.46573 (17328) Misc. bond : bond 0.00008 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 TRP cc_start: 0.8056 (t60) cc_final: 0.7841 (t60) REVERT: B 323 TRP cc_start: 0.8056 (t60) cc_final: 0.7807 (t60) REVERT: C 323 TRP cc_start: 0.8024 (t60) cc_final: 0.7808 (t60) REVERT: D 323 TRP cc_start: 0.8018 (t60) cc_final: 0.7783 (t60) outliers start: 20 outliers final: 20 residues processed: 184 average time/residue: 0.1773 time to fit residues: 53.1128 Evaluate side-chains 185 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 356 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 133 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 153 optimal weight: 0.0970 chunk 13 optimal weight: 0.0060 chunk 11 optimal weight: 6.9990 chunk 147 optimal weight: 0.0970 chunk 97 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 163 optimal weight: 30.0000 chunk 130 optimal weight: 0.7980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.097372 restraints weight = 21115.568| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.07 r_work: 0.2995 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12772 Z= 0.082 Angle : 0.424 8.773 17328 Z= 0.213 Chirality : 0.035 0.169 2100 Planarity : 0.002 0.025 2108 Dihedral : 6.474 59.943 2232 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.13 % Allowed : 13.53 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.21), residues: 1676 helix: 1.98 (0.14), residues: 1304 sheet: None (None), residues: 0 loop : -0.42 (0.36), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 221 HIS 0.002 0.000 HIS A 299 PHE 0.007 0.001 PHE A 59 TYR 0.017 0.001 TYR D 326 ARG 0.003 0.000 ARG D 287 Details of bonding type rmsd hydrogen bonds : bond 0.02787 ( 836) hydrogen bonds : angle 2.89310 ( 2472) covalent geometry : bond 0.00167 (12768) covalent geometry : angle 0.42444 (17328) Misc. bond : bond 0.00007 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 TRP cc_start: 0.8013 (t60) cc_final: 0.7787 (t60) REVERT: B 323 TRP cc_start: 0.8003 (t60) cc_final: 0.7793 (t60) REVERT: C 323 TRP cc_start: 0.8006 (t60) cc_final: 0.7780 (t60) REVERT: D 323 TRP cc_start: 0.8027 (t60) cc_final: 0.7791 (t60) outliers start: 12 outliers final: 12 residues processed: 196 average time/residue: 0.1863 time to fit residues: 59.4745 Evaluate side-chains 183 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 155 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 45 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 320 GLN A 340 HIS B 201 ASN B 320 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 201 ASN C 340 HIS D 107 GLN D 320 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096077 restraints weight = 21195.242| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.04 r_work: 0.2954 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12772 Z= 0.104 Angle : 0.446 6.922 17328 Z= 0.227 Chirality : 0.036 0.164 2100 Planarity : 0.002 0.025 2108 Dihedral : 6.593 59.906 2232 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.41 % Allowed : 13.91 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.21), residues: 1676 helix: 2.01 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -0.20 (0.37), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 221 HIS 0.002 0.001 HIS D 236 PHE 0.011 0.001 PHE B 291 TYR 0.018 0.002 TYR D 326 ARG 0.002 0.000 ARG D 287 Details of bonding type rmsd hydrogen bonds : bond 0.02997 ( 836) hydrogen bonds : angle 2.99675 ( 2472) covalent geometry : bond 0.00241 (12768) covalent geometry : angle 0.44630 (17328) Misc. bond : bond 0.00012 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 TRP cc_start: 0.7993 (t60) cc_final: 0.7774 (t60) REVERT: B 323 TRP cc_start: 0.7992 (t60) cc_final: 0.7758 (t60) REVERT: C 323 TRP cc_start: 0.8008 (t60) cc_final: 0.7781 (t60) REVERT: D 306 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8225 (tm-30) REVERT: D 323 TRP cc_start: 0.8064 (t60) cc_final: 0.7852 (t60) outliers start: 15 outliers final: 14 residues processed: 175 average time/residue: 0.1801 time to fit residues: 51.5068 Evaluate side-chains 173 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 72 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 320 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN D 107 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.097060 restraints weight = 21120.821| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.13 r_work: 0.2946 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12772 Z= 0.100 Angle : 0.447 9.199 17328 Z= 0.225 Chirality : 0.036 0.163 2100 Planarity : 0.002 0.025 2108 Dihedral : 6.577 59.882 2232 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.22 % Allowed : 14.19 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.21), residues: 1676 helix: 2.05 (0.14), residues: 1312 sheet: None (None), residues: 0 loop : -0.11 (0.38), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 221 HIS 0.003 0.001 HIS C 340 PHE 0.010 0.001 PHE B 291 TYR 0.019 0.002 TYR D 326 ARG 0.002 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 836) hydrogen bonds : angle 2.98246 ( 2472) covalent geometry : bond 0.00228 (12768) covalent geometry : angle 0.44746 (17328) Misc. bond : bond 0.00012 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6300.82 seconds wall clock time: 108 minutes 41.56 seconds (6521.56 seconds total)