Starting phenix.real_space_refine on Sat Sep 12 01:39:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6cnm_7537/09_2026/6cnm_7537.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cnm_7537/09_2026/6cnm_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6cnm_7537/09_2026/6cnm_7537.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6cnm_7537/09_2026/6cnm_7537.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cnm_7537/09_2026/6cnm_7537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cnm_7537/09_2026/6cnm_7537.map" model { file = "/net/cci-nas-00/data/ceres_data/6cnm_7537/09_2026/6cnm_7537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cnm_7537/09_2026/6cnm_7537.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 6, 'ASP:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 5, 'TYR:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} 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: {'ARG:plan': 6, 'ASP:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 5, 'TYR:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} 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: {'ARG:plan': 6, 'ASP:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 5, 'TYR:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} 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: {'ARG:plan': 6, 'ASP:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 5, 'TYR:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} 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: {'GLU:plan': 12, 'ARG:plan': 4, 'ASP:plan': 7, 'ASN:plan1': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2} 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: {'GLU:plan': 12, 'ARG:plan': 4, 'ASP:plan': 7, 'ASN:plan1': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2} 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: {'GLU:plan': 12, 'ARG:plan': 4, 'ASP:plan': 7, 'ASN:plan1': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2} 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: {'GLU:plan': 12, 'ARG:plan': 4, 'ASP:plan': 7, 'ASN:plan1': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2} 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: 32 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: 32 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: 32 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: 32 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.47, per 1000 atoms: 0.20 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: 1.05 Conformation dependent library (CDL) restraints added in 562.6 milliseconds 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: 0.31 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: 1.57 Time building geometry restraints manager: 1.40 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 - 16.57: 7090 16.57 - 33.13: 214 33.13 - 49.70: 68 49.70 - 66.27: 12 66.27 - 82.84: 8 Dihedral angle restraints: 7392 sinusoidal: 2516 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 7389 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: 1.730 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.850 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 10.533 82.836 4232 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.014 0.001 ARG A 228 TYR 0.027 0.005 TYR B 307 PHE 0.029 0.003 PHE B 291 TRP 0.026 0.003 TRP A 221 HIS 0.012 0.002 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00976 / 0.43 (12768) covalent geometry : angle 1.11404 / 0.57 (17328) hydrogen bonds : bond 0.13056 / 8.15 ( 836) hydrogen bonds : angle 6.11072 / 4.25 ( 2472) Misc. bond : bond 0.00058 / 0.04 ( 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 : 0.443 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: 0.1121 time to fit residues: 42.4276 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 : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3735 r_free = 0.3735 target = 0.135272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.097545 restraints weight = 21428.748| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.01 r_work: 0.2967 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12772 Z= 0.120 Angle : 0.534 7.759 17328 Z= 0.271 Chirality : 0.038 0.139 2100 Planarity : 0.003 0.031 2108 Dihedral : 8.539 66.260 1912 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.19), residues: 1676 helix: -0.93 (0.13), residues: 1300 sheet: None (None), residues: 0 loop : -1.13 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 317 TYR 0.018 0.002 TYR A 326 PHE 0.011 0.001 PHE B 291 TRP 0.015 0.001 TRP C 221 HIS 0.004 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12768) covalent geometry : angle 0.53400 / 0.27 (17328) hydrogen bonds : bond 0.03880 / 2.50 ( 836) hydrogen bonds : angle 3.79084 / 2.65 ( 2472) Misc. bond : bond 0.00003 / 0.00 ( 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 214 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.482 Fit side-chains REVERT: A 46 MET cc_start: 0.8710 (ttp) cc_final: 0.8343 (ttm) REVERT: A 156 MET cc_start: 0.9147 (mmm) cc_final: 0.8939 (mtp) REVERT: A 295 GLU cc_start: 0.8599 (mt-10) cc_final: 0.7925 (mt-10) REVERT: A 306 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7563 (tm-30) REVERT: A 310 GLU cc_start: 0.8720 (mp0) cc_final: 0.8284 (mp0) REVERT: A 348 ILE cc_start: 0.8855 (pt) cc_final: 0.8615 (mt) REVERT: A 356 LEU cc_start: 0.8613 (tp) cc_final: 0.8149 (mt) REVERT: B 46 MET cc_start: 0.8716 (ttp) cc_final: 0.8349 (ttm) REVERT: B 156 MET cc_start: 0.9156 (mmm) cc_final: 0.8946 (mtp) REVERT: B 295 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7998 (mt-10) REVERT: B 306 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7560 (tm-30) REVERT: B 310 GLU cc_start: 0.8745 (mp0) cc_final: 0.8320 (mp0) REVERT: B 348 ILE cc_start: 0.8844 (pt) cc_final: 0.8603 (mt) REVERT: C 46 MET cc_start: 0.8709 (ttp) cc_final: 0.8342 (ttm) REVERT: C 156 MET cc_start: 0.9149 (mmm) cc_final: 0.8938 (mtp) REVERT: C 295 GLU cc_start: 0.8603 (mt-10) cc_final: 0.7918 (mt-10) REVERT: C 306 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7566 (tm-30) REVERT: C 310 GLU cc_start: 0.8705 (mp0) cc_final: 0.8264 (mp0) REVERT: C 348 ILE cc_start: 0.8841 (pt) cc_final: 0.8600 (mt) REVERT: C 356 LEU cc_start: 0.8624 (tp) cc_final: 0.8163 (mt) REVERT: D 46 MET cc_start: 0.8693 (ttp) cc_final: 0.8316 (ttm) REVERT: D 156 MET cc_start: 0.9159 (mmm) cc_final: 0.8769 (mtp) REVERT: D 295 GLU cc_start: 0.8603 (mt-10) cc_final: 0.7920 (mt-10) REVERT: D 310 GLU cc_start: 0.8747 (mp0) cc_final: 0.8542 (mp0) REVERT: D 348 ILE cc_start: 0.8856 (pt) cc_final: 0.8620 (mt) REVERT: D 356 LEU cc_start: 0.8611 (tp) cc_final: 0.8292 (mm) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.0814 time to fit residues: 27.3248 Evaluate side-chains 172 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 16 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 147 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN B 353 GLN C 353 GLN ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096830 restraints weight = 21469.013| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.11 r_work: 0.2962 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12772 Z= 0.107 Angle : 0.472 7.170 17328 Z= 0.240 Chirality : 0.037 0.118 2100 Planarity : 0.002 0.027 2108 Dihedral : 7.463 59.084 1912 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.47 % Allowed : 11.37 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.20), residues: 1676 helix: 0.21 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.96 (0.36), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 317 TYR 0.015 0.002 TYR F 138 PHE 0.011 0.001 PHE B 291 TRP 0.012 0.001 TRP B 221 HIS 0.004 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (12768) covalent geometry : angle 0.47237 / 0.24 (17328) hydrogen bonds : bond 0.03412 / 2.20 ( 836) hydrogen bonds : angle 3.30300 / 2.32 ( 2472) Misc. bond : bond 0.00008 / 0.00 ( 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 192 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7596 (tm-30) REVERT: A 310 GLU cc_start: 0.8721 (mp0) cc_final: 0.8485 (mp0) REVERT: A 323 TRP cc_start: 0.8060 (t60) cc_final: 0.7854 (t60) REVERT: B 306 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7736 (tm-30) REVERT: B 323 TRP cc_start: 0.8041 (t60) cc_final: 0.7841 (t60) REVERT: B 356 LEU cc_start: 0.8600 (tp) cc_final: 0.8286 (mm) REVERT: C 310 GLU cc_start: 0.8720 (mp0) cc_final: 0.8472 (mp0) REVERT: C 356 LEU cc_start: 0.8604 (tp) cc_final: 0.8287 (mm) REVERT: D 156 MET cc_start: 0.9171 (mmm) cc_final: 0.8938 (mtp) REVERT: D 306 GLN cc_start: 0.8478 (tm-30) cc_final: 0.7546 (tm-30) REVERT: D 348 ILE cc_start: 0.8789 (pt) cc_final: 0.8587 (mt) outliers start: 5 outliers final: 5 residues processed: 191 average time/residue: 0.0743 time to fit residues: 23.5893 Evaluate side-chains 180 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 175 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain D residue 89 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 74 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 104 optimal weight: 0.0670 chunk 143 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097245 restraints weight = 21483.720| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.25 r_work: 0.2962 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2555 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= 0.093 Angle : 0.442 6.879 17328 Z= 0.225 Chirality : 0.036 0.116 2100 Planarity : 0.002 0.026 2108 Dihedral : 6.876 59.995 1912 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.03 % Allowed : 11.75 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1676 helix: 0.83 (0.14), residues: 1304 sheet: None (None), residues: 0 loop : -0.93 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 317 TYR 0.013 0.001 TYR D 326 PHE 0.008 0.001 PHE D 291 TRP 0.022 0.001 TRP C 323 HIS 0.004 0.001 HIS C 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (12768) covalent geometry : angle 0.44186 / 0.23 (17328) hydrogen bonds : bond 0.03148 / 2.03 ( 836) hydrogen bonds : angle 3.07689 / 2.18 ( 2472) Misc. bond : bond 0.00012 / 0.01 ( 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 203 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.9105 (mtp) cc_final: 0.8820 (mtp) REVERT: A 288 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8305 (mtmt) REVERT: A 306 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7842 (tm-30) REVERT: A 323 TRP cc_start: 0.8046 (t60) cc_final: 0.7811 (t60) REVERT: B 156 MET cc_start: 0.9102 (mtp) cc_final: 0.8813 (mtp) REVERT: B 306 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7841 (tm-30) REVERT: B 323 TRP cc_start: 0.8050 (t60) cc_final: 0.7826 (t60) REVERT: B 356 LEU cc_start: 0.8587 (tp) cc_final: 0.8271 (mm) REVERT: C 156 MET cc_start: 0.9103 (mtp) cc_final: 0.8814 (mtp) REVERT: C 288 LYS cc_start: 0.8624 (mmtt) cc_final: 0.8307 (mtmt) REVERT: C 306 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7839 (tm-30) REVERT: D 288 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8302 (mtmt) REVERT: D 306 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7976 (tm-30) REVERT: D 348 ILE cc_start: 0.8779 (pt) cc_final: 0.8523 (mt) outliers start: 11 outliers final: 11 residues processed: 200 average time/residue: 0.0747 time to fit residues: 24.4131 Evaluate side-chains 186 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 163 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 302 MET Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 302 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 133 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 107 GLN ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.093820 restraints weight = 21523.825| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.04 r_work: 0.2930 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12772 Z= 0.135 Angle : 0.486 6.948 17328 Z= 0.247 Chirality : 0.038 0.124 2100 Planarity : 0.003 0.025 2108 Dihedral : 6.829 59.904 1912 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.79 % Allowed : 12.03 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.21), residues: 1676 helix: 1.04 (0.14), residues: 1316 sheet: None (None), residues: 0 loop : -0.77 (0.37), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.019 0.002 TYR D 326 PHE 0.014 0.001 PHE B 291 TRP 0.010 0.001 TRP D 323 HIS 0.003 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (12768) covalent geometry : angle 0.48560 / 0.25 (17328) hydrogen bonds : bond 0.03454 / 2.23 ( 836) hydrogen bonds : angle 3.23742 / 2.29 ( 2472) Misc. bond : bond 0.00009 / 0.01 ( 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 191 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.9059 (mtp) cc_final: 0.8829 (mtp) REVERT: A 288 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8321 (mtmt) REVERT: B 156 MET cc_start: 0.9060 (mtp) cc_final: 0.8826 (mtp) REVERT: C 156 MET cc_start: 0.9055 (mtp) cc_final: 0.8820 (mtp) REVERT: C 288 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8324 (mtmt) REVERT: D 288 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8321 (mtmt) REVERT: D 306 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8253 (tm-30) REVERT: D 323 TRP cc_start: 0.8133 (t60) cc_final: 0.7887 (t60) outliers start: 19 outliers final: 15 residues processed: 191 average time/residue: 0.0802 time to fit residues: 25.0410 Evaluate side-chains 177 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 74 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 29 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 125 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 GLN B 320 GLN C 107 GLN C 320 GLN 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 = 0.132133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.092089 restraints weight = 21442.387| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.08 r_work: 0.2903 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12772 Z= 0.166 Angle : 0.524 8.216 17328 Z= 0.264 Chirality : 0.040 0.142 2100 Planarity : 0.003 0.026 2108 Dihedral : 6.880 58.954 1912 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.79 % Allowed : 12.22 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.21), residues: 1676 helix: 1.12 (0.14), residues: 1312 sheet: None (None), residues: 0 loop : -0.69 (0.39), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 287 TYR 0.019 0.002 TYR C 326 PHE 0.013 0.002 PHE B 291 TRP 0.029 0.002 TRP C 323 HIS 0.003 0.001 HIS D 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (12768) covalent geometry : angle 0.52444 / 0.26 (17328) hydrogen bonds : bond 0.03676 / 2.37 ( 836) hydrogen bonds : angle 3.36987 / 2.38 ( 2472) Misc. bond : bond 0.00017 / 0.01 ( 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 176 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8336 (mtmt) REVERT: A 323 TRP cc_start: 0.8196 (t60) cc_final: 0.7920 (t60) REVERT: B 323 TRP cc_start: 0.8211 (t60) cc_final: 0.7951 (t60) REVERT: C 288 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8343 (mtmt) REVERT: D 288 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8349 (mtmt) REVERT: D 306 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8322 (tm-30) REVERT: D 323 TRP cc_start: 0.8198 (t60) cc_final: 0.7970 (t60) outliers start: 19 outliers final: 19 residues processed: 175 average time/residue: 0.0820 time to fit residues: 23.4281 Evaluate side-chains 175 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 173 VAL Chi-restraints excluded: chain B residue 356 LEU 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 C residue 173 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 38 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 20 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 GLN B 320 GLN D 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096081 restraints weight = 21262.562| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.14 r_work: 0.2949 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2944 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= 0.092 Angle : 0.444 7.745 17328 Z= 0.224 Chirality : 0.036 0.155 2100 Planarity : 0.002 0.026 2108 Dihedral : 6.309 59.582 1912 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.60 % Allowed : 12.41 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.21), residues: 1676 helix: 1.51 (0.14), residues: 1304 sheet: None (None), residues: 0 loop : -0.70 (0.36), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 317 TYR 0.018 0.001 TYR D 326 PHE 0.008 0.001 PHE C 291 TRP 0.037 0.001 TRP C 323 HIS 0.004 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (12768) covalent geometry : angle 0.44405 / 0.22 (17328) hydrogen bonds : bond 0.03095 / 2.00 ( 836) hydrogen bonds : angle 3.04705 / 2.15 ( 2472) Misc. bond : bond 0.00007 / 0.00 ( 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 185 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8323 (mtmt) REVERT: A 323 TRP cc_start: 0.8172 (t60) cc_final: 0.7919 (t60) REVERT: B 288 LYS cc_start: 0.8634 (mmtt) cc_final: 0.8324 (mtmt) REVERT: B 323 TRP cc_start: 0.8176 (t60) cc_final: 0.7909 (t60) REVERT: C 288 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8326 (mtmt) REVERT: D 288 LYS cc_start: 0.8652 (mmtt) cc_final: 0.8298 (mtmt) REVERT: D 306 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8241 (tm-30) REVERT: D 323 TRP cc_start: 0.8109 (t60) cc_final: 0.7898 (t60) outliers start: 17 outliers final: 12 residues processed: 184 average time/residue: 0.0756 time to fit residues: 22.4744 Evaluate side-chains 175 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 89 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 163 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 55 optimal weight: 0.0050 chunk 150 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 320 GLN B 201 ASN B 320 GLN C 201 ASN C 320 GLN D 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.093054 restraints weight = 21385.078| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.07 r_work: 0.2918 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12772 Z= 0.142 Angle : 0.493 6.914 17328 Z= 0.249 Chirality : 0.039 0.149 2100 Planarity : 0.003 0.026 2108 Dihedral : 6.583 59.196 1912 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.79 % Allowed : 12.41 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.21), residues: 1676 helix: 1.55 (0.14), residues: 1312 sheet: None (None), residues: 0 loop : -0.59 (0.38), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 287 TYR 0.021 0.002 TYR B 326 PHE 0.014 0.001 PHE B 291 TRP 0.010 0.001 TRP D 221 HIS 0.003 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (12768) covalent geometry : angle 0.49349 / 0.25 (17328) hydrogen bonds : bond 0.03452 / 2.22 ( 836) hydrogen bonds : angle 3.24083 / 2.29 ( 2472) Misc. bond : bond 0.00011 / 0.01 ( 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 179 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8353 (mtmt) REVERT: A 323 TRP cc_start: 0.8153 (t60) cc_final: 0.7865 (t60) REVERT: B 288 LYS cc_start: 0.8676 (mmtt) cc_final: 0.8356 (mtmt) REVERT: B 323 TRP cc_start: 0.8149 (t60) cc_final: 0.7894 (t60) REVERT: C 288 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8357 (mtmt) REVERT: D 288 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8345 (mtmt) REVERT: D 306 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8323 (tm-30) outliers start: 19 outliers final: 17 residues processed: 178 average time/residue: 0.0826 time to fit residues: 23.7936 Evaluate side-chains 175 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 201 ASN Chi-restraints excluded: chain A residue 302 MET 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 201 ASN 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 C residue 201 ASN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 95 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 320 GLN D 320 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.094420 restraints weight = 21399.851| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.11 r_work: 0.2915 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12772 Z= 0.137 Angle : 0.492 8.774 17328 Z= 0.247 Chirality : 0.038 0.153 2100 Planarity : 0.002 0.026 2108 Dihedral : 6.534 58.538 1912 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.60 % Allowed : 12.31 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.21), residues: 1676 helix: 1.60 (0.14), residues: 1312 sheet: None (None), residues: 0 loop : -0.57 (0.38), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.020 0.002 TYR B 326 PHE 0.013 0.001 PHE B 291 TRP 0.036 0.001 TRP C 323 HIS 0.003 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (12768) covalent geometry : angle 0.49218 / 0.25 (17328) hydrogen bonds : bond 0.03421 / 2.20 ( 836) hydrogen bonds : angle 3.23441 / 2.28 ( 2472) Misc. bond : bond 0.00004 / 0.00 ( 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 179 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8335 (mtmt) REVERT: A 323 TRP cc_start: 0.8151 (t60) cc_final: 0.7883 (t60) REVERT: B 288 LYS cc_start: 0.8664 (mmtt) cc_final: 0.8332 (mtmt) REVERT: B 323 TRP cc_start: 0.8159 (t60) cc_final: 0.7894 (t60) REVERT: C 288 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8340 (mtmt) REVERT: C 323 TRP cc_start: 0.8268 (t60) cc_final: 0.8015 (t-100) REVERT: D 288 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8325 (mtmt) REVERT: D 306 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8304 (tm-30) outliers start: 17 outliers final: 16 residues processed: 179 average time/residue: 0.0787 time to fit residues: 22.9231 Evaluate side-chains 178 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 36 optimal weight: 1.9990 chunk 135 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 105 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.135534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.097265 restraints weight = 21354.431| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.01 r_work: 0.2972 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12772 Z= 0.092 Angle : 0.446 9.105 17328 Z= 0.224 Chirality : 0.036 0.167 2100 Planarity : 0.002 0.026 2108 Dihedral : 6.140 58.770 1912 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.22 % Allowed : 13.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.21), residues: 1676 helix: 1.88 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.49 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 317 TYR 0.019 0.002 TYR C 326 PHE 0.008 0.001 PHE B 291 TRP 0.042 0.001 TRP D 323 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (12768) covalent geometry : angle 0.44603 / 0.22 (17328) hydrogen bonds : bond 0.03014 / 1.94 ( 836) hydrogen bonds : angle 3.05048 / 2.16 ( 2472) Misc. bond : bond 0.00002 / 0.00 ( 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 184 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8255 (mtmt) REVERT: A 323 TRP cc_start: 0.8093 (t60) cc_final: 0.7816 (t60) REVERT: B 288 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8248 (mtmt) REVERT: B 323 TRP cc_start: 0.8127 (t60) cc_final: 0.7858 (t60) REVERT: C 288 LYS cc_start: 0.8635 (mmtt) cc_final: 0.8250 (mtmt) REVERT: D 288 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8297 (mtmt) outliers start: 13 outliers final: 12 residues processed: 184 average time/residue: 0.0834 time to fit residues: 24.6575 Evaluate side-chains 174 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 89 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 VAL 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 89 THR 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 57 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 114 optimal weight: 0.0070 chunk 117 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 320 GLN ** C 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 GLN D 201 ASN D 320 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095495 restraints weight = 21426.030| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.03 r_work: 0.2954 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 12772 Z= 0.097 Angle : 0.449 8.795 17328 Z= 0.225 Chirality : 0.036 0.163 2100 Planarity : 0.002 0.026 2108 Dihedral : 6.112 59.091 1912 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.32 % Allowed : 13.44 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.21), residues: 1676 helix: 1.92 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -0.22 (0.37), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 317 TYR 0.024 0.002 TYR B 326 PHE 0.010 0.001 PHE C 291 TRP 0.010 0.001 TRP D 221 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (12768) covalent geometry : angle 0.44924 / 0.23 (17328) hydrogen bonds : bond 0.03033 / 1.95 ( 836) hydrogen bonds : angle 3.05038 / 2.16 ( 2472) Misc. bond : bond 0.00009 / 0.01 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2780.53 seconds wall clock time: 48 minutes 17.92 seconds (2897.92 seconds total)