Starting phenix.real_space_refine on Thu Jul 31 01:30:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cjq_7482/07_2025/6cjq_7482.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cjq_7482/07_2025/6cjq_7482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cjq_7482/07_2025/6cjq_7482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cjq_7482/07_2025/6cjq_7482.map" model { file = "/net/cci-nas-00/data/ceres_data/6cjq_7482/07_2025/6cjq_7482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cjq_7482/07_2025/6cjq_7482.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 8472 2.51 5 N 2068 2.21 5 O 2200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12768 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "D" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'PGW': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 6, 'PGW:plan-2': 6, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'PGW': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 6, 'PGW:plan-2': 6, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 58 Restraints were copied for chains: B, C Time building chain proxies: 8.51, per 1000 atoms: 0.67 Number of scatterers: 12768 At special positions: 0 Unit cell: (106.322, 106.322, 120.571, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 2200 8.00 N 2068 7.00 C 8472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 153 " distance=0.00 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 387 " distance=0.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.7 seconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 67.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 10 through 35 removed outlier: 4.537A pdb=" N VAL A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP A 15 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 3.712A pdb=" N VAL A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 65 removed outlier: 6.464A pdb=" N LEU A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 4.101A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 4.831A pdb=" N PHE A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 91 through 98 removed outlier: 4.690A pdb=" N VAL A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 104 No H-bonds generated for 'chain 'A' and resid 103 through 104' Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.766A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 removed outlier: 4.152A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 158 removed outlier: 3.865A pdb=" N GLY A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 181 removed outlier: 4.172A pdb=" N TYR A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 224 removed outlier: 3.822A pdb=" N TYR A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.580A pdb=" N HIS A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.638A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.612A pdb=" N LEU A 276 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 278' Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.939A pdb=" N GLU A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 298' Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.857A pdb=" N ASP A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 5.129A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 394 through 403 removed outlier: 4.824A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 4.106A pdb=" N GLN A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 35 removed outlier: 4.537A pdb=" N VAL B 14 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP B 15 " --> pdb=" O TYR B 11 " (cutoff:3.500A) Proline residue: B 31 - end of helix removed outlier: 3.712A pdb=" N VAL B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 65 removed outlier: 6.464A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Proline residue: B 45 - end of helix removed outlier: 4.101A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 4.831A pdb=" N PHE B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 91 through 98 removed outlier: 4.690A pdb=" N VAL B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE B 96 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 104 No H-bonds generated for 'chain 'B' and resid 103 through 104' Processing helix chain 'B' and resid 105 through 114 removed outlier: 3.766A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 126 removed outlier: 4.152A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 158 removed outlier: 3.865A pdb=" N GLY B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 removed outlier: 4.172A pdb=" N TYR B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 224 removed outlier: 3.822A pdb=" N TYR B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 245 removed outlier: 3.580A pdb=" N HIS B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.638A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 278 removed outlier: 3.612A pdb=" N LEU B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 278' Processing helix chain 'B' and resid 281 through 292 Processing helix chain 'B' and resid 293 through 298 removed outlier: 3.939A pdb=" N GLU B 297 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 293 through 298' Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.857A pdb=" N ASP B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 5.129A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU B 373 " --> pdb=" O MET B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 394 through 403 removed outlier: 4.824A pdb=" N ARG B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 415 removed outlier: 4.106A pdb=" N GLN B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 35 removed outlier: 4.537A pdb=" N VAL C 14 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Proline residue: C 31 - end of helix removed outlier: 3.712A pdb=" N VAL C 35 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 65 removed outlier: 6.464A pdb=" N LEU C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Proline residue: C 45 - end of helix removed outlier: 4.101A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 4.831A pdb=" N PHE C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 91 through 98 removed outlier: 4.690A pdb=" N VAL C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 104 No H-bonds generated for 'chain 'C' and resid 103 through 104' Processing helix chain 'C' and resid 105 through 114 removed outlier: 3.766A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 126 removed outlier: 4.152A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 158 removed outlier: 3.865A pdb=" N GLY C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 181 removed outlier: 4.172A pdb=" N TYR C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 224 removed outlier: 3.822A pdb=" N TYR C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 245 removed outlier: 3.580A pdb=" N HIS C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.638A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 278 removed outlier: 3.612A pdb=" N LEU C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS C 277 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 278' Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 293 through 298 removed outlier: 3.939A pdb=" N GLU C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 293 through 298' Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.857A pdb=" N ASP C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 5.129A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 394 through 403 removed outlier: 4.824A pdb=" N ARG C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 415 removed outlier: 4.106A pdb=" N GLN C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU C 413 " --> pdb=" O ALA C 409 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 35 removed outlier: 4.537A pdb=" N VAL D 14 " --> pdb=" O THR D 10 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP D 15 " --> pdb=" O TYR D 11 " (cutoff:3.500A) Proline residue: D 31 - end of helix removed outlier: 3.712A pdb=" N VAL D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 65 removed outlier: 6.464A pdb=" N LEU D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Proline residue: D 45 - end of helix removed outlier: 4.101A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 4.831A pdb=" N PHE D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 91 through 98 removed outlier: 4.690A pdb=" N VAL D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE D 96 " --> pdb=" O ASP D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 104 No H-bonds generated for 'chain 'D' and resid 103 through 104' Processing helix chain 'D' and resid 105 through 114 removed outlier: 3.766A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 126 removed outlier: 4.152A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 158 removed outlier: 3.865A pdb=" N GLY D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 181 removed outlier: 4.172A pdb=" N TYR D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D 181 " --> pdb=" O THR D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 224 removed outlier: 3.822A pdb=" N TYR D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.580A pdb=" N HIS D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.638A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 278 removed outlier: 3.612A pdb=" N LEU D 276 " --> pdb=" O GLU D 272 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS D 277 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 278' Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 293 through 298 removed outlier: 3.939A pdb=" N GLU D 297 " --> pdb=" O GLY D 293 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 293 through 298' Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.857A pdb=" N ASP D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 5.129A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU D 373 " --> pdb=" O MET D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 373' Processing helix chain 'D' and resid 394 through 403 removed outlier: 4.824A pdb=" N ARG D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 415 removed outlier: 4.106A pdb=" N GLN D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU D 413 " --> pdb=" O ALA D 409 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3100 1.33 - 1.45: 2308 1.45 - 1.57: 7572 1.57 - 1.68: 0 1.68 - 1.80: 48 Bond restraints: 13028 Sorted by residual: bond pdb=" CG LEU B 43 " pdb=" CD2 LEU B 43 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" CG LEU A 43 " pdb=" CD2 LEU A 43 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" CG LEU C 43 " pdb=" CD2 LEU C 43 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" CG LEU D 43 " pdb=" CD2 LEU D 43 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" C PRO C 300 " pdb=" N LEU C 301 " ideal model delta sigma weight residual 1.332 1.307 0.025 1.40e-02 5.10e+03 3.30e+00 ... (remaining 13023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 16276 2.14 - 4.28: 972 4.28 - 6.42: 212 6.42 - 8.56: 144 8.56 - 10.70: 28 Bond angle restraints: 17632 Sorted by residual: angle pdb=" C ASP D 92 " pdb=" N LEU D 93 " pdb=" CA LEU D 93 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ASP A 92 " pdb=" N LEU A 93 " pdb=" CA LEU A 93 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ASP B 92 " pdb=" N LEU B 93 " pdb=" CA LEU B 93 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ASP C 92 " pdb=" N LEU C 93 " pdb=" CA LEU C 93 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C LEU C 39 " pdb=" N PHE C 40 " pdb=" CA PHE C 40 " ideal model delta sigma weight residual 121.54 130.33 -8.79 1.91e+00 2.74e-01 2.12e+01 ... (remaining 17627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.81: 7516 19.81 - 39.63: 320 39.63 - 59.44: 48 59.44 - 79.26: 16 79.26 - 99.07: 4 Dihedral angle restraints: 7904 sinusoidal: 3292 harmonic: 4612 Sorted by residual: dihedral pdb=" CB CYS B 153 " pdb=" SG CYS B 153 " pdb=" SG CYS B 153 " pdb=" CB CYS B 153 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS B 387 " pdb=" SG CYS B 387 " pdb=" SG CYS B 387 " pdb=" CB CYS B 387 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CA ILE A 189 " pdb=" C ILE A 189 " pdb=" N THR A 190 " pdb=" CA THR A 190 " ideal model delta harmonic sigma weight residual -180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 7901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1724 0.083 - 0.165: 316 0.165 - 0.248: 24 0.248 - 0.330: 4 0.330 - 0.413: 4 Chirality restraints: 2072 Sorted by residual: chirality pdb=" CB ILE C 58 " pdb=" CA ILE C 58 " pdb=" CG1 ILE C 58 " pdb=" CG2 ILE C 58 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CB ILE D 58 " pdb=" CA ILE D 58 " pdb=" CG1 ILE D 58 " pdb=" CG2 ILE D 58 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CB ILE A 58 " pdb=" CA ILE A 58 " pdb=" CG1 ILE A 58 " pdb=" CG2 ILE A 58 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 2069 not shown) Planarity restraints: 2156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 93 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LEU C 93 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU C 93 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU C 94 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 93 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LEU B 93 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU B 93 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 94 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 93 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LEU A 93 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU A 93 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 94 " -0.019 2.00e-02 2.50e+03 ... (remaining 2153 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 3712 2.82 - 3.34: 11504 3.34 - 3.86: 20656 3.86 - 4.38: 21964 4.38 - 4.90: 39418 Nonbonded interactions: 97254 Sorted by model distance: nonbonded pdb=" OG1 THR A 180 " pdb=" OH TYR D 186 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR C 186 " pdb=" OG1 THR D 180 " model vdw 2.306 3.040 nonbonded pdb=" OE2 GLU A 65 " pdb=" NH2 ARG A 124 " model vdw 2.309 3.120 ... (remaining 97249 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: 0.09 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 415 or resid 502 through 503 or (resid 506 and \ (name C15 or name C16 or name C19 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27)) or resid 501)) selection = (chain 'B' and (resid 10 through 415 or resid 502 through 503 or (resid 506 and \ (name C15 or name C16 or name C19 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27)) or resid 501)) selection = (chain 'C' and (resid 10 through 415 or resid 502 through 503 or (resid 506 and \ (name C15 or name C16 or name C19 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27)) or resid 501)) selection = (chain 'D' and (resid 10 through 415 or resid 501 or (resid 502 and (name C15 or \ name C16 or name C19 or name C20 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27)) or resid 505 or (resid 506 and (name C15 \ or name C16 or name C17 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24 or name C25 or name C26 or name C27)))) } 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.650 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 13028 Z= 0.387 Angle : 1.365 10.700 17634 Z= 0.671 Chirality : 0.064 0.413 2072 Planarity : 0.009 0.051 2156 Dihedral : 12.070 99.069 4924 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.60 % Allowed : 6.85 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.18), residues: 1552 helix: -2.04 (0.14), residues: 916 sheet: -1.86 (0.47), residues: 88 loop : -2.32 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP A 264 HIS 0.005 0.002 HIS C 281 PHE 0.011 0.002 PHE B 366 TYR 0.026 0.003 TYR C 211 ARG 0.006 0.001 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.09937 ( 584) hydrogen bonds : angle 5.08537 ( 1680) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00908 (13028) covalent geometry : angle 1.36477 (17632) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 268 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8855 (tp) REVERT: B 171 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8851 (tp) REVERT: C 171 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8853 (tp) REVERT: D 171 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8858 (tp) outliers start: 8 outliers final: 0 residues processed: 272 average time/residue: 0.2867 time to fit residues: 106.1231 Evaluate side-chains 131 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 171 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 30.0000 chunk 141 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 364 GLN B 159 GLN B 217 ASN B 364 GLN C 159 GLN C 217 ASN C 364 GLN D 159 GLN D 217 ASN D 364 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.120149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.089397 restraints weight = 23240.820| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.34 r_work: 0.3013 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13028 Z= 0.129 Angle : 0.692 8.724 17634 Z= 0.326 Chirality : 0.042 0.205 2072 Planarity : 0.006 0.054 2156 Dihedral : 9.487 79.985 1972 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.35 % Allowed : 9.23 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1552 helix: -0.30 (0.17), residues: 924 sheet: -1.49 (0.42), residues: 112 loop : -1.57 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 264 HIS 0.003 0.001 HIS B 281 PHE 0.010 0.001 PHE A 302 TYR 0.013 0.001 TYR D 128 ARG 0.006 0.001 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 584) hydrogen bonds : angle 3.95589 ( 1680) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00296 (13028) covalent geometry : angle 0.69240 (17632) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8530 (mm) REVERT: C 230 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8527 (mm) REVERT: D 230 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8504 (mm) outliers start: 45 outliers final: 8 residues processed: 153 average time/residue: 0.2060 time to fit residues: 49.1944 Evaluate side-chains 120 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 73 optimal weight: 0.0970 chunk 80 optimal weight: 0.0670 chunk 9 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.121363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.093296 restraints weight = 23446.915| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.37 r_work: 0.3046 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13028 Z= 0.104 Angle : 0.660 8.731 17634 Z= 0.296 Chirality : 0.042 0.198 2072 Planarity : 0.005 0.056 2156 Dihedral : 7.842 52.818 1964 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.12 % Allowed : 10.57 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.22), residues: 1552 helix: 0.48 (0.18), residues: 912 sheet: -1.22 (0.41), residues: 112 loop : -1.15 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 264 HIS 0.002 0.000 HIS A 149 PHE 0.006 0.001 PHE A 242 TYR 0.007 0.001 TYR D 128 ARG 0.003 0.000 ARG B 124 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 584) hydrogen bonds : angle 3.59570 ( 1680) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00230 (13028) covalent geometry : angle 0.66005 (17632) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9006 (tp) REVERT: A 369 MET cc_start: 0.8617 (ttm) cc_final: 0.8372 (mtp) REVERT: B 221 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9004 (tp) REVERT: B 313 ILE cc_start: 0.9296 (tp) cc_final: 0.8993 (tt) REVERT: B 369 MET cc_start: 0.8640 (ttm) cc_final: 0.8403 (mtp) REVERT: C 221 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9005 (tp) REVERT: C 230 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8568 (mm) REVERT: C 313 ILE cc_start: 0.9266 (tp) cc_final: 0.8962 (tt) REVERT: C 369 MET cc_start: 0.8609 (ttm) cc_final: 0.8359 (mtp) REVERT: D 230 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8575 (mm) REVERT: D 313 ILE cc_start: 0.9265 (tp) cc_final: 0.8967 (tt) REVERT: D 369 MET cc_start: 0.8604 (ttm) cc_final: 0.8350 (mtp) outliers start: 42 outliers final: 17 residues processed: 161 average time/residue: 0.2254 time to fit residues: 54.7556 Evaluate side-chains 125 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 401 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 chunk 114 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.120013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.091985 restraints weight = 23158.484| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.34 r_work: 0.3020 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13028 Z= 0.133 Angle : 0.665 9.704 17634 Z= 0.298 Chirality : 0.043 0.209 2072 Planarity : 0.005 0.056 2156 Dihedral : 7.280 46.281 1964 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.27 % Allowed : 12.28 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1552 helix: 0.81 (0.18), residues: 916 sheet: -0.25 (0.49), residues: 88 loop : -0.98 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 264 HIS 0.002 0.000 HIS A 281 PHE 0.016 0.001 PHE A 397 TYR 0.008 0.001 TYR A 175 ARG 0.003 0.000 ARG A 343 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 584) hydrogen bonds : angle 3.50988 ( 1680) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00327 (13028) covalent geometry : angle 0.66477 (17632) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.8483 (m-10) REVERT: A 221 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8998 (tp) REVERT: B 26 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8446 (m-10) REVERT: B 221 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8986 (tp) REVERT: C 26 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.8509 (m-10) REVERT: C 221 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8990 (tp) REVERT: C 230 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8602 (mm) REVERT: D 26 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8487 (m-10) REVERT: D 221 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8995 (tp) outliers start: 44 outliers final: 16 residues processed: 157 average time/residue: 0.2396 time to fit residues: 57.5177 Evaluate side-chains 126 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 401 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 105 optimal weight: 0.0870 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 130 optimal weight: 0.0970 chunk 111 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.120654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.092718 restraints weight = 23201.129| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.31 r_work: 0.3040 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13028 Z= 0.113 Angle : 0.652 10.843 17634 Z= 0.288 Chirality : 0.042 0.217 2072 Planarity : 0.005 0.055 2156 Dihedral : 6.708 43.375 1964 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.46 % Allowed : 14.14 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1552 helix: 1.05 (0.19), residues: 916 sheet: 0.14 (0.51), residues: 88 loop : -0.84 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 264 HIS 0.001 0.000 HIS D 281 PHE 0.007 0.001 PHE A 40 TYR 0.007 0.001 TYR A 175 ARG 0.003 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 584) hydrogen bonds : angle 3.43586 ( 1680) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00266 (13028) covalent geometry : angle 0.65209 (17632) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8451 (m-10) REVERT: A 221 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9014 (tp) REVERT: B 26 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8446 (m-10) REVERT: B 221 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9004 (tp) REVERT: C 26 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.8503 (m-10) REVERT: C 221 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9000 (tp) REVERT: C 230 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8591 (mm) REVERT: D 26 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8513 (m-10) REVERT: D 221 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9015 (tp) outliers start: 33 outliers final: 21 residues processed: 146 average time/residue: 0.2109 time to fit residues: 47.2721 Evaluate side-chains 132 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 401 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 131 optimal weight: 0.0670 chunk 117 optimal weight: 10.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.121866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.092018 restraints weight = 23410.967| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.21 r_work: 0.3062 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13028 Z= 0.097 Angle : 0.641 13.260 17634 Z= 0.280 Chirality : 0.042 0.237 2072 Planarity : 0.005 0.057 2156 Dihedral : 6.163 42.307 1964 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.60 % Allowed : 14.88 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.23), residues: 1552 helix: 1.32 (0.19), residues: 916 sheet: 0.35 (0.52), residues: 88 loop : -0.66 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 264 HIS 0.001 0.000 HIS B 149 PHE 0.006 0.001 PHE A 40 TYR 0.007 0.001 TYR D 327 ARG 0.003 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.02916 ( 584) hydrogen bonds : angle 3.31261 ( 1680) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00216 (13028) covalent geometry : angle 0.64101 (17632) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.8480 (m-10) REVERT: A 221 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9014 (tp) REVERT: B 26 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.8475 (m-10) REVERT: B 221 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9008 (tp) REVERT: B 229 LYS cc_start: 0.9443 (tttt) cc_final: 0.9240 (ttpt) REVERT: C 26 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.8477 (m-10) REVERT: C 221 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9008 (tp) REVERT: C 230 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8591 (mm) REVERT: D 26 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8498 (m-10) REVERT: D 221 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9026 (tp) outliers start: 35 outliers final: 19 residues processed: 164 average time/residue: 0.2195 time to fit residues: 54.8693 Evaluate side-chains 130 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 52 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 35 optimal weight: 0.0370 chunk 90 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.122100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.093938 restraints weight = 23283.910| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.47 r_work: 0.3066 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13028 Z= 0.098 Angle : 0.685 16.666 17634 Z= 0.288 Chirality : 0.042 0.230 2072 Planarity : 0.005 0.059 2156 Dihedral : 5.860 44.040 1964 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.53 % Allowed : 15.62 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.23), residues: 1552 helix: 1.52 (0.19), residues: 916 sheet: 0.42 (0.53), residues: 88 loop : -0.52 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 264 HIS 0.001 0.000 HIS A 149 PHE 0.007 0.001 PHE C 40 TYR 0.007 0.001 TYR D 327 ARG 0.003 0.000 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.02821 ( 584) hydrogen bonds : angle 3.20982 ( 1680) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00213 (13028) covalent geometry : angle 0.68472 (17632) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.8522 (m-10) REVERT: B 26 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8519 (m-10) REVERT: B 313 ILE cc_start: 0.9149 (tp) cc_final: 0.8911 (tt) REVERT: C 26 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8576 (m-10) REVERT: C 230 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8606 (mm) REVERT: D 26 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8481 (m-10) outliers start: 34 outliers final: 24 residues processed: 147 average time/residue: 0.2120 time to fit residues: 47.8287 Evaluate side-chains 131 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 129 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 0.0970 chunk 81 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.122344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.094447 restraints weight = 23321.293| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.32 r_work: 0.3066 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13028 Z= 0.097 Angle : 0.676 17.083 17634 Z= 0.285 Chirality : 0.042 0.239 2072 Planarity : 0.004 0.061 2156 Dihedral : 5.635 46.390 1964 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.46 % Allowed : 15.18 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.23), residues: 1552 helix: 1.65 (0.19), residues: 920 sheet: 0.43 (0.52), residues: 88 loop : -0.32 (0.30), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 264 HIS 0.001 0.000 HIS D 149 PHE 0.007 0.001 PHE C 397 TYR 0.007 0.001 TYR D 327 ARG 0.003 0.000 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.02801 ( 584) hydrogen bonds : angle 3.13256 ( 1680) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00212 (13028) covalent geometry : angle 0.67633 (17632) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8558 (m-10) REVERT: B 26 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.8576 (m-10) REVERT: B 313 ILE cc_start: 0.9164 (tp) cc_final: 0.8938 (tt) REVERT: C 26 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8566 (m-10) REVERT: C 230 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8645 (mm) REVERT: D 26 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8526 (m-10) outliers start: 33 outliers final: 22 residues processed: 148 average time/residue: 0.2233 time to fit residues: 50.2333 Evaluate side-chains 122 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 122 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 142 optimal weight: 0.0980 chunk 119 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.122817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.091611 restraints weight = 23451.012| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.35 r_work: 0.3054 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13028 Z= 0.099 Angle : 0.675 16.601 17634 Z= 0.285 Chirality : 0.042 0.304 2072 Planarity : 0.005 0.063 2156 Dihedral : 5.516 50.152 1964 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.08 % Allowed : 15.92 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.23), residues: 1552 helix: 1.80 (0.19), residues: 920 sheet: 0.45 (0.52), residues: 88 loop : -0.25 (0.30), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 264 HIS 0.001 0.000 HIS A 149 PHE 0.013 0.001 PHE B 96 TYR 0.008 0.001 TYR D 327 ARG 0.003 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.02849 ( 584) hydrogen bonds : angle 3.12203 ( 1680) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00219 (13028) covalent geometry : angle 0.67488 (17632) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8563 (m-10) REVERT: B 26 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8580 (m-10) REVERT: B 313 ILE cc_start: 0.9171 (tp) cc_final: 0.8940 (tt) REVERT: C 26 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8577 (m-10) REVERT: D 26 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8572 (m-10) outliers start: 28 outliers final: 21 residues processed: 132 average time/residue: 0.2176 time to fit residues: 43.4521 Evaluate side-chains 122 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 45 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.3980 chunk 129 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 142 optimal weight: 0.1980 chunk 97 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.122439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.094093 restraints weight = 23238.766| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.41 r_work: 0.3068 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13028 Z= 0.103 Angle : 0.683 16.427 17634 Z= 0.288 Chirality : 0.042 0.282 2072 Planarity : 0.005 0.063 2156 Dihedral : 5.450 54.505 1964 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.01 % Allowed : 16.00 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.23), residues: 1552 helix: 1.90 (0.19), residues: 936 sheet: 0.49 (0.52), residues: 88 loop : -0.16 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 264 HIS 0.001 0.000 HIS B 281 PHE 0.010 0.001 PHE B 96 TYR 0.008 0.001 TYR D 327 ARG 0.002 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.02878 ( 584) hydrogen bonds : angle 3.07971 ( 1680) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00234 (13028) covalent geometry : angle 0.68298 (17632) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8565 (m-10) REVERT: B 26 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8578 (m-10) REVERT: B 313 ILE cc_start: 0.9181 (tp) cc_final: 0.8889 (tt) REVERT: C 26 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8566 (m-10) REVERT: D 26 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8559 (m-10) outliers start: 27 outliers final: 19 residues processed: 134 average time/residue: 0.2249 time to fit residues: 45.5728 Evaluate side-chains 121 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 30 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.0040 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.119272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.088206 restraints weight = 23227.339| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.31 r_work: 0.3000 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13028 Z= 0.150 Angle : 0.717 16.668 17634 Z= 0.309 Chirality : 0.043 0.279 2072 Planarity : 0.005 0.062 2156 Dihedral : 6.027 59.823 1964 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.71 % Allowed : 16.52 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.23), residues: 1552 helix: 1.87 (0.18), residues: 936 sheet: 0.59 (0.52), residues: 88 loop : -0.19 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 176 HIS 0.002 0.000 HIS C 281 PHE 0.008 0.001 PHE D 96 TYR 0.010 0.001 TYR A 175 ARG 0.002 0.000 ARG B 124 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 584) hydrogen bonds : angle 3.20201 ( 1680) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00372 (13028) covalent geometry : angle 0.71751 (17632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5365.82 seconds wall clock time: 94 minutes 12.15 seconds (5652.15 seconds total)