Starting phenix.real_space_refine on Fri Sep 27 11:09:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7c_28902/09_2024/8f7c_28902.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7c_28902/09_2024/8f7c_28902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7c_28902/09_2024/8f7c_28902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7c_28902/09_2024/8f7c_28902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7c_28902/09_2024/8f7c_28902.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7c_28902/09_2024/8f7c_28902.cif" } resolution = 3.92 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= 0.019 sd= 0.154 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 77 5.16 5 C 10423 2.51 5 N 2716 2.21 5 O 2709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15925 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2275 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2275 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2275 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2275 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2275 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2275 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "G" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2275 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 9.75, per 1000 atoms: 0.61 Number of scatterers: 15925 At special positions: 0 Unit cell: (119.7, 118.8, 113.4, 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 77 16.00 O 2709 8.00 N 2716 7.00 C 10423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 279 " distance=2.04 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 279 " distance=2.04 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 259 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 279 " distance=2.04 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 259 " distance=2.03 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 279 " distance=2.04 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 259 " distance=2.03 Simple disulfide: pdb=" SG CYS E 81 " - pdb=" SG CYS E 279 " distance=2.04 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 259 " distance=2.03 Simple disulfide: pdb=" SG CYS F 81 " - pdb=" SG CYS F 279 " distance=2.04 Simple disulfide: pdb=" SG CYS F 99 " - pdb=" SG CYS F 259 " distance=2.03 Simple disulfide: pdb=" SG CYS G 81 " - pdb=" SG CYS G 279 " distance=2.03 Simple disulfide: pdb=" SG CYS G 99 " - pdb=" SG CYS G 259 " distance=2.03 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: 3.77 Conformation dependent library (CDL) restraints added in 2.1 seconds 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3892 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 7 sheets defined 75.1% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 48 through 59 Processing helix chain 'A' and resid 59 through 74 removed outlier: 3.770A pdb=" N ILE A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 103 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.505A pdb=" N LEU A 114 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 119 through 147 Proline residue: A 125 - end of helix removed outlier: 3.669A pdb=" N LEU A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Proline residue: A 138 - end of helix removed outlier: 3.932A pdb=" N GLU A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 removed outlier: 4.070A pdb=" N ASP A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN A 163 " --> pdb=" O GLN A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 218 removed outlier: 4.260A pdb=" N GLU A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 238 removed outlier: 4.008A pdb=" N ALA A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 removed outlier: 3.798A pdb=" N ILE A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 250 " --> pdb=" O CYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 314 removed outlier: 3.963A pdb=" N ILE A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 305 " --> pdb=" O MET A 301 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 333 through 339 removed outlier: 4.124A pdb=" N ARG A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.874A pdb=" N ILE A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 358 removed outlier: 3.560A pdb=" N ILE A 358 " --> pdb=" O ARG A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 360 through 368 removed outlier: 3.529A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 48 through 59 Processing helix chain 'B' and resid 59 through 74 removed outlier: 3.781A pdb=" N ILE B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 103 Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.502A pdb=" N LEU B 114 " --> pdb=" O ASP B 111 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 115' Processing helix chain 'B' and resid 118 through 147 removed outlier: 4.071A pdb=" N LYS B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 3.686A pdb=" N LEU B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Proline residue: B 138 - end of helix removed outlier: 3.960A pdb=" N GLU B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 164 removed outlier: 4.186A pdb=" N ASP B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN B 163 " --> pdb=" O GLN B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 218 removed outlier: 4.187A pdb=" N GLU B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 238 removed outlier: 3.923A pdb=" N ALA B 229 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS B 231 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 removed outlier: 3.786A pdb=" N ILE B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 250 " --> pdb=" O CYS B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 314 removed outlier: 3.987A pdb=" N ILE B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 330 through 339 removed outlier: 4.355A pdb=" N ARG B 334 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLN B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.914A pdb=" N ILE B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE B 350 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 358 removed outlier: 3.531A pdb=" N ILE B 358 " --> pdb=" O ARG B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 355 through 358' Processing helix chain 'B' and resid 360 through 368 removed outlier: 3.542A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 48 through 59 Processing helix chain 'C' and resid 59 through 74 removed outlier: 3.770A pdb=" N ILE C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 103 Processing helix chain 'C' and resid 111 through 115 removed outlier: 3.507A pdb=" N LEU C 114 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP C 115 " --> pdb=" O ALA C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 115' Processing helix chain 'C' and resid 119 through 147 Proline residue: C 125 - end of helix removed outlier: 3.680A pdb=" N LEU C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) Proline residue: C 138 - end of helix removed outlier: 3.899A pdb=" N GLU C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 164 removed outlier: 4.092A pdb=" N ASP C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN C 163 " --> pdb=" O GLN C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 219 removed outlier: 4.056A pdb=" N GLU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 219 " --> pdb=" O GLU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 238 removed outlier: 4.089A pdb=" N ALA C 229 " --> pdb=" O LYS C 225 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 234 " --> pdb=" O ARG C 230 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 235 " --> pdb=" O HIS C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 250 removed outlier: 3.785A pdb=" N ILE C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 250 " --> pdb=" O CYS C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 314 removed outlier: 4.032A pdb=" N ILE C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 296 " --> pdb=" O GLY C 292 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C 306 " --> pdb=" O ASN C 302 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 329 through 339 removed outlier: 4.042A pdb=" N ARG C 334 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN C 335 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER C 339 " --> pdb=" O GLN C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.870A pdb=" N ILE C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE C 350 " --> pdb=" O ILE C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 358 removed outlier: 3.569A pdb=" N ILE C 358 " --> pdb=" O ARG C 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 355 through 358' Processing helix chain 'C' and resid 360 through 368 removed outlier: 3.536A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 41 Processing helix chain 'D' and resid 48 through 59 Processing helix chain 'D' and resid 59 through 74 removed outlier: 3.771A pdb=" N ILE D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 103 Processing helix chain 'D' and resid 111 through 115 removed outlier: 3.503A pdb=" N LEU D 114 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP D 115 " --> pdb=" O ALA D 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 111 through 115' Processing helix chain 'D' and resid 118 through 147 removed outlier: 4.095A pdb=" N LYS D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Proline residue: D 125 - end of helix removed outlier: 3.687A pdb=" N LEU D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Proline residue: D 138 - end of helix removed outlier: 3.946A pdb=" N GLU D 143 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU D 145 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 164 removed outlier: 4.008A pdb=" N ASP D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN D 163 " --> pdb=" O GLN D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 218 removed outlier: 3.963A pdb=" N GLU D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 238 removed outlier: 4.017A pdb=" N ALA D 229 " --> pdb=" O LYS D 225 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 234 " --> pdb=" O ARG D 230 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 235 " --> pdb=" O HIS D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 250 removed outlier: 3.827A pdb=" N ILE D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA D 250 " --> pdb=" O CYS D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 314 removed outlier: 3.944A pdb=" N ILE D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 296 " --> pdb=" O GLY D 292 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET D 301 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 305 " --> pdb=" O MET D 301 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 306 " --> pdb=" O ASN D 302 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN D 308 " --> pdb=" O ILE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.584A pdb=" N TRP D 336 " --> pdb=" O THR D 332 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 337 " --> pdb=" O ARG D 333 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER D 339 " --> pdb=" O GLN D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 removed outlier: 3.997A pdb=" N ILE D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N MET D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE D 350 " --> pdb=" O ILE D 346 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 358 removed outlier: 3.546A pdb=" N ILE D 358 " --> pdb=" O ARG D 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 355 through 358' Processing helix chain 'D' and resid 360 through 368 removed outlier: 3.563A pdb=" N ILE D 367 " --> pdb=" O ARG D 363 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR D 368 " --> pdb=" O LEU D 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 41 Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 59 through 74 removed outlier: 3.751A pdb=" N ILE E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 103 Processing helix chain 'E' and resid 111 through 115 removed outlier: 3.503A pdb=" N LEU E 114 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP E 115 " --> pdb=" O ALA E 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 111 through 115' Processing helix chain 'E' and resid 119 through 147 Proline residue: E 125 - end of helix removed outlier: 3.680A pdb=" N LEU E 128 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA E 133 " --> pdb=" O LEU E 129 " (cutoff:3.500A) Proline residue: E 138 - end of helix removed outlier: 3.953A pdb=" N GLU E 143 " --> pdb=" O ALA E 139 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU E 145 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 161 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 209 through 218 removed outlier: 3.586A pdb=" N LEU E 214 " --> pdb=" O PHE E 210 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 238 removed outlier: 4.072A pdb=" N ALA E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE E 234 " --> pdb=" O ARG E 230 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 235 " --> pdb=" O HIS E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 250 removed outlier: 3.708A pdb=" N ILE E 242 " --> pdb=" O SER E 238 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA E 250 " --> pdb=" O CYS E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 314 removed outlier: 3.965A pdb=" N ILE E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL E 296 " --> pdb=" O GLY E 292 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET E 301 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU E 306 " --> pdb=" O ASN E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 326 removed outlier: 4.034A pdb=" N HIS E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 339 removed outlier: 4.292A pdb=" N ARG E 334 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN E 335 " --> pdb=" O LYS E 331 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER E 339 " --> pdb=" O GLN E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 354 removed outlier: 4.129A pdb=" N ILE E 346 " --> pdb=" O CYS E 342 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET E 349 " --> pdb=" O ASN E 345 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE E 350 " --> pdb=" O ILE E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 358 removed outlier: 3.569A pdb=" N ILE E 358 " --> pdb=" O ARG E 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 355 through 358' Processing helix chain 'E' and resid 360 through 368 removed outlier: 3.512A pdb=" N ILE E 367 " --> pdb=" O ARG E 363 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR E 368 " --> pdb=" O LEU E 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 48 through 59 Processing helix chain 'F' and resid 59 through 74 removed outlier: 3.768A pdb=" N ILE F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 103 Processing helix chain 'F' and resid 111 through 115 removed outlier: 3.563A pdb=" N TRP F 115 " --> pdb=" O ALA F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 135 removed outlier: 3.652A pdb=" N PHE F 123 " --> pdb=" O PHE F 119 " (cutoff:3.500A) Proline residue: F 125 - end of helix removed outlier: 3.958A pdb=" N MET F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 147 removed outlier: 3.575A pdb=" N LEU F 140 " --> pdb=" O TYR F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 160 removed outlier: 3.974A pdb=" N ASN F 155 " --> pdb=" O THR F 151 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU F 157 " --> pdb=" O GLU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 166 removed outlier: 4.107A pdb=" N HIS F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 218 removed outlier: 4.297A pdb=" N GLU F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 238 removed outlier: 4.045A pdb=" N ALA F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS F 231 " --> pdb=" O TYR F 227 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 234 " --> pdb=" O ARG F 230 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU F 235 " --> pdb=" O HIS F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 250 removed outlier: 3.771A pdb=" N ILE F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA F 250 " --> pdb=" O CYS F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 314 removed outlier: 3.997A pdb=" N ILE F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL F 296 " --> pdb=" O GLY F 292 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET F 301 " --> pdb=" O LEU F 297 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU F 306 " --> pdb=" O ASN F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 326 removed outlier: 4.217A pdb=" N HIS F 326 " --> pdb=" O PHE F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 339 removed outlier: 4.165A pdb=" N ARG F 334 " --> pdb=" O ILE F 330 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN F 335 " --> pdb=" O LYS F 331 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP F 336 " --> pdb=" O THR F 332 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG F 337 " --> pdb=" O ARG F 333 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER F 339 " --> pdb=" O GLN F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 354 removed outlier: 3.862A pdb=" N ILE F 346 " --> pdb=" O CYS F 342 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET F 349 " --> pdb=" O ASN F 345 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE F 350 " --> pdb=" O ILE F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 358 removed outlier: 3.531A pdb=" N ILE F 358 " --> pdb=" O ARG F 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 355 through 358' Processing helix chain 'F' and resid 360 through 368 removed outlier: 3.578A pdb=" N ILE F 367 " --> pdb=" O ARG F 363 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR F 368 " --> pdb=" O LEU F 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 41 Processing helix chain 'G' and resid 48 through 59 Processing helix chain 'G' and resid 59 through 74 removed outlier: 3.780A pdb=" N ILE G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.541A pdb=" N GLY G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 115 removed outlier: 3.628A pdb=" N TRP G 115 " --> pdb=" O ALA G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 147 removed outlier: 4.093A pdb=" N LYS G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Proline residue: G 125 - end of helix removed outlier: 3.671A pdb=" N LEU G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA G 133 " --> pdb=" O LEU G 129 " (cutoff:3.500A) Proline residue: G 138 - end of helix removed outlier: 3.967A pdb=" N GLU G 143 " --> pdb=" O ALA G 139 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU G 145 " --> pdb=" O GLY G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 164 removed outlier: 4.047A pdb=" N ASP G 162 " --> pdb=" O LEU G 158 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN G 163 " --> pdb=" O GLN G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 218 removed outlier: 3.606A pdb=" N LEU G 214 " --> pdb=" O PHE G 210 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 238 removed outlier: 3.966A pdb=" N ALA G 229 " --> pdb=" O LYS G 225 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS G 231 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE G 234 " --> pdb=" O ARG G 230 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU G 235 " --> pdb=" O HIS G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 250 removed outlier: 3.771A pdb=" N ILE G 242 " --> pdb=" O SER G 238 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA G 250 " --> pdb=" O CYS G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 314 removed outlier: 3.910A pdb=" N ILE G 295 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL G 296 " --> pdb=" O GLY G 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET G 301 " --> pdb=" O LEU G 297 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE G 305 " --> pdb=" O MET G 301 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU G 306 " --> pdb=" O ASN G 302 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN G 308 " --> pdb=" O ILE G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 324 Processing helix chain 'G' and resid 330 through 339 removed outlier: 4.244A pdb=" N ARG G 334 " --> pdb=" O ILE G 330 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN G 335 " --> pdb=" O LYS G 331 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP G 336 " --> pdb=" O THR G 332 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG G 337 " --> pdb=" O ARG G 333 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER G 339 " --> pdb=" O GLN G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 354 removed outlier: 3.878A pdb=" N ILE G 346 " --> pdb=" O CYS G 342 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET G 349 " --> pdb=" O ASN G 345 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE G 350 " --> pdb=" O ILE G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 358 removed outlier: 3.549A pdb=" N ILE G 358 " --> pdb=" O ARG G 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 355 through 358' Processing helix chain 'G' and resid 360 through 368 removed outlier: 3.585A pdb=" N ILE G 367 " --> pdb=" O ARG G 363 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR G 368 " --> pdb=" O LEU G 364 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.505A pdb=" N PHE A 257 " --> pdb=" O CYS A 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.540A pdb=" N TYR B 80 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 81 removed outlier: 3.619A pdb=" N TYR C 80 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 257 " --> pdb=" O CYS C 279 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.615A pdb=" N TYR D 80 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 81 removed outlier: 3.635A pdb=" N TYR F 80 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 80 through 81 820 hydrogen bonds defined for protein. 2415 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: 3.82 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5047 1.35 - 1.48: 4082 1.48 - 1.60: 7062 1.60 - 1.72: 0 1.72 - 1.85: 98 Bond restraints: 16289 Sorted by residual: bond pdb=" CB CYS D 279 " pdb=" SG CYS D 279 " ideal model delta sigma weight residual 1.808 1.846 -0.038 3.30e-02 9.18e+02 1.31e+00 bond pdb=" CB CYS E 279 " pdb=" SG CYS E 279 " ideal model delta sigma weight residual 1.808 1.845 -0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB CYS B 279 " pdb=" SG CYS B 279 " ideal model delta sigma weight residual 1.808 1.845 -0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CB CYS F 279 " pdb=" SG CYS F 279 " ideal model delta sigma weight residual 1.808 1.843 -0.035 3.30e-02 9.18e+02 1.16e+00 bond pdb=" CB CYS A 279 " pdb=" SG CYS A 279 " ideal model delta sigma weight residual 1.808 1.843 -0.035 3.30e-02 9.18e+02 1.15e+00 ... (remaining 16284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 21852 1.74 - 3.49: 208 3.49 - 5.23: 66 5.23 - 6.97: 14 6.97 - 8.72: 8 Bond angle restraints: 22148 Sorted by residual: angle pdb=" CA CYS B 81 " pdb=" CB CYS B 81 " pdb=" SG CYS B 81 " ideal model delta sigma weight residual 114.40 122.02 -7.62 2.30e+00 1.89e-01 1.10e+01 angle pdb=" CA CYS D 81 " pdb=" CB CYS D 81 " pdb=" SG CYS D 81 " ideal model delta sigma weight residual 114.40 121.71 -7.31 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CA CYS A 81 " pdb=" CB CYS A 81 " pdb=" SG CYS A 81 " ideal model delta sigma weight residual 114.40 121.70 -7.30 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CA CYS F 81 " pdb=" CB CYS F 81 " pdb=" SG CYS F 81 " ideal model delta sigma weight residual 114.40 121.66 -7.26 2.30e+00 1.89e-01 9.97e+00 angle pdb=" CA CYS E 81 " pdb=" CB CYS E 81 " pdb=" SG CYS E 81 " ideal model delta sigma weight residual 114.40 121.58 -7.18 2.30e+00 1.89e-01 9.74e+00 ... (remaining 22143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 8638 16.63 - 33.26: 828 33.26 - 49.88: 238 49.88 - 66.51: 24 66.51 - 83.14: 9 Dihedral angle restraints: 9737 sinusoidal: 3780 harmonic: 5957 Sorted by residual: dihedral pdb=" CB CYS D 81 " pdb=" SG CYS D 81 " pdb=" SG CYS D 279 " pdb=" CB CYS D 279 " ideal model delta sinusoidal sigma weight residual 93.00 47.85 45.15 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CB CYS B 81 " pdb=" SG CYS B 81 " pdb=" SG CYS B 279 " pdb=" CB CYS B 279 " ideal model delta sinusoidal sigma weight residual 93.00 47.86 45.14 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CB CYS E 81 " pdb=" SG CYS E 81 " pdb=" SG CYS E 279 " pdb=" CB CYS E 279 " ideal model delta sinusoidal sigma weight residual 93.00 48.09 44.91 1 1.00e+01 1.00e-02 2.80e+01 ... (remaining 9734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1467 0.026 - 0.052: 803 0.052 - 0.078: 218 0.078 - 0.104: 72 0.104 - 0.130: 44 Chirality restraints: 2604 Sorted by residual: chirality pdb=" CA CYS B 81 " pdb=" N CYS B 81 " pdb=" C CYS B 81 " pdb=" CB CYS B 81 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA CYS F 81 " pdb=" N CYS F 81 " pdb=" C CYS F 81 " pdb=" CB CYS F 81 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA CYS C 81 " pdb=" N CYS C 81 " pdb=" C CYS C 81 " pdb=" CB CYS C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 2601 not shown) Planarity restraints: 2758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER F 264 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO F 265 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO F 265 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 265 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 82 " -0.009 2.00e-02 2.50e+03 8.65e-03 1.50e+00 pdb=" CG TYR A 82 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 82 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 82 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 82 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 82 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 82 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 82 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 61 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO G 62 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO G 62 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 62 " -0.017 5.00e-02 4.00e+02 ... (remaining 2755 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 4 2.32 - 2.97: 6941 2.97 - 3.61: 22006 3.61 - 4.26: 30153 4.26 - 4.90: 49188 Nonbonded interactions: 108292 Sorted by model distance: nonbonded pdb=" CB GLN A 335 " pdb=" NH2 ARG A 338 " model vdw 1.675 3.520 nonbonded pdb=" OE2 GLU D 153 " pdb=" OH TYR D 213 " model vdw 2.239 3.040 nonbonded pdb=" O GLN B 252 " pdb=" NH2 ARG B 288 " model vdw 2.307 3.120 nonbonded pdb=" CA GLN A 335 " pdb=" NE ARG A 338 " model vdw 2.318 3.550 nonbonded pdb=" O GLY D 329 " pdb=" NH1 ARG D 333 " model vdw 2.332 3.120 ... (remaining 108287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 34.510 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.002 0.040 16289 Z= 0.149 Angle : 0.522 8.718 22148 Z= 0.272 Chirality : 0.036 0.130 2604 Planarity : 0.004 0.061 2758 Dihedral : 13.947 83.140 5803 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.02 (0.19), residues: 1967 helix: 0.63 (0.15), residues: 1183 sheet: 0.01 (0.59), residues: 70 loop : -0.92 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 336 HIS 0.001 0.000 HIS B 121 PHE 0.021 0.001 PHE G 210 TYR 0.022 0.001 TYR A 82 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 LEU cc_start: 0.9129 (tp) cc_final: 0.8911 (tp) REVERT: B 341 PHE cc_start: 0.7798 (m-80) cc_final: 0.7314 (m-80) REVERT: C 265 PRO cc_start: 0.7133 (Cg_endo) cc_final: 0.6841 (Cg_exo) REVERT: C 340 GLN cc_start: 0.7876 (mp-120) cc_final: 0.7094 (mm-40) REVERT: C 341 PHE cc_start: 0.7740 (m-80) cc_final: 0.7259 (m-80) REVERT: D 135 MET cc_start: 0.8183 (mmt) cc_final: 0.7942 (mmt) REVERT: D 210 PHE cc_start: 0.8062 (t80) cc_final: 0.7575 (t80) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2935 time to fit residues: 129.4495 Evaluate side-chains 247 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 20.0000 chunk 148 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 231 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16289 Z= 0.243 Angle : 0.612 7.873 22148 Z= 0.326 Chirality : 0.039 0.132 2604 Planarity : 0.004 0.048 2758 Dihedral : 4.042 18.387 2191 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.81 % Allowed : 9.09 % Favored : 88.11 % 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: 0.53 (0.19), residues: 1967 helix: 1.15 (0.15), residues: 1239 sheet: -0.10 (0.62), residues: 70 loop : -1.09 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 142 HIS 0.004 0.001 HIS B 311 PHE 0.010 0.001 PHE D 257 TYR 0.019 0.002 TYR A 213 ARG 0.005 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 251 time to evaluate : 1.878 Fit side-chains REVERT: A 323 ASP cc_start: 0.8208 (t0) cc_final: 0.7909 (t0) REVERT: A 340 GLN cc_start: 0.7799 (mp10) cc_final: 0.7511 (mp10) REVERT: B 323 ASP cc_start: 0.8226 (t0) cc_final: 0.8017 (t0) REVERT: B 341 PHE cc_start: 0.7853 (m-80) cc_final: 0.7384 (m-80) REVERT: B 352 ASN cc_start: 0.8822 (t0) cc_final: 0.8581 (t0) REVERT: C 265 PRO cc_start: 0.7420 (Cg_endo) cc_final: 0.6944 (Cg_exo) REVERT: C 304 ILE cc_start: 0.7926 (tt) cc_final: 0.7692 (tt) REVERT: C 340 GLN cc_start: 0.7997 (mp-120) cc_final: 0.7149 (mm-40) REVERT: C 341 PHE cc_start: 0.7802 (m-80) cc_final: 0.7341 (m-80) REVERT: D 210 PHE cc_start: 0.7659 (t80) cc_final: 0.7094 (t80) REVERT: E 219 ARG cc_start: 0.8830 (mmm160) cc_final: 0.8375 (mmm160) REVERT: E 334 ARG cc_start: 0.7514 (ptp90) cc_final: 0.6802 (ptp90) REVERT: E 337 ARG cc_start: 0.8238 (ptp90) cc_final: 0.7927 (ptp90) REVERT: G 265 PRO cc_start: 0.7746 (Cg_endo) cc_final: 0.7249 (Cg_exo) REVERT: G 352 ASN cc_start: 0.8946 (t0) cc_final: 0.8714 (t0) outliers start: 47 outliers final: 40 residues processed: 292 average time/residue: 0.3002 time to fit residues: 125.6734 Evaluate side-chains 274 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 234 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 307 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16289 Z= 0.172 Angle : 0.529 7.190 22148 Z= 0.279 Chirality : 0.037 0.123 2604 Planarity : 0.004 0.064 2758 Dihedral : 3.915 18.234 2191 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.93 % Allowed : 12.01 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.19), residues: 1967 helix: 1.34 (0.15), residues: 1246 sheet: -0.32 (0.63), residues: 70 loop : -1.06 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 142 HIS 0.003 0.001 HIS G 357 PHE 0.019 0.001 PHE G 210 TYR 0.017 0.001 TYR C 213 ARG 0.005 0.000 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 245 time to evaluate : 1.841 Fit side-chains REVERT: A 323 ASP cc_start: 0.8169 (t0) cc_final: 0.7916 (t0) REVERT: A 340 GLN cc_start: 0.7839 (mp10) cc_final: 0.7493 (mp10) REVERT: B 341 PHE cc_start: 0.7917 (m-80) cc_final: 0.7423 (m-80) REVERT: C 265 PRO cc_start: 0.7328 (Cg_endo) cc_final: 0.6903 (Cg_exo) REVERT: C 340 GLN cc_start: 0.8002 (mp-120) cc_final: 0.7113 (mm-40) REVERT: C 341 PHE cc_start: 0.7849 (m-80) cc_final: 0.7362 (m-80) REVERT: D 82 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8358 (m-80) REVERT: D 210 PHE cc_start: 0.7679 (t80) cc_final: 0.7099 (t80) REVERT: D 265 PRO cc_start: 0.7427 (Cg_endo) cc_final: 0.7071 (Cg_exo) REVERT: E 337 ARG cc_start: 0.8236 (ptp90) cc_final: 0.7925 (ptp90) REVERT: F 82 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.8423 (m-80) REVERT: F 135 MET cc_start: 0.8821 (tpp) cc_final: 0.8387 (mtt) REVERT: G 265 PRO cc_start: 0.7808 (Cg_endo) cc_final: 0.7477 (Cg_exo) outliers start: 49 outliers final: 32 residues processed: 277 average time/residue: 0.2669 time to fit residues: 109.6189 Evaluate side-chains 262 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 228 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 82 TYR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 242 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.0030 chunk 134 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 0.0370 chunk 85 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 0.1980 chunk 189 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.4468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2087 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: