Starting phenix.real_space_refine on Thu Jun 12 00:45:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cjt_7483/06_2025/6cjt_7483.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cjt_7483/06_2025/6cjt_7483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cjt_7483/06_2025/6cjt_7483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cjt_7483/06_2025/6cjt_7483.map" model { file = "/net/cci-nas-00/data/ceres_data/6cjt_7483/06_2025/6cjt_7483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cjt_7483/06_2025/6cjt_7483.cif" } resolution = 3.46 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 8748 2.51 5 N 2128 2.21 5 O 2296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13208 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3155 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 24, 'TRANS': 371} Chain breaks: 1 Chain: "D" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3155 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 24, 'TRANS': 371} Chain breaks: 1 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Unusual residues: {'PCG': 1, 'PGW': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGW:plan-1': 4, 'PGW:plan-2': 4, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Unusual residues: {'PCG': 1, 'PGW': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGW:plan-1': 4, 'PGW:plan-2': 4, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 44 Restraints were copied for chains: B, C Time building chain proxies: 8.71, per 1000 atoms: 0.66 Number of scatterers: 13208 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: 5 Type Number sf(0) S 28 16.00 P 8 15.00 O 2296 8.00 N 2128 7.00 C 8748 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: 3.08 Conformation dependent library (CDL) restraints added in 1.6 seconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 66.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 10 through 35 removed outlier: 4.683A pdb=" N VAL A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP A 15 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 3.732A pdb=" N VAL A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 68 removed outlier: 6.496A pdb=" N LEU A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 4.446A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 4.926A pdb=" N PHE A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ARG A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 91 through 98 removed outlier: 4.825A pdb=" N VAL A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.440A 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: 3.760A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 removed outlier: 4.056A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 158 removed outlier: 3.864A pdb=" N GLY A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 181 removed outlier: 3.868A pdb=" N TYR A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 224 removed outlier: 3.835A pdb=" N TYR A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.506A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.703A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 4.054A pdb=" N LYS A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 293 through 298 removed outlier: 4.298A pdb=" N GLU A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 6.144A 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: 3.617A pdb=" N ASP A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N HIS A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 4.837A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 5.301A 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: 4.787A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 removed outlier: 4.089A pdb=" N GLN A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 35 removed outlier: 4.683A pdb=" N VAL B 14 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP B 15 " --> pdb=" O TYR B 11 " (cutoff:3.500A) Proline residue: B 31 - end of helix removed outlier: 3.732A pdb=" N VAL B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 68 removed outlier: 6.496A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Proline residue: B 45 - end of helix removed outlier: 4.446A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 4.926A pdb=" N PHE B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ARG B 68 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 91 through 98 removed outlier: 4.825A pdb=" N VAL B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.440A 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: 3.760A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 126 removed outlier: 4.056A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 158 removed outlier: 3.864A pdb=" N GLY B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 removed outlier: 3.868A pdb=" N TYR B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 224 removed outlier: 3.835A pdb=" N TYR B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 245 removed outlier: 3.506A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.703A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 278 removed outlier: 4.054A pdb=" N LYS B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 292 Processing helix chain 'B' and resid 293 through 298 removed outlier: 4.298A pdb=" N GLU B 297 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.144A 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: 3.617A pdb=" N ASP B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N HIS B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 4.837A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 5.301A 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: 4.787A pdb=" N ARG B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 removed outlier: 4.089A pdb=" N GLN B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 35 removed outlier: 4.683A pdb=" N VAL C 14 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Proline residue: C 31 - end of helix removed outlier: 3.732A pdb=" N VAL C 35 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 68 removed outlier: 6.496A pdb=" N LEU C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Proline residue: C 45 - end of helix removed outlier: 4.446A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 4.926A pdb=" N PHE C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ARG C 68 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 91 through 98 removed outlier: 4.825A pdb=" N VAL C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.440A 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: 3.760A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 126 removed outlier: 4.056A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 158 removed outlier: 3.864A pdb=" N GLY C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 181 removed outlier: 3.868A pdb=" N TYR C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 224 removed outlier: 3.835A pdb=" N TYR C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 245 removed outlier: 3.506A pdb=" N VAL C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.703A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 278 removed outlier: 4.054A pdb=" N LYS C 277 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 293 through 298 removed outlier: 4.298A pdb=" N GLU C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 6.144A 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: 3.617A pdb=" N ASP C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N HIS C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 4.837A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 5.301A 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: 4.787A pdb=" N ARG C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 removed outlier: 4.089A pdb=" N GLN C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 35 removed outlier: 4.683A pdb=" N VAL D 14 " --> pdb=" O THR D 10 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP D 15 " --> pdb=" O TYR D 11 " (cutoff:3.500A) Proline residue: D 31 - end of helix removed outlier: 3.732A pdb=" N VAL D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 68 removed outlier: 6.496A pdb=" N LEU D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Proline residue: D 45 - end of helix removed outlier: 4.446A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 4.926A pdb=" N PHE D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ARG D 68 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 91 through 98 removed outlier: 4.825A pdb=" N VAL D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.440A 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: 3.760A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 126 removed outlier: 4.056A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 158 removed outlier: 3.864A pdb=" N GLY D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 181 removed outlier: 3.868A pdb=" N TYR D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 181 " --> pdb=" O THR D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 224 removed outlier: 3.835A pdb=" N TYR D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.506A pdb=" N VAL D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.703A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 278 removed outlier: 4.054A pdb=" N LYS D 277 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 293 through 298 removed outlier: 4.298A pdb=" N GLU D 297 " --> pdb=" O GLY D 293 " (cutoff:3.500A) removed outlier: 6.144A 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: 3.617A pdb=" N ASP D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N HIS D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 4.837A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 5.301A 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: 4.787A pdb=" N ARG D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 removed outlier: 4.089A pdb=" N GLN D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1704 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: 2.96 Time building geometry restraints manager: 3.65 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: 3220 1.33 - 1.45: 2404 1.45 - 1.57: 7788 1.57 - 1.69: 24 1.69 - 1.81: 48 Bond restraints: 13484 Sorted by residual: bond pdb=" O1A PCG A 500 " pdb=" PA PCG A 500 " ideal model delta sigma weight residual 1.582 1.457 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" O1A PCG B 500 " pdb=" PA PCG B 500 " ideal model delta sigma weight residual 1.582 1.457 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" O1A PCG D 500 " pdb=" PA PCG D 500 " ideal model delta sigma weight residual 1.582 1.457 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" O1A PCG C 500 " pdb=" PA PCG C 500 " ideal model delta sigma weight residual 1.582 1.457 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" O2A PCG C 500 " pdb=" PA PCG C 500 " ideal model delta sigma weight residual 1.473 1.584 -0.111 2.00e-02 2.50e+03 3.10e+01 ... (remaining 13479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 16656 2.11 - 4.21: 1072 4.21 - 6.32: 320 6.32 - 8.43: 140 8.43 - 10.53: 48 Bond angle restraints: 18236 Sorted by residual: angle pdb=" C ASP B 92 " pdb=" N LEU B 93 " pdb=" CA LEU B 93 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C ASP C 92 " pdb=" N LEU C 93 " pdb=" CA LEU C 93 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C ASP D 92 " pdb=" N LEU D 93 " pdb=" CA LEU D 93 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C ASP A 92 " pdb=" N LEU A 93 " pdb=" CA LEU A 93 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C LEU C 39 " pdb=" N PHE C 40 " pdb=" CA PHE C 40 " ideal model delta sigma weight residual 121.54 129.84 -8.30 1.91e+00 2.74e-01 1.89e+01 ... (remaining 18231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 8072 35.00 - 70.00: 184 70.00 - 105.01: 36 105.01 - 140.01: 28 140.01 - 175.01: 12 Dihedral angle restraints: 8332 sinusoidal: 3672 harmonic: 4660 Sorted by residual: dihedral pdb=" CA LEU D 276 " pdb=" C LEU D 276 " pdb=" N LYS D 277 " pdb=" CA LYS D 277 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LEU A 276 " pdb=" C LEU A 276 " pdb=" N LYS A 277 " pdb=" CA LYS A 277 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LEU C 276 " pdb=" C LEU C 276 " pdb=" N LYS C 277 " pdb=" CA LYS C 277 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 8329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1944 0.111 - 0.222: 164 0.222 - 0.333: 8 0.333 - 0.445: 4 0.445 - 0.556: 4 Chirality restraints: 2124 Sorted by residual: chirality pdb=" PA PCG D 500 " pdb=" O2A PCG D 500 " pdb=" O3' PCG D 500 " pdb=" O5' PCG D 500 " both_signs ideal model delta sigma weight residual True 2.70 -3.25 -0.56 2.00e-01 2.50e+01 7.72e+00 chirality pdb=" PA PCG A 500 " pdb=" O2A PCG A 500 " pdb=" O3' PCG A 500 " pdb=" O5' PCG A 500 " both_signs ideal model delta sigma weight residual True 2.70 -3.25 -0.56 2.00e-01 2.50e+01 7.72e+00 chirality pdb=" PA PCG C 500 " pdb=" O2A PCG C 500 " pdb=" O3' PCG C 500 " pdb=" O5' PCG C 500 " both_signs ideal model delta sigma weight residual True 2.70 -3.25 -0.56 2.00e-01 2.50e+01 7.72e+00 ... (remaining 2121 not shown) Planarity restraints: 2200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 93 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+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 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 93 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C LEU D 93 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU D 93 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU D 94 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 93 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+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 ... (remaining 2197 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3428 2.80 - 3.33: 11648 3.33 - 3.85: 21056 3.85 - 4.38: 23012 4.38 - 4.90: 41232 Nonbonded interactions: 100376 Sorted by model distance: nonbonded pdb=" OD2 ASP B 312 " pdb=" OH TYR B 404 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP C 312 " pdb=" OH TYR C 404 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP D 312 " pdb=" OH TYR D 404 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP A 312 " pdb=" OH TYR A 404 " model vdw 2.280 3.040 nonbonded pdb=" O12 PGW A 501 " pdb=" OAE PGW A 501 " model vdw 2.295 3.040 ... (remaining 100371 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 412 or (resid 503 and (name C15 or name C16 or \ name C17 or name C18 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 or name C28)) or (resid 505 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or resid 506 \ or (resid 501 and (name C15 or name C16 or name C17 or name C18 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 or name C28)))) selection = (chain 'B' and (resid 10 through 412 or (resid 503 and (name C15 or name C16 or \ name C17 or name C18 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 or name C28)) or (resid 505 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or resid 506 \ or (resid 501 and (name C15 or name C16 or name C17 or name C18 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 or name C28)))) selection = (chain 'C' and (resid 10 through 412 or (resid 503 and (name C15 or name C16 or \ name C17 or name C18 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 or name C28)) or (resid 505 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or resid 506 \ or (resid 501 and (name C15 or name C16 or name C17 or name C18 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 or name C28)))) selection = (chain 'D' and (resid 10 through 412 or resid 502 or (resid 504 and (name C1 or \ name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 505 and (name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or na \ me C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C30)) or (resid 506 and (name C15 or name C16 or name C17 or \ name C18 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 or name C28)))) } 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: 0.960 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.730 Find NCS groups from input model: 0.680 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.125 13484 Z= 0.430 Angle : 1.430 10.534 18238 Z= 0.674 Chirality : 0.070 0.556 2124 Planarity : 0.008 0.058 2200 Dihedral : 18.918 175.011 5320 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.59 % Allowed : 7.06 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.58 (0.18), residues: 1568 helix: -2.14 (0.14), residues: 924 sheet: -2.51 (0.39), residues: 84 loop : -2.47 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 264 HIS 0.005 0.001 HIS D 149 PHE 0.012 0.002 PHE B 36 TYR 0.030 0.004 TYR D 211 ARG 0.007 0.001 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.13946 ( 592) hydrogen bonds : angle 5.68759 ( 1704) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00962 (13484) covalent geometry : angle 1.42986 (18236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 236 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.7501 (tm) cc_final: 0.7279 (mt) REVERT: A 158 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9091 (pp) REVERT: A 229 LYS cc_start: 0.8979 (tmtp) cc_final: 0.8746 (ttmt) REVERT: A 272 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7878 (tm-30) REVERT: A 388 ASP cc_start: 0.8234 (m-30) cc_final: 0.7800 (t0) REVERT: B 77 LEU cc_start: 0.7492 (tm) cc_final: 0.7291 (mt) REVERT: B 229 LYS cc_start: 0.8974 (tmtp) cc_final: 0.8755 (ttmt) REVERT: B 272 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7858 (tm-30) REVERT: B 388 ASP cc_start: 0.8204 (m-30) cc_final: 0.7820 (t0) REVERT: C 77 LEU cc_start: 0.7528 (tm) cc_final: 0.7309 (mt) REVERT: C 272 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7938 (tm-30) REVERT: C 388 ASP cc_start: 0.8222 (m-30) cc_final: 0.7970 (t0) REVERT: D 77 LEU cc_start: 0.7519 (tm) cc_final: 0.7295 (mt) REVERT: D 158 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9066 (pp) REVERT: D 229 LYS cc_start: 0.8981 (tmtp) cc_final: 0.8738 (ttmt) REVERT: D 272 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7908 (tm-30) REVERT: D 388 ASP cc_start: 0.8216 (m-30) cc_final: 0.7815 (t0) outliers start: 8 outliers final: 0 residues processed: 240 average time/residue: 0.3267 time to fit residues: 107.2917 Evaluate side-chains 97 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain D residue 158 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 0.0270 chunk 74 optimal weight: 0.0030 chunk 91 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.4648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.120015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.092632 restraints weight = 23846.801| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.32 r_work: 0.2965 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13484 Z= 0.118 Angle : 0.706 8.588 18238 Z= 0.329 Chirality : 0.043 0.191 2124 Planarity : 0.005 0.047 2200 Dihedral : 21.754 174.367 2320 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.79 % Allowed : 11.18 % Favored : 86.03 % 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: -1.34 (0.21), residues: 1568 helix: -0.37 (0.17), residues: 948 sheet: -1.64 (0.47), residues: 92 loop : -1.47 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 264 HIS 0.002 0.001 HIS C 281 PHE 0.009 0.001 PHE A 242 TYR 0.017 0.001 TYR B 128 ARG 0.003 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 592) hydrogen bonds : angle 3.84154 ( 1704) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00256 (13484) covalent geometry : angle 0.70641 (18236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 1.382 Fit side-chains REVERT: A 77 LEU cc_start: 0.7507 (tm) cc_final: 0.7256 (mt) REVERT: A 171 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8845 (tp) REVERT: A 229 LYS cc_start: 0.9200 (tmtp) cc_final: 0.8947 (ttpt) REVERT: A 272 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7884 (tm-30) REVERT: A 369 MET cc_start: 0.8240 (mmm) cc_final: 0.8004 (mmt) REVERT: A 388 ASP cc_start: 0.8495 (m-30) cc_final: 0.7980 (t0) REVERT: B 77 LEU cc_start: 0.7477 (tm) cc_final: 0.7237 (mt) REVERT: B 229 LYS cc_start: 0.9172 (tmtp) cc_final: 0.8957 (ttpt) REVERT: B 272 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7938 (tm-30) REVERT: B 369 MET cc_start: 0.8288 (mmm) cc_final: 0.8048 (mmt) REVERT: B 388 ASP cc_start: 0.8495 (m-30) cc_final: 0.8058 (t0) REVERT: C 77 LEU cc_start: 0.7508 (tm) cc_final: 0.7265 (mt) REVERT: C 272 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7939 (tm-30) REVERT: C 369 MET cc_start: 0.8230 (mmm) cc_final: 0.7994 (mmt) REVERT: C 388 ASP cc_start: 0.8489 (m-30) cc_final: 0.8062 (t0) REVERT: D 77 LEU cc_start: 0.7514 (tm) cc_final: 0.7255 (mt) REVERT: D 171 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8843 (tp) REVERT: D 229 LYS cc_start: 0.9198 (tmtp) cc_final: 0.8969 (ttpt) REVERT: D 272 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7891 (tm-30) REVERT: D 369 MET cc_start: 0.8182 (mmm) cc_final: 0.7951 (mmt) REVERT: D 388 ASP cc_start: 0.8508 (m-30) cc_final: 0.8028 (t0) outliers start: 38 outliers final: 8 residues processed: 181 average time/residue: 0.2818 time to fit residues: 71.9615 Evaluate side-chains 113 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 203 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.116414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.089347 restraints weight = 24201.888| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.36 r_work: 0.2899 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13484 Z= 0.162 Angle : 0.715 14.477 18238 Z= 0.327 Chirality : 0.044 0.195 2124 Planarity : 0.004 0.028 2200 Dihedral : 20.443 178.404 2316 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.38 % Allowed : 13.24 % Favored : 83.38 % 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: -0.27 (0.23), residues: 1568 helix: 0.54 (0.18), residues: 956 sheet: -1.11 (0.47), residues: 92 loop : -1.22 (0.30), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 264 HIS 0.003 0.001 HIS B 149 PHE 0.007 0.001 PHE B 36 TYR 0.021 0.002 TYR B 11 ARG 0.003 0.000 ARG C 399 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 592) hydrogen bonds : angle 3.59099 ( 1704) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00392 (13484) covalent geometry : angle 0.71496 (18236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 108 time to evaluate : 1.370 Fit side-chains REVERT: A 60 LEU cc_start: 0.8242 (tp) cc_final: 0.8001 (tt) REVERT: A 77 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7137 (mt) REVERT: A 171 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8846 (tp) REVERT: A 221 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.8965 (tt) REVERT: A 334 MET cc_start: 0.7890 (ttm) cc_final: 0.7539 (mmm) REVERT: A 369 MET cc_start: 0.8242 (mmm) cc_final: 0.7976 (mmt) REVERT: A 388 ASP cc_start: 0.8597 (m-30) cc_final: 0.8371 (t0) REVERT: B 77 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7154 (mt) REVERT: B 221 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.8955 (tt) REVERT: B 369 MET cc_start: 0.8273 (mmm) cc_final: 0.8017 (mmt) REVERT: C 77 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7155 (mt) REVERT: C 221 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.8980 (tt) REVERT: C 334 MET cc_start: 0.7824 (ttm) cc_final: 0.7521 (mmm) REVERT: D 77 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7155 (mt) REVERT: D 171 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8851 (tp) REVERT: D 221 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.8985 (tt) REVERT: D 334 MET cc_start: 0.7902 (ttm) cc_final: 0.7551 (mmm) REVERT: D 369 MET cc_start: 0.8209 (mmm) cc_final: 0.7973 (mmm) outliers start: 46 outliers final: 20 residues processed: 146 average time/residue: 0.2487 time to fit residues: 53.5310 Evaluate side-chains 114 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.8315 > 50: distance: 52 - 60: 34.612 distance: 60 - 61: 40.251 distance: 61 - 62: 67.172 distance: 62 - 63: 39.446 distance: 62 - 71: 7.575 distance: 64 - 65: 40.693 distance: 65 - 66: 40.219 distance: 65 - 67: 38.710 distance: 66 - 68: 40.635 distance: 67 - 69: 39.434 distance: 68 - 70: 57.681 distance: 69 - 70: 57.018 distance: 72 - 73: 40.007 distance: 73 - 74: 39.090 distance: 73 - 75: 39.468 distance: 75 - 76: 53.987 distance: 76 - 77: 57.409 distance: 76 - 79: 41.243 distance: 77 - 84: 39.406 distance: 79 - 80: 38.801 distance: 80 - 81: 56.178 distance: 81 - 82: 56.186 distance: 81 - 83: 40.114 distance: 84 - 85: 40.644 distance: 85 - 86: 38.892 distance: 85 - 88: 56.024 distance: 86 - 87: 41.172 distance: 88 - 89: 57.357 distance: 89 - 90: 56.897 distance: 90 - 91: 31.995 distance: 92 - 93: 69.308 distance: 93 - 94: 39.243 distance: 94 - 97: 40.152 distance: 97 - 98: 56.325 distance: 98 - 99: 39.204 distance: 98 - 101: 39.001 distance: 99 - 100: 56.642 distance: 99 - 105: 68.176 distance: 101 - 102: 57.519 distance: 102 - 103: 55.386 distance: 102 - 104: 39.493 distance: 105 - 106: 41.301 distance: 106 - 107: 56.039 distance: 106 - 109: 69.714 distance: 107 - 108: 40.263 distance: 107 - 113: 38.904 distance: 109 - 111: 57.028 distance: 110 - 112: 38.762 distance: 113 - 114: 40.747 distance: 115 - 116: 55.546 distance: 115 - 121: 57.686 distance: 117 - 118: 68.978 distance: 118 - 119: 55.996 distance: 121 - 122: 38.727 distance: 122 - 123: 41.064 distance: 122 - 125: 55.959 distance: 123 - 124: 55.832 distance: 125 - 126: 70.363 distance: 127 - 128: 56.613 distance: 128 - 129: 39.490 distance: 129 - 130: 56.127 distance: 129 - 131: 69.436 distance: 132 - 133: 39.339 distance: 133 - 134: 39.502 distance: 133 - 136: 39.086 distance: 134 - 135: 56.290 distance: 134 - 137: 34.060