Starting phenix.real_space_refine on Fri Sep 11 14:45:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7egk_31135/09_2026/7egk_31135.cif Found real_map, /net/cci-nas-00/data/ceres_data/7egk_31135/09_2026/7egk_31135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7egk_31135/09_2026/7egk_31135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7egk_31135/09_2026/7egk_31135.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7egk_31135/09_2026/7egk_31135.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7egk_31135/09_2026/7egk_31135.cif" model { file = "/net/cci-nas-00/data/ceres_data/7egk_31135/09_2026/7egk_31135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7egk_31135/09_2026/7egk_31135.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 51 5.16 5 Na 3 4.78 5 C 6444 2.51 5 N 1602 2.21 5 O 1791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9894 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2443 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "C" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2443 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "E" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2443 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 2.17, per 1000 atoms: 0.22 Number of scatterers: 9894 At special positions: 0 Unit cell: (98.0343, 100.189, 88.3386, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 3 15.00 Na 3 11.00 O 1791 8.00 N 1602 7.00 C 6444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 105 " - pdb=" SG CYS D 110 " distance=2.02 Simple disulfide: pdb=" SG CYS F 105 " - pdb=" SG CYS F 110 " distance=2.02 Simple disulfide: pdb=" SG CYS B 105 " - pdb=" SG CYS B 110 " distance=2.02 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: 0.89 Conformation dependent library (CDL) restraints added in 388.9 milliseconds 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 3 sheets defined 73.0% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 removed outlier: 3.600A pdb=" N LEU A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 32 Processing helix chain 'A' and resid 39 through 61 removed outlier: 4.041A pdb=" N GLY A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 91 removed outlier: 4.074A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 95 removed outlier: 3.515A pdb=" N LEU A 95 " --> pdb=" O LEU A 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 95' Processing helix chain 'A' and resid 99 through 112 removed outlier: 3.594A pdb=" N ALA A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 133 through 138 removed outlier: 4.193A pdb=" N GLY A 137 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 164 removed outlier: 3.500A pdb=" N MET A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Proline residue: A 146 - end of helix Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 221 through 237 removed outlier: 3.615A pdb=" N ALA A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 250 through 269 removed outlier: 3.560A pdb=" N ILE A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY A 263 " --> pdb=" O MET A 259 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ALA A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.597A pdb=" N ARG A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL A 276 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 304 removed outlier: 3.533A pdb=" N VAL A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Proline residue: A 288 - end of helix removed outlier: 3.520A pdb=" N ILE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.504A pdb=" N VAL A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 336 removed outlier: 3.612A pdb=" N THR A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 334 " --> pdb=" O PRO A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.846A pdb=" N TYR A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 359 through 371 removed outlier: 3.773A pdb=" N THR A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 27 removed outlier: 3.540A pdb=" N ALA D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 68 through 83 removed outlier: 3.654A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'C' and resid 3 through 16 removed outlier: 3.600A pdb=" N LEU C 8 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 39 through 61 removed outlier: 4.041A pdb=" N GLY C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 91 removed outlier: 4.074A pdb=" N VAL C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 90 " --> pdb=" O PHE C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 95 removed outlier: 3.515A pdb=" N LEU C 95 " --> pdb=" O LEU C 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 92 through 95' Processing helix chain 'C' and resid 99 through 112 removed outlier: 3.594A pdb=" N ALA C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 133 through 138 removed outlier: 4.193A pdb=" N GLY C 137 " --> pdb=" O ALA C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 164 removed outlier: 3.500A pdb=" N MET C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Proline residue: C 146 - end of helix Processing helix chain 'C' and resid 211 through 220 Processing helix chain 'C' and resid 221 through 237 removed outlier: 3.615A pdb=" N ALA C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 246 Processing helix chain 'C' and resid 250 through 269 removed outlier: 3.559A pdb=" N ILE C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY C 263 " --> pdb=" O MET C 259 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ALA C 266 " --> pdb=" O MET C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 276 removed outlier: 3.596A pdb=" N ARG C 274 " --> pdb=" O GLY C 271 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL C 276 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 304 removed outlier: 3.534A pdb=" N VAL C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Proline residue: C 288 - end of helix removed outlier: 3.521A pdb=" N ILE C 301 " --> pdb=" O GLY C 297 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.505A pdb=" N VAL C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 336 removed outlier: 3.541A pdb=" N ALA C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 351 removed outlier: 3.846A pdb=" N TYR C 344 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 351 " --> pdb=" O SER C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 359 Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.773A pdb=" N THR C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 27 removed outlier: 3.540A pdb=" N ALA F 21 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS F 22 " --> pdb=" O LYS F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 55 Processing helix chain 'F' and resid 68 through 83 removed outlier: 3.654A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'E' and resid 3 through 16 removed outlier: 3.601A pdb=" N LEU E 8 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR E 9 " --> pdb=" O SER E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 32 Processing helix chain 'E' and resid 39 through 61 removed outlier: 4.040A pdb=" N GLY E 59 " --> pdb=" O GLY E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 91 removed outlier: 4.073A pdb=" N VAL E 85 " --> pdb=" O GLY E 81 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 95 removed outlier: 3.516A pdb=" N LEU E 95 " --> pdb=" O LEU E 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 99 through 112 removed outlier: 3.593A pdb=" N ALA E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 128 Processing helix chain 'E' and resid 133 through 138 removed outlier: 4.193A pdb=" N GLY E 137 " --> pdb=" O ALA E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 164 Proline residue: E 146 - end of helix Processing helix chain 'E' and resid 211 through 220 Processing helix chain 'E' and resid 221 through 237 removed outlier: 3.615A pdb=" N ALA E 226 " --> pdb=" O PRO E 222 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR E 237 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 250 through 269 removed outlier: 3.558A pdb=" N ILE E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY E 263 " --> pdb=" O MET E 259 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ALA E 266 " --> pdb=" O MET E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 276 removed outlier: 3.596A pdb=" N ARG E 274 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS E 275 " --> pdb=" O GLU E 272 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL E 276 " --> pdb=" O LEU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 304 removed outlier: 3.534A pdb=" N VAL E 282 " --> pdb=" O GLN E 278 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Proline residue: E 288 - end of helix removed outlier: 3.521A pdb=" N ILE E 301 " --> pdb=" O GLY E 297 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 322 removed outlier: 3.504A pdb=" N VAL E 314 " --> pdb=" O LEU E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 336 removed outlier: 4.024A pdb=" N THR E 331 " --> pdb=" O SER E 327 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E 334 " --> pdb=" O PRO E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 351 removed outlier: 3.846A pdb=" N TYR E 344 " --> pdb=" O ASN E 340 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE E 351 " --> pdb=" O SER E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 359 Processing helix chain 'E' and resid 359 through 371 removed outlier: 3.772A pdb=" N THR E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 27 removed outlier: 3.540A pdb=" N ALA B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 22 " --> pdb=" O LYS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 68 through 83 removed outlier: 3.655A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 Processing sheet with id=AA1, first strand: chain 'F' and resid 32 through 40 removed outlier: 5.387A pdb=" N ASN F 36 " --> pdb=" O ASN D 36 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ASN D 36 " --> pdb=" O ASN F 36 " (cutoff:3.500A) removed outlier: 13.271A pdb=" N GLY F 38 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 16.687A pdb=" N VAL D 34 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 23.016A pdb=" N LYS F 40 " --> pdb=" O TYR D 32 " (cutoff:3.500A) removed outlier: 26.353A pdb=" N TYR D 32 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N GLY D 89 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY F 101 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE D 91 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER D 95 " --> pdb=" O SER F 95 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N SER F 95 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 14.511A pdb=" N GLU D 97 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 17.549A pdb=" N ILE F 93 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 23.260A pdb=" N LEU D 99 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 26.793A pdb=" N ILE F 91 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 29.801A pdb=" N GLY D 101 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 33.445A pdb=" N GLY F 89 " --> pdb=" O GLY D 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 59 through 66 current: chain 'B' and resid 32 through 40 removed outlier: 5.384A pdb=" N ASN B 36 " --> pdb=" O ASN F 36 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN F 36 " --> pdb=" O ASN B 36 " (cutoff:3.500A) removed outlier: 13.254A pdb=" N GLY B 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 16.669A pdb=" N VAL F 34 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 22.997A pdb=" N LYS B 40 " --> pdb=" O TYR F 32 " (cutoff:3.500A) removed outlier: 26.335A pdb=" N TYR F 32 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 32 through 40 removed outlier: 26.442A pdb=" N TYR B 32 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 23.106A pdb=" N LYS D 40 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 16.757A pdb=" N VAL B 34 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 13.339A pdb=" N GLY D 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASN B 36 " --> pdb=" O ASN D 36 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASN D 36 " --> pdb=" O ASN B 36 " (cutoff:3.500A) removed outlier: 33.529A pdb=" N GLY D 89 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 29.903A pdb=" N GLY B 101 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 26.870A pdb=" N ILE D 91 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 23.336A pdb=" N LEU B 99 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 17.604A pdb=" N ILE D 93 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 14.555A pdb=" N GLU B 97 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N SER D 95 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER B 95 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 91 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY D 101 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N GLY B 89 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 59 through 66 removed outlier: 33.445A pdb=" N GLY B 89 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 29.804A pdb=" N GLY F 101 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 26.795A pdb=" N ILE B 91 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 23.261A pdb=" N LEU F 99 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 17.551A pdb=" N ILE B 93 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 14.510A pdb=" N GLU F 97 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N SER B 95 " --> pdb=" O SER F 95 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER F 95 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE F 91 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY B 101 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N GLY F 89 " --> pdb=" O GLY B 101 " (cutoff:3.500A) 727 hydrogen bonds defined for protein. 2100 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3044 1.34 - 1.45: 1492 1.45 - 1.57: 5454 1.57 - 1.69: 3 1.69 - 1.80: 90 Bond restraints: 10083 Sorted by residual: bond pdb=" N ILE C 326 " pdb=" CA ILE C 326 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.20e+00 bond pdb=" N ILE E 326 " pdb=" CA ILE E 326 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.15e+00 bond pdb=" N ILE A 326 " pdb=" CA ILE A 326 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.57e+00 bond pdb=" N SER A 322 " pdb=" CA SER A 322 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.31e-02 5.83e+03 6.26e+00 bond pdb=" N SER E 322 " pdb=" CA SER E 322 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.31e-02 5.83e+03 6.07e+00 ... (remaining 10078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 12953 1.86 - 3.71: 571 3.71 - 5.57: 133 5.57 - 7.43: 34 7.43 - 9.28: 16 Bond angle restraints: 13707 Sorted by residual: angle pdb=" N LEU A 20 " pdb=" CA LEU A 20 " pdb=" C LEU A 20 " ideal model delta sigma weight residual 114.04 107.61 6.43 1.24e+00 6.50e-01 2.69e+01 angle pdb=" N LEU C 20 " pdb=" CA LEU C 20 " pdb=" C LEU C 20 " ideal model delta sigma weight residual 114.04 107.62 6.42 1.24e+00 6.50e-01 2.68e+01 angle pdb=" N LEU E 20 " pdb=" CA LEU E 20 " pdb=" C LEU E 20 " ideal model delta sigma weight residual 114.04 107.62 6.42 1.24e+00 6.50e-01 2.68e+01 angle pdb=" C PRO A 18 " pdb=" N THR A 19 " pdb=" CA THR A 19 " ideal model delta sigma weight residual 121.54 129.50 -7.96 1.91e+00 2.74e-01 1.74e+01 angle pdb=" C PRO E 18 " pdb=" N THR E 19 " pdb=" CA THR E 19 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.71e+01 ... (remaining 13702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 5255 15.75 - 31.50: 502 31.50 - 47.25: 156 47.25 - 63.00: 39 63.00 - 78.75: 15 Dihedral angle restraints: 5967 sinusoidal: 2247 harmonic: 3720 Sorted by residual: dihedral pdb=" CA SER C 323 " pdb=" C SER C 323 " pdb=" N SER C 324 " pdb=" CA SER C 324 " ideal model delta harmonic sigma weight residual -180.00 -151.83 -28.17 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA SER A 323 " pdb=" C SER A 323 " pdb=" N SER A 324 " pdb=" CA SER A 324 " ideal model delta harmonic sigma weight residual -180.00 -151.92 -28.08 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA GLY E 263 " pdb=" C GLY E 263 " pdb=" N MET E 264 " pdb=" CA MET E 264 " ideal model delta harmonic sigma weight residual 180.00 155.38 24.62 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 5964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1027 0.044 - 0.087: 475 0.087 - 0.131: 132 0.131 - 0.174: 19 0.174 - 0.218: 9 Chirality restraints: 1662 Sorted by residual: chirality pdb=" C2' AMP B 201 " pdb=" C1' AMP B 201 " pdb=" C3' AMP B 201 " pdb=" O2' AMP B 201 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C2' AMP D 201 " pdb=" C1' AMP D 201 " pdb=" C3' AMP D 201 " pdb=" O2' AMP D 201 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C2' AMP F 200 " pdb=" C1' AMP F 200 " pdb=" C3' AMP F 200 " pdb=" O2' AMP F 200 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1659 not shown) Planarity restraints: 1686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 323 " -0.020 2.00e-02 2.50e+03 4.17e-02 1.74e+01 pdb=" C SER E 323 " 0.072 2.00e-02 2.50e+03 pdb=" O SER E 323 " -0.028 2.00e-02 2.50e+03 pdb=" N SER E 324 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 329 " 0.044 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO E 330 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO E 330 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 330 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 329 " 0.044 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO A 330 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " 0.037 5.00e-02 4.00e+02 ... (remaining 1683 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2263 2.77 - 3.30: 8494 3.30 - 3.84: 16423 3.84 - 4.37: 20037 4.37 - 4.90: 34778 Nonbonded interactions: 81995 Sorted by model distance: nonbonded pdb=" OD2 ASP E 325 " pdb=" OG1 THR E 353 " model vdw 2.240 3.040 nonbonded pdb=" OD2 ASP A 325 " pdb=" OG1 THR A 353 " model vdw 2.267 3.040 nonbonded pdb=" OD1 ASP A 325 " pdb=" OG SER A 348 " model vdw 2.279 3.040 nonbonded pdb=" O THR A 124 " pdb=" OG SER A 128 " model vdw 2.285 3.040 nonbonded pdb=" O THR E 124 " pdb=" OG SER E 128 " model vdw 2.286 3.040 ... (remaining 81990 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'B' } 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: 0.910 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.720 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 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 : 0.008 0.073 10086 Z= 0.329 Angle : 0.997 9.282 13713 Z= 0.549 Chirality : 0.054 0.218 1662 Planarity : 0.008 0.066 1686 Dihedral : 14.739 78.745 3588 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.23 % Favored : 96.54 % Rotamer: Outliers : 8.02 % Allowed : 5.41 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.67 (0.14), residues: 1299 helix: -4.31 (0.07), residues: 861 sheet: -1.54 (0.48), residues: 99 loop : -1.97 (0.24), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 252 TYR 0.016 0.002 TYR E 344 PHE 0.016 0.003 PHE E 296 TRP 0.016 0.003 TRP C 212 HIS 0.003 0.001 HIS E 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00770 / 0.33 (10083) covalent geometry : angle 0.99758 / 0.55 (13707) SS BOND : bond 0.00707 / 0.36 ( 3) SS BOND : angle 0.38014 / 0.20 ( 6) hydrogen bonds : bond 0.29616 / 19.33 ( 667) hydrogen bonds : angle 10.08184 / 6.87 ( 2100) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 223 time to evaluate : 0.367 Fit side-chains REVERT: A 10 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6766 (t0) REVERT: A 70 MET cc_start: 0.8566 (ptm) cc_final: 0.8129 (ptt) REVERT: A 133 GLU cc_start: 0.8460 (mp0) cc_final: 0.8259 (mp0) REVERT: A 161 LYS cc_start: 0.7767 (mtmt) cc_final: 0.7334 (mmtm) REVERT: D 40 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8359 (ttpm) REVERT: D 50 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: D 78 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7522 (mtp85) REVERT: C 70 MET cc_start: 0.8490 (ptm) cc_final: 0.8056 (ptp) REVERT: C 133 GLU cc_start: 0.8481 (mp0) cc_final: 0.8105 (mp0) REVERT: C 300 MET cc_start: 0.8911 (mmm) cc_final: 0.8689 (mmm) REVERT: C 323 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8634 (p) REVERT: F 40 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8380 (ttpm) REVERT: F 43 ARG cc_start: 0.8478 (mtt90) cc_final: 0.8139 (mtt180) REVERT: F 50 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: F 78 ARG cc_start: 0.7806 (mtp180) cc_final: 0.7603 (mtp85) REVERT: E 10 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6897 (t0) REVERT: E 70 MET cc_start: 0.8456 (ptm) cc_final: 0.7986 (ptt) REVERT: E 133 GLU cc_start: 0.8255 (mp0) cc_final: 0.7893 (mp0) REVERT: E 161 LYS cc_start: 0.7682 (mtmt) cc_final: 0.7430 (mptt) REVERT: E 300 MET cc_start: 0.8965 (mmm) cc_final: 0.8585 (mmm) REVERT: B 40 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8500 (tttm) REVERT: B 78 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7508 (mtp180) outliers start: 83 outliers final: 14 residues processed: 275 average time/residue: 0.6216 time to fit residues: 181.1487 Evaluate side-chains 198 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 348 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN A 156 ASN A 291 HIS A 303 HIS D 36 ASN C 14 GLN C 291 HIS C 303 HIS E 14 GLN E 97 ASN E 291 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.088057 restraints weight = 12653.422| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.58 r_work: 0.2821 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10086 Z= 0.151 Angle : 0.705 7.307 13713 Z= 0.351 Chirality : 0.043 0.136 1662 Planarity : 0.006 0.042 1686 Dihedral : 7.058 63.339 1444 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.77 % Allowed : 14.11 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.20), residues: 1299 helix: -1.20 (0.15), residues: 861 sheet: -0.76 (0.46), residues: 99 loop : -1.28 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 333 TYR 0.017 0.002 TYR A 344 PHE 0.013 0.001 PHE B 62 TRP 0.015 0.002 TRP C 212 HIS 0.001 0.000 HIS E 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (10083) covalent geometry : angle 0.70564 / 0.35 (13707) SS BOND : bond 0.00224 / 0.11 ( 3) SS BOND : angle 0.06052 / 0.03 ( 6) hydrogen bonds : bond 0.04977 / 3.25 ( 667) hydrogen bonds : angle 4.95863 / 3.38 ( 2100) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.254 Fit side-chains REVERT: A 133 GLU cc_start: 0.8671 (mp0) cc_final: 0.8280 (mp0) REVERT: A 161 LYS cc_start: 0.7362 (mtmt) cc_final: 0.6900 (mmtm) REVERT: D 40 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8544 (ttpt) REVERT: D 45 VAL cc_start: 0.9302 (p) cc_final: 0.9084 (t) REVERT: D 52 ASN cc_start: 0.8475 (t0) cc_final: 0.8230 (t0) REVERT: D 74 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8241 (tm-30) REVERT: D 78 ARG cc_start: 0.8262 (mtp180) cc_final: 0.7950 (mtp85) REVERT: C 40 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7591 (pp20) REVERT: C 129 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8408 (mttp) REVERT: C 133 GLU cc_start: 0.8694 (mp0) cc_final: 0.8294 (mp0) REVERT: C 161 LYS cc_start: 0.7434 (mtmt) cc_final: 0.7214 (mptt) REVERT: F 40 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8520 (ttpt) REVERT: F 50 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: F 67 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: F 78 ARG cc_start: 0.8357 (mtp180) cc_final: 0.8077 (mtp85) REVERT: F 82 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8545 (tttp) REVERT: E 133 GLU cc_start: 0.8633 (mp0) cc_final: 0.8289 (mp0) REVERT: E 161 LYS cc_start: 0.7388 (mtmt) cc_final: 0.7131 (mptt) REVERT: E 300 MET cc_start: 0.9091 (mmm) cc_final: 0.8869 (mmm) REVERT: B 40 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8437 (tttm) REVERT: B 78 ARG cc_start: 0.8185 (mtp180) cc_final: 0.7929 (mtp180) outliers start: 39 outliers final: 11 residues processed: 214 average time/residue: 0.7091 time to fit residues: 159.8377 Evaluate side-chains 203 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain B residue 67 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 113 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 116 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 36 ASN B 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.091284 restraints weight = 12607.036| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.55 r_work: 0.2854 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10086 Z= 0.133 Angle : 0.658 6.828 13713 Z= 0.320 Chirality : 0.043 0.133 1662 Planarity : 0.005 0.035 1686 Dihedral : 5.953 52.057 1425 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.57 % Allowed : 14.69 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1299 helix: 0.28 (0.17), residues: 888 sheet: -0.42 (0.46), residues: 99 loop : -0.85 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 69 TYR 0.016 0.001 TYR A 344 PHE 0.011 0.001 PHE D 62 TRP 0.013 0.002 TRP C 267 HIS 0.002 0.000 HIS C 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (10083) covalent geometry : angle 0.65852 / 0.32 (13707) SS BOND : bond 0.00166 / 0.08 ( 3) SS BOND : angle 0.04202 / 0.02 ( 6) hydrogen bonds : bond 0.04376 / 2.86 ( 667) hydrogen bonds : angle 4.49993 / 3.04 ( 2100) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8630 (mp0) cc_final: 0.8322 (mp0) REVERT: A 161 LYS cc_start: 0.7295 (mtmt) cc_final: 0.6844 (mmtm) REVERT: A 224 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8579 (tt) REVERT: D 40 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8520 (ttpt) REVERT: D 67 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: D 78 ARG cc_start: 0.8206 (mtp180) cc_final: 0.7934 (mtp85) REVERT: C 40 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7456 (tm-30) REVERT: C 133 GLU cc_start: 0.8685 (mp0) cc_final: 0.8343 (mp0) REVERT: C 161 LYS cc_start: 0.7411 (mtmt) cc_final: 0.7169 (mptt) REVERT: F 40 LYS cc_start: 0.8860 (ttmm) cc_final: 0.8557 (ttpt) REVERT: F 50 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8103 (pt0) REVERT: F 67 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: F 78 ARG cc_start: 0.8313 (mtp180) cc_final: 0.8003 (mtp85) REVERT: F 82 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8583 (tttp) REVERT: E 161 LYS cc_start: 0.7455 (mtmt) cc_final: 0.7153 (mptt) REVERT: E 300 MET cc_start: 0.9041 (mmm) cc_final: 0.8718 (mmm) REVERT: B 18 LYS cc_start: 0.9178 (tppt) cc_final: 0.8842 (mptt) REVERT: B 40 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8415 (mptt) outliers start: 37 outliers final: 12 residues processed: 213 average time/residue: 0.7039 time to fit residues: 158.0270 Evaluate side-chains 206 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain B residue 85 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 12 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 80 optimal weight: 0.0470 chunk 74 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.091451 restraints weight = 12351.134| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.60 r_work: 0.2885 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10086 Z= 0.126 Angle : 0.647 6.375 13713 Z= 0.313 Chirality : 0.043 0.134 1662 Planarity : 0.004 0.035 1686 Dihedral : 5.591 55.384 1424 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.00 % Allowed : 16.43 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.23), residues: 1299 helix: 1.05 (0.18), residues: 867 sheet: -0.28 (0.46), residues: 99 loop : -0.43 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 274 TYR 0.016 0.001 TYR E 344 PHE 0.012 0.001 PHE D 62 TRP 0.014 0.002 TRP E 267 HIS 0.001 0.000 HIS C 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (10083) covalent geometry : angle 0.64692 / 0.31 (13707) SS BOND : bond 0.00114 / 0.06 ( 3) SS BOND : angle 0.03322 / 0.02 ( 6) hydrogen bonds : bond 0.04059 / 2.65 ( 667) hydrogen bonds : angle 4.30562 / 2.90 ( 2100) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.7295 (mtmt) cc_final: 0.6849 (mmtm) REVERT: A 224 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8560 (tt) REVERT: D 40 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8544 (ttpt) REVERT: D 67 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: C 40 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: C 129 LYS cc_start: 0.8960 (mppt) cc_final: 0.8744 (mmtm) REVERT: C 133 GLU cc_start: 0.8657 (mp0) cc_final: 0.8237 (mp0) REVERT: C 161 LYS cc_start: 0.7440 (mtmt) cc_final: 0.7103 (mptt) REVERT: F 40 LYS cc_start: 0.8867 (ttmm) cc_final: 0.8560 (ttpt) REVERT: F 50 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8086 (pt0) REVERT: F 67 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: F 78 ARG cc_start: 0.8437 (mtp180) cc_final: 0.8089 (mtp85) REVERT: F 82 LYS cc_start: 0.8887 (ttpt) cc_final: 0.8583 (tttp) REVERT: E 129 LYS cc_start: 0.8815 (mmtm) cc_final: 0.8600 (mmtm) REVERT: E 133 GLU cc_start: 0.8551 (mp0) cc_final: 0.8197 (mp0) REVERT: E 265 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8361 (tp30) REVERT: E 300 MET cc_start: 0.9009 (mmm) cc_final: 0.8798 (mmm) REVERT: B 18 LYS cc_start: 0.9158 (tppt) cc_final: 0.8795 (mptt) REVERT: B 40 LYS cc_start: 0.8928 (ttmm) cc_final: 0.8409 (mptt) outliers start: 31 outliers final: 14 residues processed: 209 average time/residue: 0.7042 time to fit residues: 154.7960 Evaluate side-chains 206 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 85 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 56 optimal weight: 0.0970 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.090619 restraints weight = 12222.114| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.59 r_work: 0.2832 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10086 Z= 0.149 Angle : 0.661 6.857 13713 Z= 0.321 Chirality : 0.044 0.139 1662 Planarity : 0.004 0.035 1686 Dihedral : 5.696 69.797 1423 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.29 % Allowed : 16.52 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.24), residues: 1299 helix: 1.26 (0.18), residues: 870 sheet: -0.29 (0.46), residues: 99 loop : -0.20 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 46 TYR 0.015 0.002 TYR A 344 PHE 0.011 0.001 PHE C 246 TRP 0.015 0.002 TRP E 267 HIS 0.002 0.001 HIS C 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (10083) covalent geometry : angle 0.66158 / 0.32 (13707) SS BOND : bond 0.00219 / 0.11 ( 3) SS BOND : angle 0.06138 / 0.03 ( 6) hydrogen bonds : bond 0.04365 / 2.85 ( 667) hydrogen bonds : angle 4.35474 / 2.93 ( 2100) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.7326 (mtmt) cc_final: 0.6856 (mmtm) REVERT: A 224 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8540 (tt) REVERT: A 227 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8646 (tmm) REVERT: D 40 LYS cc_start: 0.8916 (ttmm) cc_final: 0.8478 (tttm) REVERT: D 67 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: C 40 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: C 71 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8053 (tm) REVERT: C 133 GLU cc_start: 0.8650 (mp0) cc_final: 0.8282 (mp0) REVERT: C 161 LYS cc_start: 0.7440 (mtmt) cc_final: 0.7092 (mptt) REVERT: C 367 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8931 (tt) REVERT: F 40 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8569 (ttpt) REVERT: F 50 GLN cc_start: 0.8524 (pt0) cc_final: 0.8292 (pt0) REVERT: F 67 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8251 (mt-10) REVERT: F 78 ARG cc_start: 0.8415 (mtp180) cc_final: 0.8090 (mtp85) REVERT: F 82 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8582 (tttp) REVERT: E 129 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8578 (mmtp) REVERT: E 133 GLU cc_start: 0.8571 (mp0) cc_final: 0.8071 (mp0) REVERT: E 161 LYS cc_start: 0.7522 (ttmt) cc_final: 0.7150 (tttm) REVERT: E 300 MET cc_start: 0.9022 (mmm) cc_final: 0.8788 (mmm) REVERT: B 18 LYS cc_start: 0.9174 (tppt) cc_final: 0.8800 (mptt) REVERT: B 40 LYS cc_start: 0.8933 (ttmm) cc_final: 0.8419 (mptt) outliers start: 34 outliers final: 16 residues processed: 210 average time/residue: 0.6999 time to fit residues: 154.9193 Evaluate side-chains 211 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 85 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 87 optimal weight: 4.9990 chunk 109 optimal weight: 0.2980 chunk 95 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.087714 restraints weight = 12260.882| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.75 r_work: 0.2812 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10086 Z= 0.163 Angle : 0.674 6.959 13713 Z= 0.329 Chirality : 0.045 0.139 1662 Planarity : 0.005 0.036 1686 Dihedral : 5.422 44.051 1419 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.57 % Allowed : 17.00 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.24), residues: 1299 helix: 1.40 (0.18), residues: 861 sheet: -0.35 (0.46), residues: 99 loop : -0.33 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 46 TYR 0.017 0.002 TYR A 140 PHE 0.013 0.001 PHE C 246 TRP 0.016 0.002 TRP E 267 HIS 0.002 0.001 HIS C 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (10083) covalent geometry : angle 0.67435 / 0.33 (13707) SS BOND : bond 0.00240 / 0.12 ( 3) SS BOND : angle 0.11154 / 0.06 ( 6) hydrogen bonds : bond 0.04534 / 2.95 ( 667) hydrogen bonds : angle 4.40805 / 2.97 ( 2100) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.7273 (mtmt) cc_final: 0.6781 (mmtm) REVERT: A 224 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8501 (tt) REVERT: A 227 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8633 (tmm) REVERT: A 259 MET cc_start: 0.9261 (mmp) cc_final: 0.8975 (mmm) REVERT: D 40 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8420 (tttm) REVERT: D 67 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8172 (mt-10) REVERT: C 40 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: C 71 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8090 (tm) REVERT: C 133 GLU cc_start: 0.8572 (mp0) cc_final: 0.8139 (mp0) REVERT: C 161 LYS cc_start: 0.7374 (mtmt) cc_final: 0.7015 (mptt) REVERT: F 40 LYS cc_start: 0.8933 (ttmm) cc_final: 0.8549 (ttpt) REVERT: F 50 GLN cc_start: 0.8504 (pt0) cc_final: 0.8232 (pt0) REVERT: F 67 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8277 (mt-10) REVERT: F 82 LYS cc_start: 0.8895 (ttpt) cc_final: 0.8538 (tttp) REVERT: E 129 LYS cc_start: 0.8829 (mmtm) cc_final: 0.8603 (mmtp) REVERT: E 133 GLU cc_start: 0.8613 (mp0) cc_final: 0.8206 (mp0) REVERT: E 274 ARG cc_start: 0.7991 (mtt90) cc_final: 0.7603 (mmt180) REVERT: E 300 MET cc_start: 0.9009 (mmm) cc_final: 0.8730 (mmm) REVERT: B 18 LYS cc_start: 0.9168 (tppt) cc_final: 0.8792 (mptt) REVERT: B 40 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8307 (mptt) outliers start: 37 outliers final: 13 residues processed: 208 average time/residue: 0.7174 time to fit residues: 157.2609 Evaluate side-chains 208 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 85 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 120 optimal weight: 2.9990 chunk 13 optimal weight: 0.0070 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 156 ASN E 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.092288 restraints weight = 12204.980| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.64 r_work: 0.2843 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10086 Z= 0.127 Angle : 0.643 7.296 13713 Z= 0.310 Chirality : 0.043 0.134 1662 Planarity : 0.004 0.036 1686 Dihedral : 5.231 41.325 1419 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.19 % Allowed : 17.78 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.24), residues: 1299 helix: 1.55 (0.18), residues: 867 sheet: -0.28 (0.46), residues: 99 loop : -0.11 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 78 TYR 0.016 0.001 TYR A 344 PHE 0.013 0.001 PHE B 62 TRP 0.014 0.002 TRP E 267 HIS 0.001 0.000 HIS C 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (10083) covalent geometry : angle 0.64344 / 0.31 (13707) SS BOND : bond 0.00136 / 0.07 ( 3) SS BOND : angle 0.05198 / 0.03 ( 6) hydrogen bonds : bond 0.04015 / 2.62 ( 667) hydrogen bonds : angle 4.24514 / 2.85 ( 2100) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.7398 (mtmt) cc_final: 0.6954 (mmtp) REVERT: A 224 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8567 (tt) REVERT: A 259 MET cc_start: 0.9234 (mmp) cc_final: 0.8958 (mmm) REVERT: D 40 LYS cc_start: 0.8933 (ttmm) cc_final: 0.8502 (tttm) REVERT: D 67 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: C 40 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: C 161 LYS cc_start: 0.7478 (mtmt) cc_final: 0.7127 (mptt) REVERT: F 40 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8558 (ttpt) REVERT: F 50 GLN cc_start: 0.8568 (pt0) cc_final: 0.8299 (pt0) REVERT: F 67 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8269 (mt-10) REVERT: F 82 LYS cc_start: 0.8900 (ttpt) cc_final: 0.8543 (tttp) REVERT: E 129 LYS cc_start: 0.8820 (mmtm) cc_final: 0.8616 (mmtp) REVERT: E 133 GLU cc_start: 0.8572 (mp0) cc_final: 0.8196 (mp0) REVERT: E 274 ARG cc_start: 0.7989 (mtt90) cc_final: 0.7668 (mmt180) REVERT: B 18 LYS cc_start: 0.9182 (tppt) cc_final: 0.8820 (mptt) REVERT: B 40 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8399 (mptt) outliers start: 33 outliers final: 15 residues processed: 205 average time/residue: 0.7004 time to fit residues: 151.2274 Evaluate side-chains 205 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 85 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 24 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.666 > 50:) chunk 70 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.090812 restraints weight = 12581.825| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.54 r_work: 0.2864 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10086 Z= 0.139 Angle : 0.654 7.612 13713 Z= 0.316 Chirality : 0.043 0.137 1662 Planarity : 0.004 0.036 1686 Dihedral : 5.269 42.188 1419 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.19 % Allowed : 18.16 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.24), residues: 1299 helix: 1.62 (0.18), residues: 861 sheet: -0.25 (0.46), residues: 99 loop : -0.22 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 78 TYR 0.016 0.002 TYR A 344 PHE 0.013 0.001 PHE B 62 TRP 0.015 0.002 TRP E 267 HIS 0.001 0.001 HIS C 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10083) covalent geometry : angle 0.65452 / 0.32 (13707) SS BOND : bond 0.00174 / 0.09 ( 3) SS BOND : angle 0.07923 / 0.04 ( 6) hydrogen bonds : bond 0.04187 / 2.73 ( 667) hydrogen bonds : angle 4.26662 / 2.87 ( 2100) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.7353 (mtmt) cc_final: 0.6941 (mmtp) REVERT: A 224 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8585 (tt) REVERT: A 259 MET cc_start: 0.9205 (mmp) cc_final: 0.8941 (mmm) REVERT: A 272 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: D 18 LYS cc_start: 0.9152 (tppt) cc_final: 0.8814 (mptt) REVERT: D 40 LYS cc_start: 0.8924 (ttmm) cc_final: 0.8549 (ttpt) REVERT: D 67 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: C 40 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: C 133 GLU cc_start: 0.8738 (mp0) cc_final: 0.8532 (mp0) REVERT: C 161 LYS cc_start: 0.7431 (mtmt) cc_final: 0.7077 (mptt) REVERT: F 40 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8558 (ttpt) REVERT: F 50 GLN cc_start: 0.8559 (pt0) cc_final: 0.8296 (pt0) REVERT: F 67 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: F 82 LYS cc_start: 0.8896 (ttpt) cc_final: 0.8575 (tttp) REVERT: E 129 LYS cc_start: 0.8820 (mmtm) cc_final: 0.8618 (mmtp) REVERT: E 133 GLU cc_start: 0.8577 (mp0) cc_final: 0.8270 (mp0) REVERT: E 274 ARG cc_start: 0.8004 (mtt90) cc_final: 0.7694 (mmt180) REVERT: B 18 LYS cc_start: 0.9159 (tppt) cc_final: 0.8785 (mptt) REVERT: B 40 LYS cc_start: 0.8924 (ttmm) cc_final: 0.8395 (mptt) outliers start: 33 outliers final: 16 residues processed: 207 average time/residue: 0.7159 time to fit residues: 156.1057 Evaluate side-chains 210 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 85 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 118 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 80 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.093093 restraints weight = 12127.444| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.57 r_work: 0.2902 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10086 Z= 0.119 Angle : 0.646 8.736 13713 Z= 0.307 Chirality : 0.043 0.133 1662 Planarity : 0.004 0.036 1686 Dihedral : 5.146 40.286 1419 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.61 % Allowed : 18.45 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.24), residues: 1299 helix: 1.64 (0.18), residues: 867 sheet: -0.18 (0.47), residues: 99 loop : -0.03 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 78 TYR 0.016 0.001 TYR C 344 PHE 0.013 0.001 PHE D 62 TRP 0.014 0.002 TRP E 267 HIS 0.001 0.000 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (10083) covalent geometry : angle 0.64660 / 0.31 (13707) SS BOND : bond 0.00095 / 0.05 ( 3) SS BOND : angle 0.05979 / 0.03 ( 6) hydrogen bonds : bond 0.03840 / 2.51 ( 667) hydrogen bonds : angle 4.17145 / 2.80 ( 2100) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.7408 (mtmt) cc_final: 0.6977 (mmtp) REVERT: A 224 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8514 (tt) REVERT: A 259 MET cc_start: 0.9199 (mmp) cc_final: 0.8920 (mmm) REVERT: A 272 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: D 18 LYS cc_start: 0.9158 (tppt) cc_final: 0.8797 (mptt) REVERT: D 40 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8588 (ttpt) REVERT: D 67 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: C 40 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: C 129 LYS cc_start: 0.9022 (mppt) cc_final: 0.8807 (mmtm) REVERT: C 133 GLU cc_start: 0.8756 (mp0) cc_final: 0.8442 (mp0) REVERT: C 161 LYS cc_start: 0.7416 (mtmt) cc_final: 0.7075 (mptt) REVERT: F 40 LYS cc_start: 0.8842 (ttmm) cc_final: 0.8549 (ttpt) REVERT: F 67 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8250 (mt-10) REVERT: F 82 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8533 (tttp) REVERT: E 129 LYS cc_start: 0.8827 (mmtm) cc_final: 0.8623 (mmtp) REVERT: E 133 GLU cc_start: 0.8596 (mp0) cc_final: 0.8247 (mp0) REVERT: E 274 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7602 (mmt180) REVERT: B 18 LYS cc_start: 0.9158 (tppt) cc_final: 0.8781 (mptt) REVERT: B 40 LYS cc_start: 0.8954 (ttmm) cc_final: 0.8387 (mptt) outliers start: 27 outliers final: 15 residues processed: 209 average time/residue: 0.6942 time to fit residues: 152.9324 Evaluate side-chains 208 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain B residue 67 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 128 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.092079 restraints weight = 12406.429| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.54 r_work: 0.2876 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10086 Z= 0.128 Angle : 0.661 10.370 13713 Z= 0.315 Chirality : 0.043 0.135 1662 Planarity : 0.004 0.036 1686 Dihedral : 5.170 41.049 1419 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.32 % Allowed : 18.65 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.24), residues: 1299 helix: 1.68 (0.18), residues: 864 sheet: -0.16 (0.47), residues: 99 loop : 0.14 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 78 TYR 0.016 0.001 TYR E 344 PHE 0.013 0.001 PHE D 62 TRP 0.014 0.002 TRP E 267 HIS 0.001 0.000 HIS C 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10083) covalent geometry : angle 0.66130 / 0.31 (13707) SS BOND : bond 0.00127 / 0.06 ( 3) SS BOND : angle 0.08205 / 0.04 ( 6) hydrogen bonds : bond 0.03989 / 2.61 ( 667) hydrogen bonds : angle 4.17584 / 2.80 ( 2100) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.7433 (mtmt) cc_final: 0.7031 (mmtp) REVERT: A 224 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8589 (tt) REVERT: A 259 MET cc_start: 0.9181 (mmp) cc_final: 0.8918 (mmm) REVERT: A 272 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: D 18 LYS cc_start: 0.9148 (tppt) cc_final: 0.8803 (mptt) REVERT: D 40 LYS cc_start: 0.8953 (ttmm) cc_final: 0.8633 (ttpt) REVERT: D 67 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: C 40 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: C 129 LYS cc_start: 0.9011 (mppt) cc_final: 0.8800 (mmtm) REVERT: C 133 GLU cc_start: 0.8770 (mp0) cc_final: 0.8505 (mp0) REVERT: C 161 LYS cc_start: 0.7427 (mtmt) cc_final: 0.7101 (mptt) REVERT: F 40 LYS cc_start: 0.8812 (ttmm) cc_final: 0.8518 (ttpt) REVERT: F 67 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8283 (mt-10) REVERT: F 82 LYS cc_start: 0.8887 (ttpt) cc_final: 0.8576 (tttp) REVERT: E 129 LYS cc_start: 0.8802 (mmtm) cc_final: 0.8596 (mmtp) REVERT: E 133 GLU cc_start: 0.8606 (mp0) cc_final: 0.8309 (mp0) REVERT: E 274 ARG cc_start: 0.7937 (mtt90) cc_final: 0.7637 (mmt180) REVERT: B 18 LYS cc_start: 0.9137 (tppt) cc_final: 0.8753 (mptt) REVERT: B 40 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8365 (mptt) outliers start: 24 outliers final: 14 residues processed: 206 average time/residue: 0.7085 time to fit residues: 153.8953 Evaluate side-chains 209 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain B residue 67 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.091786 restraints weight = 12603.772| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.53 r_work: 0.2880 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10086 Z= 0.133 Angle : 0.669 11.737 13713 Z= 0.319 Chirality : 0.044 0.137 1662 Planarity : 0.004 0.036 1686 Dihedral : 5.203 41.230 1419 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.03 % Allowed : 19.03 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.24), residues: 1299 helix: 1.67 (0.18), residues: 864 sheet: -0.18 (0.47), residues: 99 loop : -0.05 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 78 TYR 0.016 0.002 TYR A 344 PHE 0.013 0.001 PHE D 62 TRP 0.014 0.002 TRP E 267 HIS 0.001 0.000 HIS C 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (10083) covalent geometry : angle 0.66924 / 0.32 (13707) SS BOND : bond 0.00149 / 0.07 ( 3) SS BOND : angle 0.08196 / 0.05 ( 6) hydrogen bonds : bond 0.04055 / 2.65 ( 667) hydrogen bonds : angle 4.20555 / 2.82 ( 2100) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3685.97 seconds wall clock time: 63 minutes 17.62 seconds (3797.62 seconds total)