Starting phenix.real_space_refine on Mon Jul 28 01:58:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7egk_31135/07_2025/7egk_31135.cif Found real_map, /net/cci-nas-00/data/ceres_data/7egk_31135/07_2025/7egk_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_31135/07_2025/7egk_31135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7egk_31135/07_2025/7egk_31135.map" model { file = "/net/cci-nas-00/data/ceres_data/7egk_31135/07_2025/7egk_31135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7egk_31135/07_2025/7egk_31135.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 Unusual residues: {'AMP%rna3p': 1} Classifications: {'RNA_mixed': 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 Unusual residues: {'AMP%rna3p': 1} Classifications: {'RNA_mixed': 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 Unusual residues: {'AMP%rna3p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 7.08, per 1000 atoms: 0.72 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: 2.95 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.28 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: 3.24 Time building geometry restraints manager: 3.33 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 2.090 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.620 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.003 TRP C 212 HIS 0.003 0.001 HIS E 291 PHE 0.016 0.003 PHE E 296 TYR 0.016 0.002 TYR E 344 ARG 0.002 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.29616 ( 667) hydrogen bonds : angle 10.08184 ( 2100) SS BOND : bond 0.00707 ( 3) SS BOND : angle 0.38014 ( 6) covalent geometry : bond 0.00770 (10083) covalent geometry : angle 0.99758 (13707) *********************** 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 : 1.246 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: 1.7532 time to fit residues: 510.7657 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 : 1.097 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 156 ASN A 291 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.089763 restraints weight = 12557.533| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.57 r_work: 0.2870 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2420 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= 0.140 Angle : 0.696 7.186 13713 Z= 0.345 Chirality : 0.043 0.134 1662 Planarity : 0.006 0.042 1686 Dihedral : 6.965 62.052 1444 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.48 % Allowed : 14.49 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.19), residues: 1299 helix: -1.34 (0.15), residues: 879 sheet: -0.71 (0.46), residues: 99 loop : -1.44 (0.29), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 212 HIS 0.001 0.000 HIS E 291 PHE 0.014 0.001 PHE B 62 TYR 0.017 0.002 TYR A 344 ARG 0.001 0.000 ARG C 333 Details of bonding type rmsd hydrogen bonds : bond 0.04696 ( 667) hydrogen bonds : angle 4.90940 ( 2100) SS BOND : bond 0.00226 ( 3) SS BOND : angle 0.08568 ( 6) covalent geometry : bond 0.00310 (10083) covalent geometry : angle 0.69595 (13707) *********************** 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 233 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 1.149 Fit side-chains REVERT: A 10 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6990 (t0) REVERT: A 133 GLU cc_start: 0.8665 (mp0) cc_final: 0.8320 (mp0) REVERT: A 161 LYS cc_start: 0.7351 (mtmt) cc_final: 0.6904 (mmtm) REVERT: D 40 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8557 (ttpt) REVERT: D 45 VAL cc_start: 0.9279 (p) cc_final: 0.9070 (t) REVERT: D 78 ARG cc_start: 0.8263 (mtp180) cc_final: 0.7947 (mtp85) REVERT: C 40 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7618 (pp20) REVERT: C 129 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8428 (mttp) REVERT: C 133 GLU cc_start: 0.8685 (mp0) cc_final: 0.8323 (mp0) REVERT: C 161 LYS cc_start: 0.7444 (mtmt) cc_final: 0.7242 (mptt) REVERT: F 40 LYS cc_start: 0.8826 (ttmm) cc_final: 0.8529 (ttpt) REVERT: F 50 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8085 (pt0) REVERT: F 67 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: F 78 ARG cc_start: 0.8380 (mtp180) cc_final: 0.8102 (mtp85) REVERT: F 82 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8546 (tttp) REVERT: E 10 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7182 (t0) REVERT: E 70 MET cc_start: 0.8816 (ptm) cc_final: 0.8285 (ptt) REVERT: E 133 GLU cc_start: 0.8611 (mp0) cc_final: 0.8309 (mp0) REVERT: E 161 LYS cc_start: 0.7462 (mtmt) cc_final: 0.7174 (mptt) REVERT: E 300 MET cc_start: 0.9086 (mmm) cc_final: 0.8765 (mmm) REVERT: B 40 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8451 (tttm) REVERT: B 48 SER cc_start: 0.8276 (m) cc_final: 0.8059 (p) REVERT: B 78 ARG cc_start: 0.8163 (mtp180) cc_final: 0.7829 (mtp180) outliers start: 36 outliers final: 8 residues processed: 214 average time/residue: 1.6390 time to fit residues: 369.7692 Evaluate side-chains 204 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 323 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 F residue 50 GLN Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 323 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 5 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS D 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.090005 restraints weight = 12683.181| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.55 r_work: 0.2839 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2535 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= 0.152 Angle : 0.676 6.703 13713 Z= 0.331 Chirality : 0.044 0.137 1662 Planarity : 0.005 0.036 1686 Dihedral : 6.303 56.898 1428 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.96 % Allowed : 14.88 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1299 helix: 0.36 (0.17), residues: 864 sheet: -0.48 (0.46), residues: 99 loop : -0.79 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 267 HIS 0.002 0.001 HIS C 291 PHE 0.012 0.001 PHE C 246 TYR 0.015 0.002 TYR A 344 ARG 0.001 0.000 ARG D 46 Details of bonding type rmsd hydrogen bonds : bond 0.04701 ( 667) hydrogen bonds : angle 4.58932 ( 2100) SS BOND : bond 0.00189 ( 3) SS BOND : angle 0.05296 ( 6) covalent geometry : bond 0.00359 (10083) covalent geometry : angle 0.67626 (13707) *********************** 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: 41 poor density : 193 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8656 (mp0) cc_final: 0.8343 (mp0) REVERT: A 161 LYS cc_start: 0.7320 (mtmt) cc_final: 0.6868 (mmtm) REVERT: A 224 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8576 (tt) REVERT: D 40 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8540 (ttpt) REVERT: D 45 VAL cc_start: 0.9318 (p) cc_final: 0.9111 (t) REVERT: D 67 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: C 40 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: C 133 GLU cc_start: 0.8699 (mp0) cc_final: 0.8357 (mp0) REVERT: C 161 LYS cc_start: 0.7418 (mtmt) cc_final: 0.7156 (mptt) REVERT: F 40 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8571 (ttpt) REVERT: F 50 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8092 (pt0) REVERT: F 67 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: F 78 ARG cc_start: 0.8371 (mtp180) cc_final: 0.8045 (mtp85) REVERT: F 82 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8578 (tttp) REVERT: E 161 LYS cc_start: 0.7391 (mtmt) cc_final: 0.7148 (mptt) REVERT: E 300 MET cc_start: 0.9066 (mmm) cc_final: 0.8755 (mmm) REVERT: B 18 LYS cc_start: 0.9194 (tppt) cc_final: 0.8854 (mptt) REVERT: B 40 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8405 (mptt) outliers start: 41 outliers final: 18 residues processed: 212 average time/residue: 1.8176 time to fit residues: 405.9134 Evaluate side-chains 214 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 1.998 ------------------------------------------------------------------------------- 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 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 67 GLU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain C residue 4 LEU 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 4 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain B residue 67 GLU 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 33 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3238 r_free = 0.3238 target = 0.108508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.088243 restraints weight = 12604.435| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.53 r_work: 0.2813 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10086 Z= 0.188 Angle : 0.708 7.265 13713 Z= 0.347 Chirality : 0.046 0.141 1662 Planarity : 0.005 0.036 1686 Dihedral : 6.187 66.743 1424 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1299 helix: 0.86 (0.18), residues: 864 sheet: -0.44 (0.46), residues: 99 loop : -0.63 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 267 HIS 0.002 0.001 HIS C 291 PHE 0.015 0.002 PHE C 246 TYR 0.019 0.002 TYR A 140 ARG 0.002 0.000 ARG D 46 Details of bonding type rmsd hydrogen bonds : bond 0.04902 ( 667) hydrogen bonds : angle 4.59104 ( 2100) SS BOND : bond 0.00333 ( 3) SS BOND : angle 0.09643 ( 6) covalent geometry : bond 0.00457 (10083) covalent geometry : angle 0.70843 (13707) *********************** 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 230 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7966 (pp20) cc_final: 0.7751 (pp20) REVERT: A 133 GLU cc_start: 0.8665 (mp0) cc_final: 0.8347 (mp0) REVERT: A 161 LYS cc_start: 0.7337 (mtmt) cc_final: 0.6863 (mmtm) REVERT: A 224 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8578 (tt) REVERT: D 40 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8524 (ttpt) REVERT: D 45 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.9078 (t) REVERT: D 52 ASN cc_start: 0.8465 (t0) cc_final: 0.8215 (t0) REVERT: D 67 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: C 40 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: C 71 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8200 (tm) REVERT: C 129 LYS cc_start: 0.8938 (mppt) cc_final: 0.8733 (mmtm) REVERT: C 133 GLU cc_start: 0.8659 (mp0) cc_final: 0.8243 (mp0) REVERT: C 161 LYS cc_start: 0.7397 (mtmt) cc_final: 0.7165 (mptt) REVERT: C 210 LYS cc_start: 0.8325 (mmmt) cc_final: 0.8037 (mmmt) REVERT: C 367 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8963 (tt) REVERT: F 40 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8583 (ttpt) REVERT: F 50 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8297 (pt0) REVERT: F 67 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8273 (mt-10) REVERT: F 78 ARG cc_start: 0.8309 (mtp180) cc_final: 0.7988 (mtp85) REVERT: F 82 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8586 (tttp) REVERT: E 133 GLU cc_start: 0.8619 (mp0) cc_final: 0.8173 (mp0) REVERT: E 300 MET cc_start: 0.9078 (mmm) cc_final: 0.8764 (mmm) REVERT: B 18 LYS cc_start: 0.9175 (tppt) cc_final: 0.8815 (mptt) REVERT: B 40 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8394 (mptt) REVERT: B 48 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8391 (p) outliers start: 34 outliers final: 16 residues processed: 212 average time/residue: 1.6644 time to fit residues: 371.3174 Evaluate side-chains 218 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 D residue 22 LYS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 45 VAL 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 4 LEU 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 C residue 367 LEU Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 81 VAL 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 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 49 optimal weight: 0.0370 chunk 72 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 98 optimal weight: 0.2980 chunk 71 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3317 r_free = 0.3317 target = 0.115395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.092650 restraints weight = 12033.429| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.75 r_work: 0.2862 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2904 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= 0.116 Angle : 0.634 6.387 13713 Z= 0.306 Chirality : 0.042 0.130 1662 Planarity : 0.004 0.037 1686 Dihedral : 5.722 84.103 1423 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.29 % Allowed : 17.10 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1299 helix: 1.31 (0.18), residues: 867 sheet: -0.24 (0.47), residues: 99 loop : -0.30 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 267 HIS 0.001 0.000 HIS B 102 PHE 0.012 0.001 PHE D 62 TYR 0.017 0.001 TYR E 344 ARG 0.002 0.000 ARG E 252 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 667) hydrogen bonds : angle 4.24233 ( 2100) SS BOND : bond 0.00111 ( 3) SS BOND : angle 0.03438 ( 6) covalent geometry : bond 0.00256 (10083) covalent geometry : angle 0.63455 (13707) *********************** 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 230 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7821 (pp20) cc_final: 0.7525 (pp20) REVERT: A 161 LYS cc_start: 0.7325 (mtmt) cc_final: 0.6818 (mmtm) REVERT: A 224 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8492 (tt) REVERT: D 40 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8472 (ttpt) REVERT: D 67 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: C 40 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: C 71 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7915 (tm) REVERT: C 133 GLU cc_start: 0.8556 (mp0) cc_final: 0.8226 (mp0) REVERT: C 161 LYS cc_start: 0.7398 (mtmt) cc_final: 0.7028 (mptt) REVERT: F 40 LYS cc_start: 0.8878 (ttmm) cc_final: 0.8495 (ttpt) REVERT: F 67 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: F 82 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8514 (tttp) REVERT: E 127 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7866 (pt0) REVERT: E 129 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8599 (mmtp) REVERT: E 133 GLU cc_start: 0.8562 (mp0) cc_final: 0.8135 (mp0) REVERT: E 161 LYS cc_start: 0.7427 (ttmt) cc_final: 0.7043 (tttm) REVERT: E 274 ARG cc_start: 0.7987 (mtt90) cc_final: 0.7560 (mmt180) REVERT: B 18 LYS cc_start: 0.9147 (tppt) cc_final: 0.8763 (mptt) REVERT: B 40 LYS cc_start: 0.8921 (ttmm) cc_final: 0.8256 (mptt) REVERT: B 48 SER cc_start: 0.8615 (p) cc_final: 0.8381 (p) outliers start: 34 outliers final: 9 residues processed: 212 average time/residue: 1.6649 time to fit residues: 372.2321 Evaluate side-chains 200 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 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 71 LEU 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 71 LEU Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 323 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 19 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 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 = 0.3296 r_free = 0.3296 target = 0.113691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.091330 restraints weight = 12118.119| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.65 r_work: 0.2868 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2973 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= 0.127 Angle : 0.641 6.443 13713 Z= 0.309 Chirality : 0.043 0.136 1662 Planarity : 0.004 0.036 1686 Dihedral : 5.198 40.544 1420 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.29 % Allowed : 17.87 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.24), residues: 1299 helix: 1.48 (0.18), residues: 867 sheet: -0.16 (0.47), residues: 99 loop : -0.16 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 267 HIS 0.001 0.000 HIS C 291 PHE 0.011 0.001 PHE D 62 TYR 0.015 0.001 TYR A 344 ARG 0.002 0.000 ARG D 78 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 667) hydrogen bonds : angle 4.23395 ( 2100) SS BOND : bond 0.00137 ( 3) SS BOND : angle 0.05821 ( 6) covalent geometry : bond 0.00289 (10083) covalent geometry : angle 0.64069 (13707) *********************** 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 226 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8628 (tp) REVERT: A 40 GLU cc_start: 0.7945 (pp20) cc_final: 0.7677 (pp20) REVERT: A 161 LYS cc_start: 0.7382 (mtmt) cc_final: 0.6929 (mmtp) REVERT: A 224 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8544 (tt) REVERT: A 227 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8567 (tmm) REVERT: A 259 MET cc_start: 0.9213 (mmp) cc_final: 0.8943 (mmm) REVERT: D 40 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8583 (ttpt) REVERT: D 67 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: C 40 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: C 71 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7944 (tm) REVERT: C 133 GLU cc_start: 0.8593 (mp0) cc_final: 0.8206 (mp0) REVERT: C 161 LYS cc_start: 0.7428 (mtmt) cc_final: 0.7083 (mptt) REVERT: F 40 LYS cc_start: 0.8872 (ttmm) cc_final: 0.8577 (ttpt) REVERT: F 67 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8275 (mt-10) REVERT: F 82 LYS cc_start: 0.8895 (ttpt) cc_final: 0.8573 (tttp) REVERT: E 129 LYS cc_start: 0.8821 (mmtm) cc_final: 0.8620 (mmtp) REVERT: E 133 GLU cc_start: 0.8581 (mp0) cc_final: 0.8107 (mp0) REVERT: E 274 ARG cc_start: 0.7976 (mtt90) cc_final: 0.7619 (mmt180) REVERT: B 18 LYS cc_start: 0.9170 (tppt) cc_final: 0.8801 (mptt) REVERT: B 40 LYS cc_start: 0.8961 (ttmm) cc_final: 0.8390 (mptt) REVERT: B 48 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8461 (p) outliers start: 34 outliers final: 12 residues processed: 212 average time/residue: 1.6039 time to fit residues: 359.5369 Evaluate side-chains 202 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 20 LEU 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 85 ASN Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 71 LEU 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 71 LEU Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 127 optimal weight: 0.0970 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 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 = 0.3297 r_free = 0.3297 target = 0.112675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.092293 restraints weight = 12627.170| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.55 r_work: 0.2870 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3036 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= 0.123 Angle : 0.637 7.040 13713 Z= 0.307 Chirality : 0.043 0.134 1662 Planarity : 0.004 0.036 1686 Dihedral : 5.148 40.471 1419 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.71 % Allowed : 18.94 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1299 helix: 1.59 (0.18), residues: 867 sheet: -0.16 (0.47), residues: 99 loop : -0.09 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 267 HIS 0.001 0.000 HIS C 291 PHE 0.013 0.001 PHE D 62 TYR 0.016 0.001 TYR E 344 ARG 0.004 0.000 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 667) hydrogen bonds : angle 4.19142 ( 2100) SS BOND : bond 0.00120 ( 3) SS BOND : angle 0.05742 ( 6) covalent geometry : bond 0.00279 (10083) covalent geometry : angle 0.63737 (13707) *********************** 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 218 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7863 (pp20) cc_final: 0.7585 (pp20) REVERT: A 161 LYS cc_start: 0.7388 (mtmt) cc_final: 0.6944 (mmtp) REVERT: A 224 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8557 (tt) REVERT: A 227 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8605 (tmm) REVERT: A 259 MET cc_start: 0.9195 (mmp) cc_final: 0.8930 (mmm) REVERT: D 18 LYS cc_start: 0.9162 (tppt) cc_final: 0.8804 (mptt) REVERT: D 40 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8574 (ttpt) REVERT: D 67 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8113 (mt-10) REVERT: C 40 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: C 71 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7923 (tm) REVERT: C 161 LYS cc_start: 0.7429 (mtmt) cc_final: 0.7100 (mptt) REVERT: F 40 LYS cc_start: 0.8841 (ttmm) cc_final: 0.8549 (ttpt) REVERT: F 67 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8297 (mt-10) REVERT: F 82 LYS cc_start: 0.8887 (ttpt) cc_final: 0.8573 (tttp) REVERT: E 129 LYS cc_start: 0.8841 (mmtm) cc_final: 0.8635 (mmtp) REVERT: E 274 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7646 (mmt180) REVERT: B 18 LYS cc_start: 0.9151 (tppt) cc_final: 0.8771 (mptt) REVERT: B 40 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8364 (mptt) REVERT: B 48 SER cc_start: 0.8689 (OUTLIER) cc_final: 0.8443 (p) outliers start: 28 outliers final: 11 residues processed: 204 average time/residue: 1.7380 time to fit residues: 373.6084 Evaluate side-chains 203 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU 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 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 71 LEU 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 71 LEU Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain B residue 48 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 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 = 0.3290 r_free = 0.3290 target = 0.112092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.091768 restraints weight = 12595.967| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.54 r_work: 0.2874 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3080 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= 0.129 Angle : 0.647 7.481 13713 Z= 0.311 Chirality : 0.043 0.135 1662 Planarity : 0.004 0.036 1686 Dihedral : 5.164 40.870 1419 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.71 % Allowed : 18.94 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.24), residues: 1299 helix: 1.67 (0.18), residues: 861 sheet: -0.18 (0.47), residues: 99 loop : -0.16 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 267 HIS 0.001 0.000 HIS C 291 PHE 0.013 0.001 PHE B 62 TYR 0.016 0.001 TYR A 344 ARG 0.003 0.000 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 667) hydrogen bonds : angle 4.19991 ( 2100) SS BOND : bond 0.00137 ( 3) SS BOND : angle 0.06385 ( 6) covalent geometry : bond 0.00294 (10083) covalent geometry : angle 0.64670 (13707) *********************** 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 219 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7881 (pp20) cc_final: 0.7610 (pp20) REVERT: A 161 LYS cc_start: 0.7428 (mtmt) cc_final: 0.7002 (mmtp) REVERT: A 224 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8571 (tt) REVERT: A 227 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8607 (tmm) REVERT: A 259 MET cc_start: 0.9187 (mmp) cc_final: 0.8918 (mmm) REVERT: D 18 LYS cc_start: 0.9170 (tppt) cc_final: 0.8813 (mptt) REVERT: D 40 LYS cc_start: 0.8911 (ttmm) cc_final: 0.8590 (ttpt) REVERT: D 67 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: C 40 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: C 71 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7941 (tm) REVERT: C 129 LYS cc_start: 0.9012 (mppt) cc_final: 0.8809 (mmtm) REVERT: C 161 LYS cc_start: 0.7427 (mtmt) cc_final: 0.7083 (mptt) REVERT: F 40 LYS cc_start: 0.8830 (ttmm) cc_final: 0.8541 (ttpt) REVERT: F 67 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: F 82 LYS cc_start: 0.8888 (ttpt) cc_final: 0.8586 (tttp) REVERT: E 40 GLU cc_start: 0.7839 (pp20) cc_final: 0.7565 (pt0) REVERT: E 129 LYS cc_start: 0.8807 (mmtm) cc_final: 0.8597 (mmtp) REVERT: E 274 ARG cc_start: 0.7952 (mtt90) cc_final: 0.7662 (mmt180) REVERT: B 18 LYS cc_start: 0.9156 (tppt) cc_final: 0.8777 (mptt) REVERT: B 40 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8381 (mptt) REVERT: B 48 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8441 (p) outliers start: 28 outliers final: 9 residues processed: 204 average time/residue: 1.8095 time to fit residues: 389.8380 Evaluate side-chains 203 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 71 LEU 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 E residue 323 SER Chi-restraints excluded: chain B residue 48 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 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 = 0.3257 r_free = 0.3257 target = 0.110043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.089633 restraints weight = 12565.725| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.55 r_work: 0.2835 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3008 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= 0.159 Angle : 0.690 8.274 13713 Z= 0.333 Chirality : 0.044 0.140 1662 Planarity : 0.005 0.035 1686 Dihedral : 5.347 43.407 1419 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.51 % Allowed : 19.42 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1299 helix: 1.61 (0.18), residues: 861 sheet: -0.17 (0.47), residues: 99 loop : -0.19 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 267 HIS 0.002 0.001 HIS C 291 PHE 0.013 0.001 PHE C 246 TYR 0.016 0.002 TYR A 140 ARG 0.004 0.000 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 667) hydrogen bonds : angle 4.33298 ( 2100) SS BOND : bond 0.00230 ( 3) SS BOND : angle 0.10596 ( 6) covalent geometry : bond 0.00381 (10083) covalent geometry : angle 0.69002 (13707) *********************** 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 218 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.8028 (pp20) cc_final: 0.7786 (pp20) REVERT: A 161 LYS cc_start: 0.7382 (mtmt) cc_final: 0.6970 (mmtp) REVERT: A 224 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8583 (tt) REVERT: A 227 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8642 (tmm) REVERT: A 259 MET cc_start: 0.9201 (mmp) cc_final: 0.8928 (mmm) REVERT: D 18 LYS cc_start: 0.9143 (tppt) cc_final: 0.8786 (mptt) REVERT: D 40 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8592 (ttpt) REVERT: D 67 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: C 40 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: C 71 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8057 (tm) REVERT: C 129 LYS cc_start: 0.9002 (mppt) cc_final: 0.8800 (mmtm) REVERT: C 161 LYS cc_start: 0.7419 (mtmt) cc_final: 0.7071 (mptt) REVERT: F 40 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8545 (ttpt) REVERT: F 67 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: F 82 LYS cc_start: 0.8896 (ttpt) cc_final: 0.8569 (tttp) REVERT: E 40 GLU cc_start: 0.7954 (pp20) cc_final: 0.7605 (pt0) REVERT: E 129 LYS cc_start: 0.8770 (mmtm) cc_final: 0.8563 (mmtp) REVERT: E 274 ARG cc_start: 0.7993 (mtt90) cc_final: 0.7672 (mmt180) REVERT: E 325 ASP cc_start: 0.6357 (OUTLIER) cc_final: 0.6131 (m-30) REVERT: B 18 LYS cc_start: 0.9140 (tppt) cc_final: 0.8752 (mptt) REVERT: B 40 LYS cc_start: 0.8902 (ttmm) cc_final: 0.8371 (mptt) REVERT: B 48 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8548 (p) outliers start: 26 outliers final: 12 residues processed: 204 average time/residue: 1.9465 time to fit residues: 417.3571 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 : 1.886 ------------------------------------------------------------------------------- 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 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 35 MET Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 71 LEU 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 E residue 323 SER Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain B residue 48 SER 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 67 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN C 156 ASN B 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.092295 restraints weight = 12506.090| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.47 r_work: 0.2874 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3113 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= 0.129 Angle : 0.661 10.376 13713 Z= 0.317 Chirality : 0.043 0.134 1662 Planarity : 0.004 0.036 1686 Dihedral : 5.217 41.079 1419 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.51 % Allowed : 19.13 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.24), residues: 1299 helix: 1.71 (0.18), residues: 858 sheet: -0.17 (0.47), residues: 99 loop : -0.17 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 267 HIS 0.001 0.000 HIS D 102 PHE 0.014 0.001 PHE D 62 TYR 0.016 0.001 TYR A 344 ARG 0.003 0.000 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 667) hydrogen bonds : angle 4.21414 ( 2100) SS BOND : bond 0.00131 ( 3) SS BOND : angle 0.06755 ( 6) covalent geometry : bond 0.00293 (10083) covalent geometry : angle 0.66100 (13707) ********************** 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 216 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7940 (pp20) cc_final: 0.7687 (pp20) REVERT: A 161 LYS cc_start: 0.7427 (mtmt) cc_final: 0.7015 (mmtp) REVERT: A 224 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8565 (tt) REVERT: A 227 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8591 (tmm) REVERT: A 259 MET cc_start: 0.9183 (mmp) cc_final: 0.8913 (mmm) REVERT: D 18 LYS cc_start: 0.9116 (tppt) cc_final: 0.8754 (mptt) REVERT: D 40 LYS cc_start: 0.8917 (ttmm) cc_final: 0.8591 (ttpt) REVERT: D 67 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: C 40 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7575 (tt0) REVERT: C 71 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7957 (tm) REVERT: C 161 LYS cc_start: 0.7394 (mtmt) cc_final: 0.7060 (mptt) REVERT: F 40 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8504 (ttpt) REVERT: F 67 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8254 (mt-10) REVERT: F 82 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8552 (tttp) REVERT: E 40 GLU cc_start: 0.7821 (pp20) cc_final: 0.7580 (pt0) REVERT: E 129 LYS cc_start: 0.8760 (mmtm) cc_final: 0.8551 (mmtp) REVERT: E 274 ARG cc_start: 0.7967 (mtt90) cc_final: 0.7651 (mmt180) REVERT: E 325 ASP cc_start: 0.6038 (OUTLIER) cc_final: 0.5794 (m-30) REVERT: B 18 LYS cc_start: 0.9116 (tppt) cc_final: 0.8727 (mptt) REVERT: B 40 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8333 (mptt) REVERT: B 48 SER cc_start: 0.8701 (p) cc_final: 0.8473 (p) outliers start: 26 outliers final: 12 residues processed: 203 average time/residue: 1.6290 time to fit residues: 348.5224 Evaluate side-chains 206 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 67 GLU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 71 LEU 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 E residue 323 SER Chi-restraints excluded: chain E residue 325 ASP 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 122 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN C 156 ASN B 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.092415 restraints weight = 12556.468| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.44 r_work: 0.2875 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3090 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= 0.138 Angle : 0.673 10.602 13713 Z= 0.323 Chirality : 0.044 0.138 1662 Planarity : 0.004 0.036 1686 Dihedral : 5.253 41.658 1419 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.22 % Allowed : 19.32 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.24), residues: 1299 helix: 1.72 (0.18), residues: 858 sheet: -0.13 (0.48), residues: 99 loop : -0.17 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 267 HIS 0.001 0.000 HIS D 102 PHE 0.014 0.001 PHE D 62 TYR 0.016 0.002 TYR A 344 ARG 0.003 0.000 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 667) hydrogen bonds : angle 4.23058 ( 2100) SS BOND : bond 0.00165 ( 3) SS BOND : angle 0.08977 ( 6) covalent geometry : bond 0.00320 (10083) covalent geometry : angle 0.67285 (13707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8876.57 seconds wall clock time: 158 minutes 46.50 seconds (9526.50 seconds total)