Starting phenix.real_space_refine on Fri Jun 20 17:04:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k04_36757/06_2025/8k04_36757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k04_36757/06_2025/8k04_36757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k04_36757/06_2025/8k04_36757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k04_36757/06_2025/8k04_36757.map" model { file = "/net/cci-nas-00/data/ceres_data/8k04_36757/06_2025/8k04_36757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k04_36757/06_2025/8k04_36757.cif" } resolution = 2.72 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 15400 2.51 5 N 4170 2.21 5 O 4440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 330 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24120 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2412 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 292} Chain: "B" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2412 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 292} Chain: "C" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2412 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 292} Chain: "D" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2412 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 292} Chain: "E" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2412 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 292} Chain: "F" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2412 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 292} Chain: "G" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2412 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 292} Chain: "H" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2412 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 292} Chain: "I" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2412 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 292} Chain: "J" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2412 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 292} Time building chain proxies: 15.29, per 1000 atoms: 0.63 Number of scatterers: 24120 At special positions: 0 Unit cell: (145.634, 139.401, 90.1005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 4440 8.00 N 4170 7.00 C 15400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 6.49 Conformation dependent library (CDL) restraints added in 3.2 seconds 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5740 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 20 sheets defined 51.6% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 20 through 42 Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 114 through 126 Proline residue: A 120 - end of helix Processing helix chain 'A' and resid 147 through 163 Processing helix chain 'A' and resid 190 through 199 removed outlier: 3.700A pdb=" N GLY A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.599A pdb=" N ASP A 203 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 204 " --> pdb=" O GLY A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 204' Processing helix chain 'A' and resid 205 through 226 Processing helix chain 'A' and resid 234 through 247 Processing helix chain 'A' and resid 249 through 256 removed outlier: 3.674A pdb=" N ALA A 255 " --> pdb=" O GLU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.612A pdb=" N HIS A 270 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 283 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'B' and resid 20 through 42 Processing helix chain 'B' and resid 76 through 79 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 114 through 126 Proline residue: B 120 - end of helix Processing helix chain 'B' and resid 147 through 163 Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.700A pdb=" N GLY B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.599A pdb=" N ASP B 203 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 204 " --> pdb=" O GLY B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 200 through 204' Processing helix chain 'B' and resid 205 through 226 Processing helix chain 'B' and resid 234 through 247 Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.674A pdb=" N ALA B 255 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.612A pdb=" N HIS B 270 " --> pdb=" O LYS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 283 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'C' and resid 20 through 42 Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 114 through 126 Proline residue: C 120 - end of helix Processing helix chain 'C' and resid 147 through 163 Processing helix chain 'C' and resid 190 through 199 removed outlier: 3.699A pdb=" N GLY C 199 " --> pdb=" O ASP C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.598A pdb=" N ASP C 203 " --> pdb=" O SER C 200 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 204 " --> pdb=" O GLY C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 200 through 204' Processing helix chain 'C' and resid 205 through 226 Processing helix chain 'C' and resid 234 through 247 Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.674A pdb=" N ALA C 255 " --> pdb=" O GLU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 266 Processing helix chain 'C' and resid 267 through 271 removed outlier: 3.612A pdb=" N HIS C 270 " --> pdb=" O LYS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 283 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'D' and resid 20 through 42 Processing helix chain 'D' and resid 76 through 79 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 114 through 126 Proline residue: D 120 - end of helix Processing helix chain 'D' and resid 147 through 163 Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.700A pdb=" N GLY D 199 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 3.599A pdb=" N ASP D 203 " --> pdb=" O SER D 200 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 204 " --> pdb=" O GLY D 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 200 through 204' Processing helix chain 'D' and resid 205 through 226 Processing helix chain 'D' and resid 234 through 247 Processing helix chain 'D' and resid 249 through 256 removed outlier: 3.673A pdb=" N ALA D 255 " --> pdb=" O GLU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 266 Processing helix chain 'D' and resid 267 through 271 removed outlier: 3.612A pdb=" N HIS D 270 " --> pdb=" O LYS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 283 Processing helix chain 'D' and resid 284 through 286 No H-bonds generated for 'chain 'D' and resid 284 through 286' Processing helix chain 'E' and resid 20 through 42 Processing helix chain 'E' and resid 76 through 79 Processing helix chain 'E' and resid 87 through 102 Processing helix chain 'E' and resid 114 through 126 Proline residue: E 120 - end of helix Processing helix chain 'E' and resid 147 through 163 Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.700A pdb=" N GLY E 199 " --> pdb=" O ASP E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 204 removed outlier: 3.599A pdb=" N ASP E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU E 204 " --> pdb=" O GLY E 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 200 through 204' Processing helix chain 'E' and resid 205 through 226 Processing helix chain 'E' and resid 234 through 247 Processing helix chain 'E' and resid 249 through 256 removed outlier: 3.673A pdb=" N ALA E 255 " --> pdb=" O GLU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 266 Processing helix chain 'E' and resid 267 through 271 removed outlier: 3.613A pdb=" N HIS E 270 " --> pdb=" O LYS E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 283 Processing helix chain 'E' and resid 284 through 286 No H-bonds generated for 'chain 'E' and resid 284 through 286' Processing helix chain 'F' and resid 20 through 42 Processing helix chain 'F' and resid 76 through 79 Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'F' and resid 114 through 126 Proline residue: F 120 - end of helix Processing helix chain 'F' and resid 147 through 163 Processing helix chain 'F' and resid 190 through 199 removed outlier: 3.700A pdb=" N GLY F 199 " --> pdb=" O ASP F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 204 removed outlier: 3.599A pdb=" N ASP F 203 " --> pdb=" O SER F 200 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU F 204 " --> pdb=" O GLY F 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 200 through 204' Processing helix chain 'F' and resid 205 through 226 Processing helix chain 'F' and resid 234 through 247 Processing helix chain 'F' and resid 249 through 256 removed outlier: 3.674A pdb=" N ALA F 255 " --> pdb=" O GLU F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 266 Processing helix chain 'F' and resid 267 through 271 removed outlier: 3.613A pdb=" N HIS F 270 " --> pdb=" O LYS F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 283 Processing helix chain 'F' and resid 284 through 286 No H-bonds generated for 'chain 'F' and resid 284 through 286' Processing helix chain 'G' and resid 20 through 42 Processing helix chain 'G' and resid 76 through 79 Processing helix chain 'G' and resid 87 through 102 Processing helix chain 'G' and resid 114 through 126 Proline residue: G 120 - end of helix Processing helix chain 'G' and resid 147 through 163 Processing helix chain 'G' and resid 190 through 199 removed outlier: 3.700A pdb=" N GLY G 199 " --> pdb=" O ASP G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.599A pdb=" N ASP G 203 " --> pdb=" O SER G 200 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU G 204 " --> pdb=" O GLY G 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 200 through 204' Processing helix chain 'G' and resid 205 through 226 Processing helix chain 'G' and resid 234 through 247 Processing helix chain 'G' and resid 249 through 256 removed outlier: 3.673A pdb=" N ALA G 255 " --> pdb=" O GLU G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 266 Processing helix chain 'G' and resid 267 through 271 removed outlier: 3.612A pdb=" N HIS G 270 " --> pdb=" O LYS G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 283 Processing helix chain 'G' and resid 284 through 286 No H-bonds generated for 'chain 'G' and resid 284 through 286' Processing helix chain 'H' and resid 20 through 42 Processing helix chain 'H' and resid 76 through 79 Processing helix chain 'H' and resid 87 through 102 Processing helix chain 'H' and resid 114 through 126 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 147 through 163 Processing helix chain 'H' and resid 190 through 199 removed outlier: 3.700A pdb=" N GLY H 199 " --> pdb=" O ASP H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 204 removed outlier: 3.598A pdb=" N ASP H 203 " --> pdb=" O SER H 200 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU H 204 " --> pdb=" O GLY H 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 200 through 204' Processing helix chain 'H' and resid 205 through 226 Processing helix chain 'H' and resid 234 through 247 Processing helix chain 'H' and resid 249 through 256 removed outlier: 3.673A pdb=" N ALA H 255 " --> pdb=" O GLU H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 266 Processing helix chain 'H' and resid 267 through 271 removed outlier: 3.612A pdb=" N HIS H 270 " --> pdb=" O LYS H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 272 through 283 Processing helix chain 'H' and resid 284 through 286 No H-bonds generated for 'chain 'H' and resid 284 through 286' Processing helix chain 'I' and resid 20 through 42 Processing helix chain 'I' and resid 76 through 79 Processing helix chain 'I' and resid 87 through 102 Processing helix chain 'I' and resid 114 through 126 Proline residue: I 120 - end of helix Processing helix chain 'I' and resid 147 through 163 Processing helix chain 'I' and resid 190 through 199 removed outlier: 3.700A pdb=" N GLY I 199 " --> pdb=" O ASP I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 204 removed outlier: 3.599A pdb=" N ASP I 203 " --> pdb=" O SER I 200 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU I 204 " --> pdb=" O GLY I 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 200 through 204' Processing helix chain 'I' and resid 205 through 226 Processing helix chain 'I' and resid 234 through 247 Processing helix chain 'I' and resid 249 through 256 removed outlier: 3.673A pdb=" N ALA I 255 " --> pdb=" O GLU I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 266 Processing helix chain 'I' and resid 267 through 271 removed outlier: 3.613A pdb=" N HIS I 270 " --> pdb=" O LYS I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 283 Processing helix chain 'I' and resid 284 through 286 No H-bonds generated for 'chain 'I' and resid 284 through 286' Processing helix chain 'J' and resid 20 through 42 Processing helix chain 'J' and resid 76 through 79 Processing helix chain 'J' and resid 87 through 102 Processing helix chain 'J' and resid 114 through 126 Proline residue: J 120 - end of helix Processing helix chain 'J' and resid 147 through 163 Processing helix chain 'J' and resid 190 through 199 removed outlier: 3.700A pdb=" N GLY J 199 " --> pdb=" O ASP J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 204 removed outlier: 3.599A pdb=" N ASP J 203 " --> pdb=" O SER J 200 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU J 204 " --> pdb=" O GLY J 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 200 through 204' Processing helix chain 'J' and resid 205 through 226 Processing helix chain 'J' and resid 234 through 247 Processing helix chain 'J' and resid 249 through 256 removed outlier: 3.674A pdb=" N ALA J 255 " --> pdb=" O GLU J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 266 Processing helix chain 'J' and resid 267 through 271 removed outlier: 3.613A pdb=" N HIS J 270 " --> pdb=" O LYS J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 283 Processing helix chain 'J' and resid 284 through 286 No H-bonds generated for 'chain 'J' and resid 284 through 286' Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 108 removed outlier: 6.784A pdb=" N PHE A 65 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N SER A 108 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 67 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL A 46 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL A 136 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU A 48 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE A 138 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA A 50 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 169 " --> pdb=" O HIS A 2 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA A 3 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER A 309 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY A 292 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG A 311 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER A 290 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 83 Processing sheet with id=AA3, first strand: chain 'B' and resid 106 through 108 removed outlier: 6.784A pdb=" N PHE B 65 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N SER B 108 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 67 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL B 46 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL B 136 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU B 48 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE B 138 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA B 50 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 169 " --> pdb=" O HIS B 2 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA B 3 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE B 305 " --> pdb=" O TYR B 295 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR B 295 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER B 307 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG B 293 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 83 Processing sheet with id=AA5, first strand: chain 'C' and resid 106 through 108 removed outlier: 6.783A pdb=" N PHE C 65 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N SER C 108 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 67 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL C 46 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL C 136 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU C 48 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE C 138 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA C 50 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 169 " --> pdb=" O HIS C 2 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA C 3 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE C 305 " --> pdb=" O TYR C 295 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR C 295 " --> pdb=" O PHE C 305 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER C 307 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG C 293 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 81 through 83 Processing sheet with id=AA7, first strand: chain 'D' and resid 106 through 108 removed outlier: 6.784A pdb=" N PHE D 65 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N SER D 108 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU D 67 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL D 46 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL D 136 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU D 48 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE D 138 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA D 50 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 169 " --> pdb=" O HIS D 2 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA D 3 " --> pdb=" O THR D 312 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE D 305 " --> pdb=" O TYR D 295 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR D 295 " --> pdb=" O PHE D 305 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER D 307 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG D 293 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 81 through 83 Processing sheet with id=AA9, first strand: chain 'E' and resid 106 through 108 removed outlier: 6.784A pdb=" N PHE E 65 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N SER E 108 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU E 67 " --> pdb=" O SER E 108 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL E 46 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL E 136 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU E 48 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE E 138 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA E 50 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 169 " --> pdb=" O HIS E 2 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA E 3 " --> pdb=" O THR E 312 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER E 309 " --> pdb=" O GLY E 292 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLY E 292 " --> pdb=" O SER E 309 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ARG E 311 " --> pdb=" O SER E 290 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER E 290 " --> pdb=" O ARG E 311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 81 through 83 Processing sheet with id=AB2, first strand: chain 'F' and resid 106 through 108 removed outlier: 6.783A pdb=" N PHE F 65 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N SER F 108 " --> pdb=" O PHE F 65 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU F 67 " --> pdb=" O SER F 108 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL F 46 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL F 136 " --> pdb=" O VAL F 46 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU F 48 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE F 138 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA F 50 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL F 169 " --> pdb=" O HIS F 2 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA F 3 " --> pdb=" O THR F 312 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE F 305 " --> pdb=" O TYR F 295 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR F 295 " --> pdb=" O PHE F 305 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N SER F 307 " --> pdb=" O ARG F 293 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG F 293 " --> pdb=" O SER F 307 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 81 through 83 Processing sheet with id=AB4, first strand: chain 'G' and resid 106 through 108 removed outlier: 6.784A pdb=" N PHE G 65 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N SER G 108 " --> pdb=" O PHE G 65 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU G 67 " --> pdb=" O SER G 108 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL G 46 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL G 136 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU G 48 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE G 138 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA G 50 " --> pdb=" O ILE G 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL G 169 " --> pdb=" O HIS G 2 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA G 3 " --> pdb=" O THR G 312 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE G 305 " --> pdb=" O TYR G 295 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR G 295 " --> pdb=" O PHE G 305 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER G 307 " --> pdb=" O ARG G 293 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG G 293 " --> pdb=" O SER G 307 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 81 through 83 Processing sheet with id=AB6, first strand: chain 'H' and resid 106 through 108 removed outlier: 6.784A pdb=" N PHE H 65 " --> pdb=" O ALA H 106 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N SER H 108 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU H 67 " --> pdb=" O SER H 108 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL H 46 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL H 136 " --> pdb=" O VAL H 46 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU H 48 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE H 138 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA H 50 " --> pdb=" O ILE H 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL H 169 " --> pdb=" O HIS H 2 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA H 3 " --> pdb=" O THR H 312 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE H 305 " --> pdb=" O TYR H 295 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR H 295 " --> pdb=" O PHE H 305 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER H 307 " --> pdb=" O ARG H 293 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG H 293 " --> pdb=" O SER H 307 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 81 through 83 Processing sheet with id=AB8, first strand: chain 'I' and resid 106 through 108 removed outlier: 6.784A pdb=" N PHE I 65 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N SER I 108 " --> pdb=" O PHE I 65 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU I 67 " --> pdb=" O SER I 108 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL I 46 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL I 136 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU I 48 " --> pdb=" O VAL I 136 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE I 138 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA I 50 " --> pdb=" O ILE I 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL I 169 " --> pdb=" O HIS I 2 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA I 3 " --> pdb=" O THR I 312 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER I 309 " --> pdb=" O GLY I 292 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY I 292 " --> pdb=" O SER I 309 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ARG I 311 " --> pdb=" O SER I 290 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER I 290 " --> pdb=" O ARG I 311 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 81 through 83 Processing sheet with id=AC1, first strand: chain 'J' and resid 106 through 108 removed outlier: 6.784A pdb=" N PHE J 65 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N SER J 108 " --> pdb=" O PHE J 65 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU J 67 " --> pdb=" O SER J 108 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL J 46 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL J 136 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU J 48 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE J 138 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA J 50 " --> pdb=" O ILE J 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL J 169 " --> pdb=" O HIS J 2 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA J 3 " --> pdb=" O THR J 312 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE J 305 " --> pdb=" O TYR J 295 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR J 295 " --> pdb=" O PHE J 305 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER J 307 " --> pdb=" O ARG J 293 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG J 293 " --> pdb=" O SER J 307 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 81 through 83 1300 hydrogen bonds defined for protein. 3690 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: 8.87 Time building geometry restraints manager: 7.65 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: 8110 1.34 - 1.46: 4637 1.46 - 1.57: 11813 1.57 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 24740 Sorted by residual: bond pdb=" CA HIS E 6 " pdb=" CB HIS E 6 " ideal model delta sigma weight residual 1.533 1.499 0.034 1.72e-02 3.38e+03 3.99e+00 bond pdb=" CA HIS I 6 " pdb=" CB HIS I 6 " ideal model delta sigma weight residual 1.533 1.499 0.034 1.72e-02 3.38e+03 3.95e+00 bond pdb=" CA HIS J 6 " pdb=" CB HIS J 6 " ideal model delta sigma weight residual 1.533 1.500 0.034 1.72e-02 3.38e+03 3.87e+00 bond pdb=" CA HIS H 6 " pdb=" CB HIS H 6 " ideal model delta sigma weight residual 1.533 1.500 0.034 1.72e-02 3.38e+03 3.86e+00 bond pdb=" CA HIS B 6 " pdb=" CB HIS B 6 " ideal model delta sigma weight residual 1.533 1.500 0.033 1.72e-02 3.38e+03 3.79e+00 ... (remaining 24735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 29852 1.11 - 2.22: 2956 2.22 - 3.33: 688 3.33 - 4.45: 104 4.45 - 5.56: 50 Bond angle restraints: 33650 Sorted by residual: angle pdb=" CA VAL E 131 " pdb=" C VAL E 131 " pdb=" N PRO E 132 " ideal model delta sigma weight residual 116.57 119.72 -3.15 9.80e-01 1.04e+00 1.03e+01 angle pdb=" CA VAL A 131 " pdb=" C VAL A 131 " pdb=" N PRO A 132 " ideal model delta sigma weight residual 116.57 119.71 -3.14 9.80e-01 1.04e+00 1.03e+01 angle pdb=" CA VAL G 131 " pdb=" C VAL G 131 " pdb=" N PRO G 132 " ideal model delta sigma weight residual 116.57 119.70 -3.13 9.80e-01 1.04e+00 1.02e+01 angle pdb=" CA VAL B 131 " pdb=" C VAL B 131 " pdb=" N PRO B 132 " ideal model delta sigma weight residual 116.57 119.70 -3.13 9.80e-01 1.04e+00 1.02e+01 angle pdb=" CA VAL F 131 " pdb=" C VAL F 131 " pdb=" N PRO F 132 " ideal model delta sigma weight residual 116.57 119.69 -3.12 9.80e-01 1.04e+00 1.01e+01 ... (remaining 33645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 13454 16.60 - 33.19: 1008 33.19 - 49.79: 138 49.79 - 66.39: 50 66.39 - 82.98: 40 Dihedral angle restraints: 14690 sinusoidal: 5750 harmonic: 8940 Sorted by residual: dihedral pdb=" CA GLU J 259 " pdb=" C GLU J 259 " pdb=" N GLU J 260 " pdb=" CA GLU J 260 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLU D 259 " pdb=" C GLU D 259 " pdb=" N GLU D 260 " pdb=" CA GLU D 260 " ideal model delta harmonic sigma weight residual 180.00 157.45 22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA GLU H 259 " pdb=" C GLU H 259 " pdb=" N GLU H 260 " pdb=" CA GLU H 260 " ideal model delta harmonic sigma weight residual 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 14687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1711 0.027 - 0.054: 1061 0.054 - 0.081: 565 0.081 - 0.107: 240 0.107 - 0.134: 103 Chirality restraints: 3680 Sorted by residual: chirality pdb=" CA GLU B 259 " pdb=" N GLU B 259 " pdb=" C GLU B 259 " pdb=" CB GLU B 259 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA GLU A 259 " pdb=" N GLU A 259 " pdb=" C GLU A 259 " pdb=" CB GLU A 259 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA GLU I 259 " pdb=" N GLU I 259 " pdb=" C GLU I 259 " pdb=" CB GLU I 259 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 3677 not shown) Planarity restraints: 4460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 131 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO D 132 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 132 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 132 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 131 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO F 132 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO F 132 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 132 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 131 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO H 132 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO H 132 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 132 " -0.025 5.00e-02 4.00e+02 ... (remaining 4457 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 633 2.67 - 3.23: 25085 3.23 - 3.79: 38581 3.79 - 4.34: 50063 4.34 - 4.90: 83484 Nonbonded interactions: 197846 Sorted by model distance: nonbonded pdb=" OE1 GLN A 240 " pdb=" OG1 THR E 164 " model vdw 2.118 3.040 nonbonded pdb=" OG1 THR B 164 " pdb=" OE1 GLN C 240 " model vdw 2.125 3.040 nonbonded pdb=" NE2 GLN D 180 " pdb=" O HIS D 231 " model vdw 2.179 3.120 nonbonded pdb=" NE2 GLN J 180 " pdb=" O HIS J 231 " model vdw 2.179 3.120 nonbonded pdb=" NE2 GLN A 180 " pdb=" O HIS A 231 " model vdw 2.179 3.120 ... (remaining 197841 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: 0.21 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 6.650 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: 0.040 Extract box with map and model: 1.120 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 56.810 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.160 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 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 : 0.011 0.058 24740 Z= 0.491 Angle : 0.776 5.558 33650 Z= 0.436 Chirality : 0.047 0.134 3680 Planarity : 0.005 0.044 4460 Dihedral : 12.967 82.985 8950 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3120 helix: 1.70 (0.14), residues: 1280 sheet: -0.89 (0.19), residues: 640 loop : -1.07 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 237 HIS 0.006 0.001 HIS A 2 PHE 0.010 0.002 PHE D 58 TYR 0.010 0.001 TYR E 109 ARG 0.004 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.14276 ( 1300) hydrogen bonds : angle 7.18000 ( 3690) covalent geometry : bond 0.01098 (24740) covalent geometry : angle 0.77572 (33650) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 2.871 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 2.0865 time to fit residues: 385.7749 Evaluate side-chains 147 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 0.9990 chunk 94 optimal weight: 0.0050 chunk 147 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 281 optimal weight: 5.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.101024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.060744 restraints weight = 60133.772| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 4.83 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24740 Z= 0.115 Angle : 0.554 5.172 33650 Z= 0.285 Chirality : 0.041 0.163 3680 Planarity : 0.004 0.044 4460 Dihedral : 4.588 16.844 3380 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.63 % Allowed : 5.00 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.91 (0.15), residues: 3120 helix: 2.59 (0.14), residues: 1300 sheet: -0.58 (0.20), residues: 640 loop : -1.00 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 237 HIS 0.003 0.001 HIS D 10 PHE 0.011 0.001 PHE J 161 TYR 0.010 0.001 TYR E 54 ARG 0.005 0.000 ARG C 160 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 1300) hydrogen bonds : angle 5.05544 ( 3690) covalent geometry : bond 0.00251 (24740) covalent geometry : angle 0.55448 (33650) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 2.437 Fit side-chains REVERT: A 231 HIS cc_start: 0.9044 (t-90) cc_final: 0.8774 (t-170) REVERT: C 130 LYS cc_start: 0.9262 (mmmm) cc_final: 0.9015 (mmmm) REVERT: C 153 MET cc_start: 0.9245 (mmp) cc_final: 0.9030 (mmm) REVERT: C 231 HIS cc_start: 0.9057 (t-90) cc_final: 0.8847 (t-170) REVERT: D 231 HIS cc_start: 0.9059 (t-90) cc_final: 0.8816 (t-170) REVERT: D 252 GLU cc_start: 0.8178 (mp0) cc_final: 0.7804 (mp0) REVERT: E 231 HIS cc_start: 0.9043 (t-90) cc_final: 0.8824 (t-170) REVERT: F 231 HIS cc_start: 0.9050 (t-90) cc_final: 0.8803 (t-170) REVERT: H 231 HIS cc_start: 0.9067 (t-90) cc_final: 0.8819 (t-170) REVERT: H 252 GLU cc_start: 0.8195 (mp0) cc_final: 0.7831 (mp0) REVERT: I 231 HIS cc_start: 0.9096 (t-90) cc_final: 0.8822 (t-170) REVERT: I 252 GLU cc_start: 0.8187 (mp0) cc_final: 0.7813 (mp0) REVERT: J 231 HIS cc_start: 0.9027 (t-90) cc_final: 0.8808 (t-170) REVERT: J 252 GLU cc_start: 0.8196 (mp0) cc_final: 0.7993 (mp0) outliers start: 16 outliers final: 0 residues processed: 169 average time/residue: 1.6770 time to fit residues: 321.1955 Evaluate side-chains 139 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 20 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 chunk 309 optimal weight: 20.0000 chunk 266 optimal weight: 50.0000 chunk 302 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.097695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.057472 restraints weight = 60289.762| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 4.71 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 24740 Z= 0.245 Angle : 0.579 5.310 33650 Z= 0.298 Chirality : 0.042 0.151 3680 Planarity : 0.004 0.046 4460 Dihedral : 4.543 15.277 3380 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.79 % Allowed : 7.94 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.01 (0.16), residues: 3120 helix: 2.69 (0.14), residues: 1300 sheet: -0.51 (0.20), residues: 640 loop : -0.96 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 237 HIS 0.003 0.001 HIS B 10 PHE 0.011 0.001 PHE G 58 TYR 0.007 0.001 TYR E 54 ARG 0.002 0.000 ARG H 152 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 1300) hydrogen bonds : angle 5.02225 ( 3690) covalent geometry : bond 0.00561 (24740) covalent geometry : angle 0.57903 (33650) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 2.536 Fit side-chains REVERT: A 130 LYS cc_start: 0.9226 (mmmm) cc_final: 0.9015 (mmmm) REVERT: A 231 HIS cc_start: 0.9061 (t-90) cc_final: 0.8838 (t-170) REVERT: A 252 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8580 (mp0) REVERT: C 130 LYS cc_start: 0.9347 (mmmm) cc_final: 0.9082 (mmmm) REVERT: D 231 HIS cc_start: 0.9071 (t-90) cc_final: 0.8867 (t-170) REVERT: E 231 HIS cc_start: 0.9059 (t-90) cc_final: 0.8847 (t-170) REVERT: F 130 LYS cc_start: 0.9233 (mmmm) cc_final: 0.9011 (mmmm) REVERT: F 252 GLU cc_start: 0.8294 (mp0) cc_final: 0.7928 (mp0) REVERT: H 231 HIS cc_start: 0.9072 (t-90) cc_final: 0.8862 (t-170) REVERT: H 252 GLU cc_start: 0.8336 (mp0) cc_final: 0.8078 (mp0) REVERT: J 231 HIS cc_start: 0.9057 (t-90) cc_final: 0.8843 (t-170) outliers start: 20 outliers final: 7 residues processed: 162 average time/residue: 1.7952 time to fit residues: 330.2636 Evaluate side-chains 138 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 250 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 153 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 276 optimal weight: 7.9990 chunk 262 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 268 optimal weight: 50.0000 chunk 42 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.099105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.058689 restraints weight = 60733.007| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 4.76 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24740 Z= 0.166 Angle : 0.547 5.422 33650 Z= 0.280 Chirality : 0.040 0.148 3680 Planarity : 0.004 0.046 4460 Dihedral : 4.378 14.598 3380 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.63 % Allowed : 8.77 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.25 (0.16), residues: 3120 helix: 2.81 (0.14), residues: 1300 sheet: -0.38 (0.21), residues: 640 loop : -0.75 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 237 HIS 0.003 0.001 HIS A 10 PHE 0.009 0.001 PHE C 161 TYR 0.007 0.001 TYR F 54 ARG 0.002 0.000 ARG F 152 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 1300) hydrogen bonds : angle 4.76590 ( 3690) covalent geometry : bond 0.00380 (24740) covalent geometry : angle 0.54684 (33650) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 2.642 Fit side-chains REVERT: A 231 HIS cc_start: 0.9098 (t-90) cc_final: 0.8815 (t-170) REVERT: B 252 GLU cc_start: 0.8412 (mp0) cc_final: 0.8193 (mp0) REVERT: C 130 LYS cc_start: 0.9356 (mmmm) cc_final: 0.9105 (mmmm) REVERT: D 231 HIS cc_start: 0.9116 (t-90) cc_final: 0.8880 (t-170) REVERT: E 231 HIS cc_start: 0.9100 (t-90) cc_final: 0.8855 (t-170) REVERT: E 252 GLU cc_start: 0.8550 (mp0) cc_final: 0.8173 (mp0) REVERT: F 231 HIS cc_start: 0.9101 (t-90) cc_final: 0.8830 (t-170) REVERT: G 252 GLU cc_start: 0.8408 (mp0) cc_final: 0.8187 (mp0) REVERT: H 153 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.9070 (mmm) REVERT: H 231 HIS cc_start: 0.9105 (t-90) cc_final: 0.8859 (t-170) REVERT: J 231 HIS cc_start: 0.9093 (t-90) cc_final: 0.8852 (t-170) REVERT: J 252 GLU cc_start: 0.8404 (mp0) cc_final: 0.8005 (mp0) outliers start: 41 outliers final: 15 residues processed: 197 average time/residue: 1.6936 time to fit residues: 378.6880 Evaluate side-chains 158 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain H residue 153 MET Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain J residue 38 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 213 optimal weight: 0.9980 chunk 250 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 206 optimal weight: 50.0000 chunk 222 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 304 optimal weight: 9.9990 chunk 232 optimal weight: 7.9990 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.099080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.058402 restraints weight = 60534.645| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 4.78 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 24740 Z= 0.157 Angle : 0.538 5.749 33650 Z= 0.274 Chirality : 0.040 0.146 3680 Planarity : 0.004 0.048 4460 Dihedral : 4.273 14.946 3380 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.63 % Allowed : 9.33 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.16), residues: 3120 helix: 2.91 (0.14), residues: 1300 sheet: -0.38 (0.21), residues: 640 loop : -0.67 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 237 HIS 0.003 0.001 HIS E 179 PHE 0.009 0.001 PHE I 58 TYR 0.006 0.001 TYR F 54 ARG 0.003 0.000 ARG C 160 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 1300) hydrogen bonds : angle 4.63000 ( 3690) covalent geometry : bond 0.00359 (24740) covalent geometry : angle 0.53830 (33650) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 2.533 Fit side-chains REVERT: A 231 HIS cc_start: 0.9037 (t-90) cc_final: 0.8784 (t-170) REVERT: C 130 LYS cc_start: 0.9369 (mmmm) cc_final: 0.9133 (mmmm) REVERT: C 231 HIS cc_start: 0.9087 (t-90) cc_final: 0.8868 (t-170) REVERT: D 231 HIS cc_start: 0.9055 (t-90) cc_final: 0.8846 (t-170) REVERT: D 252 GLU cc_start: 0.8604 (mp0) cc_final: 0.8247 (mp0) REVERT: E 231 HIS cc_start: 0.9075 (t-90) cc_final: 0.8862 (t-170) REVERT: E 252 GLU cc_start: 0.8516 (mp0) cc_final: 0.8058 (mp0) REVERT: F 231 HIS cc_start: 0.9055 (t-90) cc_final: 0.8849 (t-170) REVERT: H 231 HIS cc_start: 0.9066 (t-90) cc_final: 0.8856 (t-170) REVERT: I 252 GLU cc_start: 0.8601 (mp0) cc_final: 0.8242 (mp0) REVERT: J 231 HIS cc_start: 0.9053 (t-90) cc_final: 0.8842 (t-170) outliers start: 41 outliers final: 24 residues processed: 179 average time/residue: 1.3938 time to fit residues: 287.9978 Evaluate side-chains 170 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 250 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 185 optimal weight: 0.4980 chunk 124 optimal weight: 9.9990 chunk 250 optimal weight: 6.9990 chunk 176 optimal weight: 50.0000 chunk 307 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 291 optimal weight: 8.9990 overall best weight: 6.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.097195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.057076 restraints weight = 60464.016| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 4.71 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 24740 Z= 0.289 Angle : 0.611 5.980 33650 Z= 0.315 Chirality : 0.042 0.146 3680 Planarity : 0.005 0.052 4460 Dihedral : 4.423 16.375 3380 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.87 % Allowed : 9.52 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.27 (0.16), residues: 3120 helix: 2.90 (0.14), residues: 1300 sheet: -0.43 (0.20), residues: 640 loop : -0.78 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 237 HIS 0.003 0.001 HIS J 179 PHE 0.012 0.001 PHE D 58 TYR 0.009 0.001 TYR I 109 ARG 0.002 0.000 ARG F 152 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 1300) hydrogen bonds : angle 4.87127 ( 3690) covalent geometry : bond 0.00662 (24740) covalent geometry : angle 0.61123 (33650) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 2.731 Fit side-chains revert: symmetry clash REVERT: A 231 HIS cc_start: 0.9117 (t-90) cc_final: 0.8834 (t-170) REVERT: C 130 LYS cc_start: 0.9399 (mmmm) cc_final: 0.9171 (mmmm) REVERT: C 231 HIS cc_start: 0.9124 (t-90) cc_final: 0.8880 (t-170) REVERT: D 231 HIS cc_start: 0.9121 (t-90) cc_final: 0.8874 (t-170) REVERT: E 130 LYS cc_start: 0.9449 (mmmm) cc_final: 0.9215 (mmmm) REVERT: E 231 HIS cc_start: 0.9105 (t-90) cc_final: 0.8857 (t-170) REVERT: E 252 GLU cc_start: 0.8548 (mp0) cc_final: 0.8202 (mp0) REVERT: F 231 HIS cc_start: 0.9113 (t-90) cc_final: 0.8864 (t-170) REVERT: G 130 LYS cc_start: 0.9414 (mmmm) cc_final: 0.9164 (mmmm) REVERT: H 130 LYS cc_start: 0.9421 (mmmm) cc_final: 0.9170 (mmmm) REVERT: H 231 HIS cc_start: 0.9108 (t-90) cc_final: 0.8857 (t-170) REVERT: I 130 LYS cc_start: 0.9429 (mmmm) cc_final: 0.9191 (mmmm) REVERT: J 130 LYS cc_start: 0.9441 (mmmm) cc_final: 0.9204 (mmmm) REVERT: J 231 HIS cc_start: 0.9109 (t-90) cc_final: 0.8862 (t-170) outliers start: 47 outliers final: 24 residues processed: 177 average time/residue: 1.4920 time to fit residues: 301.8227 Evaluate side-chains 166 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 143 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 136 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 52 optimal weight: 50.0000 chunk 131 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 112 optimal weight: 40.0000 chunk 230 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 83 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.097329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.057283 restraints weight = 60736.575| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 4.70 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 24740 Z= 0.243 Angle : 0.588 6.334 33650 Z= 0.301 Chirality : 0.041 0.146 3680 Planarity : 0.005 0.048 4460 Dihedral : 4.373 15.910 3380 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.59 % Allowed : 10.56 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.33 (0.16), residues: 3120 helix: 2.92 (0.14), residues: 1300 sheet: -0.39 (0.21), residues: 640 loop : -0.72 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 237 HIS 0.003 0.001 HIS J 179 PHE 0.011 0.001 PHE D 58 TYR 0.008 0.001 TYR D 109 ARG 0.002 0.000 ARG J 152 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 1300) hydrogen bonds : angle 4.76742 ( 3690) covalent geometry : bond 0.00558 (24740) covalent geometry : angle 0.58775 (33650) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 2.968 Fit side-chains revert: symmetry clash REVERT: A 130 LYS cc_start: 0.9409 (mmmm) cc_final: 0.9185 (mmmm) REVERT: A 231 HIS cc_start: 0.9075 (t-90) cc_final: 0.8827 (t-170) REVERT: A 267 LYS cc_start: 0.9354 (ptpp) cc_final: 0.9140 (pmtt) REVERT: C 130 LYS cc_start: 0.9374 (mmmm) cc_final: 0.9166 (mmmm) REVERT: C 231 HIS cc_start: 0.9090 (t-90) cc_final: 0.8873 (t-170) REVERT: D 130 LYS cc_start: 0.9436 (mmmm) cc_final: 0.9207 (mmmm) REVERT: D 231 HIS cc_start: 0.9070 (t-90) cc_final: 0.8858 (t-170) REVERT: E 130 LYS cc_start: 0.9467 (mmmm) cc_final: 0.9242 (mmmm) REVERT: E 231 HIS cc_start: 0.9067 (t-90) cc_final: 0.8853 (t-170) REVERT: F 130 LYS cc_start: 0.9402 (mmmm) cc_final: 0.9168 (mmmm) REVERT: F 231 HIS cc_start: 0.9077 (t-90) cc_final: 0.8838 (t-170) REVERT: F 267 LYS cc_start: 0.9346 (ptpp) cc_final: 0.9142 (pmtt) REVERT: G 130 LYS cc_start: 0.9429 (mmmm) cc_final: 0.9181 (mmmm) REVERT: H 130 LYS cc_start: 0.9442 (mmmm) cc_final: 0.9194 (mmmm) REVERT: H 231 HIS cc_start: 0.9080 (t-90) cc_final: 0.8866 (t-170) REVERT: I 130 LYS cc_start: 0.9451 (mmmm) cc_final: 0.9227 (mmmm) REVERT: J 130 LYS cc_start: 0.9458 (mmmm) cc_final: 0.9229 (mmmm) REVERT: J 231 HIS cc_start: 0.9068 (t-90) cc_final: 0.8829 (t-170) outliers start: 40 outliers final: 23 residues processed: 176 average time/residue: 1.6910 time to fit residues: 342.5425 Evaluate side-chains 169 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 143 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 61 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 chunk 269 optimal weight: 50.0000 chunk 231 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 285 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 241 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.099105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.059102 restraints weight = 60119.839| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 4.71 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24740 Z= 0.131 Angle : 0.536 6.716 33650 Z= 0.274 Chirality : 0.039 0.146 3680 Planarity : 0.004 0.047 4460 Dihedral : 4.194 14.642 3380 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.47 % Allowed : 10.99 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.45 (0.16), residues: 3120 helix: 3.00 (0.14), residues: 1300 sheet: -0.31 (0.21), residues: 640 loop : -0.64 (0.20), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 237 HIS 0.003 0.001 HIS J 179 PHE 0.010 0.001 PHE C 161 TYR 0.007 0.001 TYR E 54 ARG 0.002 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 1300) hydrogen bonds : angle 4.53698 ( 3690) covalent geometry : bond 0.00299 (24740) covalent geometry : angle 0.53610 (33650) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 2.467 Fit side-chains REVERT: A 130 LYS cc_start: 0.9421 (mmmm) cc_final: 0.9209 (mmmm) REVERT: A 231 HIS cc_start: 0.9043 (t-90) cc_final: 0.8773 (t-170) REVERT: A 267 LYS cc_start: 0.9302 (ptpp) cc_final: 0.9098 (pmtt) REVERT: B 130 LYS cc_start: 0.9410 (mmmm) cc_final: 0.9156 (mmmm) REVERT: C 130 LYS cc_start: 0.9334 (mmmm) cc_final: 0.8813 (mppt) REVERT: C 231 HIS cc_start: 0.9096 (t-90) cc_final: 0.8849 (t-170) REVERT: D 130 LYS cc_start: 0.9443 (mmmm) cc_final: 0.9217 (mmmm) REVERT: D 231 HIS cc_start: 0.9069 (t-90) cc_final: 0.8827 (t-170) REVERT: E 130 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9253 (mmmm) REVERT: E 231 HIS cc_start: 0.9073 (t-90) cc_final: 0.8826 (t-170) REVERT: F 130 LYS cc_start: 0.9405 (mmmm) cc_final: 0.9171 (mmmm) REVERT: F 231 HIS cc_start: 0.9043 (t-90) cc_final: 0.8808 (t-170) REVERT: F 267 LYS cc_start: 0.9318 (ptpp) cc_final: 0.9104 (pmtt) REVERT: G 130 LYS cc_start: 0.9428 (mmmm) cc_final: 0.9183 (mmmm) REVERT: H 130 LYS cc_start: 0.9434 (mmmm) cc_final: 0.9198 (mmmm) REVERT: H 231 HIS cc_start: 0.9088 (t-90) cc_final: 0.8845 (t-170) REVERT: I 130 LYS cc_start: 0.9457 (mmmm) cc_final: 0.9245 (mmmm) REVERT: J 130 LYS cc_start: 0.9464 (mmmm) cc_final: 0.9242 (mmmm) REVERT: J 231 HIS cc_start: 0.9080 (t-90) cc_final: 0.8839 (t-170) outliers start: 37 outliers final: 20 residues processed: 189 average time/residue: 1.4738 time to fit residues: 319.5687 Evaluate side-chains 180 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 143 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 39 optimal weight: 5.9990 chunk 179 optimal weight: 0.9980 chunk 250 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 253 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 279 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.099100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.058995 restraints weight = 60581.476| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 4.72 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24740 Z= 0.136 Angle : 0.538 6.999 33650 Z= 0.272 Chirality : 0.039 0.146 3680 Planarity : 0.004 0.047 4460 Dihedral : 4.104 14.840 3380 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.11 % Allowed : 11.07 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.16), residues: 3120 helix: 3.03 (0.15), residues: 1300 sheet: -0.31 (0.21), residues: 640 loop : -0.65 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 237 HIS 0.004 0.001 HIS B 179 PHE 0.009 0.001 PHE H 161 TYR 0.006 0.001 TYR J 54 ARG 0.003 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 1300) hydrogen bonds : angle 4.47804 ( 3690) covalent geometry : bond 0.00316 (24740) covalent geometry : angle 0.53803 (33650) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 2.771 Fit side-chains REVERT: A 130 LYS cc_start: 0.9448 (mmmm) cc_final: 0.8856 (mppt) REVERT: A 231 HIS cc_start: 0.9022 (t-90) cc_final: 0.8781 (t-170) REVERT: A 252 GLU cc_start: 0.8548 (mp0) cc_final: 0.8335 (mp0) REVERT: A 267 LYS cc_start: 0.9313 (ptpp) cc_final: 0.9089 (pmtt) REVERT: B 130 LYS cc_start: 0.9437 (mmmm) cc_final: 0.9189 (mmmm) REVERT: C 130 LYS cc_start: 0.9290 (mmmm) cc_final: 0.8768 (mppt) REVERT: C 231 HIS cc_start: 0.9040 (t-90) cc_final: 0.8834 (t-170) REVERT: C 252 GLU cc_start: 0.8650 (mp0) cc_final: 0.8371 (mp0) REVERT: D 130 LYS cc_start: 0.9474 (mmmm) cc_final: 0.8815 (mppt) REVERT: D 231 HIS cc_start: 0.8990 (t-90) cc_final: 0.8749 (t-170) REVERT: E 130 LYS cc_start: 0.9477 (mmmm) cc_final: 0.9262 (mmmm) REVERT: E 231 HIS cc_start: 0.9039 (t-90) cc_final: 0.8828 (t-170) REVERT: F 130 LYS cc_start: 0.9432 (mmmm) cc_final: 0.9206 (mmmm) REVERT: F 231 HIS cc_start: 0.9010 (t-90) cc_final: 0.8773 (t-170) REVERT: F 267 LYS cc_start: 0.9314 (ptpp) cc_final: 0.9089 (pmtt) REVERT: G 130 LYS cc_start: 0.9437 (mmmm) cc_final: 0.9207 (mmmm) REVERT: H 130 LYS cc_start: 0.9436 (mmmm) cc_final: 0.9212 (mmmm) REVERT: H 231 HIS cc_start: 0.9039 (t-90) cc_final: 0.8808 (t-170) REVERT: I 130 LYS cc_start: 0.9466 (mmmm) cc_final: 0.9194 (mmmm) REVERT: J 130 LYS cc_start: 0.9475 (mmmm) cc_final: 0.9257 (mmmm) REVERT: J 231 HIS cc_start: 0.9027 (t-90) cc_final: 0.8796 (t-170) outliers start: 28 outliers final: 17 residues processed: 189 average time/residue: 1.4705 time to fit residues: 317.7386 Evaluate side-chains 189 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 38 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 114 optimal weight: 20.0000 chunk 168 optimal weight: 4.9990 chunk 84 optimal weight: 40.0000 chunk 79 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 chunk 52 optimal weight: 40.0000 chunk 41 optimal weight: 10.0000 chunk 208 optimal weight: 20.0000 chunk 300 optimal weight: 30.0000 chunk 86 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.095678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.055365 restraints weight = 61525.090| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 4.73 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.046 24740 Z= 0.428 Angle : 0.717 6.885 33650 Z= 0.369 Chirality : 0.045 0.141 3680 Planarity : 0.005 0.057 4460 Dihedral : 4.510 17.573 3380 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.83 % Allowed : 11.23 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.16 (0.16), residues: 3120 helix: 2.81 (0.14), residues: 1300 sheet: -0.45 (0.20), residues: 640 loop : -0.88 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 237 HIS 0.004 0.001 HIS H 179 PHE 0.015 0.002 PHE G 58 TYR 0.009 0.001 TYR D 109 ARG 0.004 0.000 ARG F 152 Details of bonding type rmsd hydrogen bonds : bond 0.05102 ( 1300) hydrogen bonds : angle 5.03546 ( 3690) covalent geometry : bond 0.00974 (24740) covalent geometry : angle 0.71675 (33650) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 3.714 Fit side-chains REVERT: A 130 LYS cc_start: 0.9478 (mmmm) cc_final: 0.9270 (mmmm) REVERT: A 231 HIS cc_start: 0.9084 (t-90) cc_final: 0.8799 (t-170) REVERT: A 267 LYS cc_start: 0.9397 (ptpp) cc_final: 0.9129 (pmtt) REVERT: B 130 LYS cc_start: 0.9461 (mmmm) cc_final: 0.9212 (mmmm) REVERT: C 130 LYS cc_start: 0.9379 (mmmm) cc_final: 0.9169 (mmmm) REVERT: C 231 HIS cc_start: 0.9105 (t-90) cc_final: 0.8852 (t-170) REVERT: D 130 LYS cc_start: 0.9493 (mmmm) cc_final: 0.9202 (mmmm) REVERT: D 231 HIS cc_start: 0.9110 (t-90) cc_final: 0.8852 (t-170) REVERT: E 130 LYS cc_start: 0.9497 (mmmm) cc_final: 0.9273 (mmmm) REVERT: E 231 HIS cc_start: 0.9112 (t-90) cc_final: 0.8846 (t-170) REVERT: F 130 LYS cc_start: 0.9463 (mmmm) cc_final: 0.9230 (mmmm) REVERT: F 231 HIS cc_start: 0.9080 (t-90) cc_final: 0.8824 (t-170) REVERT: F 267 LYS cc_start: 0.9401 (ptpp) cc_final: 0.9135 (pmtt) REVERT: G 130 LYS cc_start: 0.9466 (mmmm) cc_final: 0.9230 (mmmm) REVERT: H 130 LYS cc_start: 0.9468 (mmmm) cc_final: 0.9251 (mmmm) REVERT: H 231 HIS cc_start: 0.9114 (t-90) cc_final: 0.8853 (t-170) REVERT: I 130 LYS cc_start: 0.9503 (mmmm) cc_final: 0.9224 (mmmm) REVERT: J 130 LYS cc_start: 0.9495 (mmmm) cc_final: 0.9270 (mmmm) REVERT: J 231 HIS cc_start: 0.9124 (t-90) cc_final: 0.8860 (t-170) outliers start: 21 outliers final: 15 residues processed: 171 average time/residue: 2.1913 time to fit residues: 437.7414 Evaluate side-chains 164 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain I residue 143 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 280 optimal weight: 50.0000 chunk 283 optimal weight: 4.9990 chunk 269 optimal weight: 40.0000 chunk 139 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 114 optimal weight: 40.0000 chunk 279 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.098676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.058484 restraints weight = 60194.185| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 4.72 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24740 Z= 0.147 Angle : 0.560 6.887 33650 Z= 0.285 Chirality : 0.040 0.153 3680 Planarity : 0.004 0.048 4460 Dihedral : 4.262 15.190 3380 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.87 % Allowed : 11.35 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.16), residues: 3120 helix: 2.99 (0.15), residues: 1300 sheet: -0.37 (0.21), residues: 640 loop : -0.82 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 237 HIS 0.005 0.001 HIS H 179 PHE 0.011 0.001 PHE C 161 TYR 0.010 0.001 TYR J 54 ARG 0.001 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 1300) hydrogen bonds : angle 4.56929 ( 3690) covalent geometry : bond 0.00338 (24740) covalent geometry : angle 0.55964 (33650) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13989.75 seconds wall clock time: 245 minutes 53.55 seconds (14753.55 seconds total)