Starting phenix.real_space_refine on Fri May 23 07:54:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k04_36757/05_2025/8k04_36757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k04_36757/05_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_36757/05_2025/8k04_36757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k04_36757/05_2025/8k04_36757.map" model { file = "/net/cci-nas-00/data/ceres_data/8k04_36757/05_2025/8k04_36757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k04_36757/05_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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 14.90, per 1000 atoms: 0.62 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: 6.23 Conformation dependent library (CDL) restraints added in 3.1 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: 3.05 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: 8.04 Time building geometry restraints manager: 7.18 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: 0.22 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: 5.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.300 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 53.950 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.120 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:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.340 ------------------------------------------------------------------------------- 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 : 2.954 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 1.9578 time to fit residues: 362.2282 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 : 2.539 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.100926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.061348 restraints weight = 59908.614| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 4.75 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 : 2.638 Fit side-chains REVERT: A 231 HIS cc_start: 0.9042 (t-90) cc_final: 0.8773 (t-170) REVERT: C 130 LYS cc_start: 0.9279 (mmmm) cc_final: 0.9032 (mmmm) REVERT: C 153 MET cc_start: 0.9253 (mmp) cc_final: 0.9040 (mmm) REVERT: C 231 HIS cc_start: 0.9051 (t-90) cc_final: 0.8842 (t-170) REVERT: D 231 HIS cc_start: 0.9056 (t-90) cc_final: 0.8815 (t-170) REVERT: D 252 GLU cc_start: 0.8182 (mp0) cc_final: 0.7808 (mp0) REVERT: E 231 HIS cc_start: 0.9042 (t-90) cc_final: 0.8827 (t-170) REVERT: F 231 HIS cc_start: 0.9048 (t-90) cc_final: 0.8803 (t-170) REVERT: H 231 HIS cc_start: 0.9064 (t-90) cc_final: 0.8815 (t-170) REVERT: H 252 GLU cc_start: 0.8196 (mp0) cc_final: 0.7832 (mp0) REVERT: I 231 HIS cc_start: 0.9093 (t-90) cc_final: 0.8823 (t-170) REVERT: I 252 GLU cc_start: 0.8191 (mp0) cc_final: 0.7815 (mp0) REVERT: J 231 HIS cc_start: 0.9023 (t-90) cc_final: 0.8805 (t-170) REVERT: J 252 GLU cc_start: 0.8197 (mp0) cc_final: 0.7994 (mp0) outliers start: 16 outliers final: 0 residues processed: 169 average time/residue: 1.5285 time to fit residues: 294.3311 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 : 2.579 ------------------------------------------------------------------------------- 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: 9.9990 chunk 252 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 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: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.097997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.057526 restraints weight = 60353.369| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 4.73 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 24740 Z= 0.232 Angle : 0.569 5.279 33650 Z= 0.293 Chirality : 0.041 0.148 3680 Planarity : 0.004 0.046 4460 Dihedral : 4.515 14.970 3380 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.79 % Allowed : 7.78 % Favored : 91.43 % 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: 1.04 (0.16), residues: 3120 helix: 2.70 (0.14), residues: 1300 sheet: -0.51 (0.20), residues: 640 loop : -0.94 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 237 HIS 0.003 0.001 HIS A 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 0.04333 ( 1300) hydrogen bonds : angle 4.99134 ( 3690) covalent geometry : bond 0.00532 (24740) covalent geometry : angle 0.56877 (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 164 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 2.739 Fit side-chains REVERT: A 130 LYS cc_start: 0.9241 (mmmm) cc_final: 0.9028 (mmmm) REVERT: A 231 HIS cc_start: 0.9062 (t-90) cc_final: 0.8811 (t-170) REVERT: A 252 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8585 (mp0) REVERT: C 130 LYS cc_start: 0.9361 (mmmm) cc_final: 0.9098 (mmmm) REVERT: C 153 MET cc_start: 0.9298 (mmp) cc_final: 0.9064 (mmm) REVERT: E 231 HIS cc_start: 0.9066 (t-90) cc_final: 0.8858 (t-170) REVERT: F 130 LYS cc_start: 0.9255 (mmmm) cc_final: 0.9033 (mmmm) REVERT: F 252 GLU cc_start: 0.8291 (mp0) cc_final: 0.7938 (mp0) REVERT: H 231 HIS cc_start: 0.9075 (t-90) cc_final: 0.8873 (t-170) REVERT: J 231 HIS cc_start: 0.9053 (t-90) cc_final: 0.8848 (t-170) outliers start: 20 outliers final: 7 residues processed: 163 average time/residue: 1.5725 time to fit residues: 291.2695 Evaluate side-chains 139 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 2.563 ------------------------------------------------------------------------------- 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: 4.9990 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 276 optimal weight: 7.9990 chunk 262 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 268 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.099805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.059384 restraints weight = 60645.002| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 4.75 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24740 Z= 0.130 Angle : 0.531 5.264 33650 Z= 0.270 Chirality : 0.039 0.149 3680 Planarity : 0.004 0.045 4460 Dihedral : 4.328 14.374 3380 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.55 % Allowed : 8.69 % Favored : 89.76 % 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: 1.28 (0.16), residues: 3120 helix: 2.81 (0.14), residues: 1300 sheet: -0.36 (0.21), residues: 640 loop : -0.70 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 237 HIS 0.003 0.001 HIS A 10 PHE 0.009 0.001 PHE C 161 TYR 0.006 0.001 TYR F 54 ARG 0.002 0.000 ARG F 249 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 1300) hydrogen bonds : angle 4.69809 ( 3690) covalent geometry : bond 0.00297 (24740) covalent geometry : angle 0.53084 (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 211 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 2.671 Fit side-chains REVERT: A 231 HIS cc_start: 0.9078 (t-90) cc_final: 0.8804 (t-170) REVERT: B 252 GLU cc_start: 0.8381 (mp0) cc_final: 0.8174 (mp0) REVERT: C 130 LYS cc_start: 0.9350 (mmmm) cc_final: 0.9095 (mmmm) REVERT: C 153 MET cc_start: 0.9272 (mmp) cc_final: 0.9033 (mmm) REVERT: E 231 HIS cc_start: 0.9094 (t-90) cc_final: 0.8857 (t-170) REVERT: E 252 GLU cc_start: 0.8526 (mp0) cc_final: 0.8171 (mp0) REVERT: G 252 GLU cc_start: 0.8374 (mp0) cc_final: 0.8164 (mp0) REVERT: H 231 HIS cc_start: 0.9091 (t-90) cc_final: 0.8856 (t-170) REVERT: H 252 GLU cc_start: 0.8397 (mp0) cc_final: 0.8039 (mp0) REVERT: J 231 HIS cc_start: 0.9076 (t-90) cc_final: 0.8811 (t-170) REVERT: J 252 GLU cc_start: 0.8391 (mp0) cc_final: 0.8012 (mp0) outliers start: 39 outliers final: 14 residues processed: 201 average time/residue: 1.5145 time to fit residues: 345.7931 Evaluate side-chains 160 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 2.542 ------------------------------------------------------------------------------- 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 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 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: 8.9990 chunk 250 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 222 optimal weight: 0.2980 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 232 optimal weight: 0.8980 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.099759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.059975 restraints weight = 60083.877| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 4.65 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24740 Z= 0.126 Angle : 0.520 5.772 33650 Z= 0.264 Chirality : 0.039 0.147 3680 Planarity : 0.004 0.048 4460 Dihedral : 4.193 14.675 3380 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.43 % Allowed : 9.48 % Favored : 89.09 % 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: 1.40 (0.16), residues: 3120 helix: 2.92 (0.14), residues: 1300 sheet: -0.34 (0.21), residues: 640 loop : -0.63 (0.20), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 237 HIS 0.003 0.001 HIS B 179 PHE 0.009 0.001 PHE B 161 TYR 0.006 0.001 TYR A 54 ARG 0.002 0.000 ARG C 160 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 1300) hydrogen bonds : angle 4.55074 ( 3690) covalent geometry : bond 0.00289 (24740) covalent geometry : angle 0.51995 (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 196 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 2.783 Fit side-chains REVERT: A 231 HIS cc_start: 0.9010 (t-90) cc_final: 0.8781 (t-170) REVERT: B 153 MET cc_start: 0.9254 (mmp) cc_final: 0.9013 (mmm) REVERT: C 130 LYS cc_start: 0.9345 (mmmm) cc_final: 0.9106 (mmmm) REVERT: C 153 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.9038 (mmm) REVERT: C 231 HIS cc_start: 0.9074 (t-90) cc_final: 0.8835 (t-170) REVERT: D 252 GLU cc_start: 0.8615 (mp0) cc_final: 0.8269 (mp0) REVERT: E 231 HIS cc_start: 0.9029 (t-90) cc_final: 0.8824 (t-170) REVERT: E 252 GLU cc_start: 0.8499 (mp0) cc_final: 0.8055 (mp0) REVERT: I 252 GLU cc_start: 0.8612 (mp0) cc_final: 0.8268 (mp0) REVERT: J 231 HIS cc_start: 0.9031 (t-90) cc_final: 0.8827 (t-170) REVERT: J 252 GLU cc_start: 0.8476 (mp0) cc_final: 0.8122 (mp0) outliers start: 36 outliers final: 21 residues processed: 183 average time/residue: 1.3641 time to fit residues: 288.9954 Evaluate side-chains 172 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 2.568 ------------------------------------------------------------------------------- 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 153 MET 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 F residue 143 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 143 THR 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 I residue 250 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 143 THR 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: 9.9990 chunk 41 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 250 optimal weight: 3.9990 chunk 176 optimal weight: 20.0000 chunk 307 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.096541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.056243 restraints weight = 60685.166| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 4.70 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 24740 Z= 0.355 Angle : 0.654 6.021 33650 Z= 0.337 Chirality : 0.044 0.145 3680 Planarity : 0.005 0.052 4460 Dihedral : 4.509 17.421 3380 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.98 % Allowed : 9.09 % Favored : 88.93 % 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: 1.22 (0.16), residues: 3120 helix: 2.85 (0.14), residues: 1300 sheet: -0.41 (0.21), residues: 640 loop : -0.83 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 237 HIS 0.003 0.001 HIS A 6 PHE 0.014 0.002 PHE I 58 TYR 0.009 0.001 TYR D 109 ARG 0.002 0.000 ARG F 152 Details of bonding type rmsd hydrogen bonds : bond 0.04871 ( 1300) hydrogen bonds : angle 4.99630 ( 3690) covalent geometry : bond 0.00812 (24740) covalent geometry : angle 0.65417 (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 191 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 2.607 Fit side-chains revert: symmetry clash REVERT: A 231 HIS cc_start: 0.9119 (t-90) cc_final: 0.8863 (t-170) REVERT: C 130 LYS cc_start: 0.9410 (mmmm) cc_final: 0.9181 (mmmm) REVERT: C 153 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.9068 (mmm) REVERT: C 231 HIS cc_start: 0.9125 (t-90) cc_final: 0.8893 (t-170) REVERT: E 130 LYS cc_start: 0.9466 (mmmm) cc_final: 0.9238 (mmmm) REVERT: E 231 HIS cc_start: 0.9105 (t-90) cc_final: 0.8878 (t-170) REVERT: G 130 LYS cc_start: 0.9435 (mmmm) cc_final: 0.9185 (mmmm) REVERT: I 130 LYS cc_start: 0.9446 (mmmm) cc_final: 0.9208 (mmmm) REVERT: J 130 LYS cc_start: 0.9454 (mmmm) cc_final: 0.9218 (mmmm) REVERT: J 231 HIS cc_start: 0.9117 (t-90) cc_final: 0.8866 (t-170) outliers start: 50 outliers final: 25 residues processed: 178 average time/residue: 1.4961 time to fit residues: 303.8350 Evaluate side-chains 168 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 2.575 ------------------------------------------------------------------------------- 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 153 MET 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 133 VAL 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 I residue 250 ILE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 250 ILE 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: 8.9990 chunk 52 optimal weight: 50.0000 chunk 131 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 112 optimal weight: 30.0000 chunk 230 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 245 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 83 optimal weight: 50.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.097850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.058019 restraints weight = 60556.735| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 4.68 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 24740 Z= 0.202 Angle : 0.568 6.346 33650 Z= 0.291 Chirality : 0.040 0.145 3680 Planarity : 0.005 0.047 4460 Dihedral : 4.339 15.601 3380 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.75 % Allowed : 10.12 % Favored : 88.13 % 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: 1.38 (0.16), residues: 3120 helix: 2.97 (0.14), residues: 1300 sheet: -0.34 (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 I 179 PHE 0.010 0.001 PHE J 58 TYR 0.008 0.001 TYR E 54 ARG 0.002 0.000 ARG F 152 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 1300) hydrogen bonds : angle 4.68552 ( 3690) covalent geometry : bond 0.00463 (24740) covalent geometry : angle 0.56850 (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 193 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 2.818 Fit side-chains revert: symmetry clash REVERT: A 130 LYS cc_start: 0.9403 (mmmm) cc_final: 0.9174 (mmmm) REVERT: A 231 HIS cc_start: 0.9057 (t-90) cc_final: 0.8817 (t-170) REVERT: C 130 LYS cc_start: 0.9365 (mmmm) cc_final: 0.9156 (mmmm) REVERT: C 153 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.9071 (mmm) REVERT: C 231 HIS cc_start: 0.9070 (t-90) cc_final: 0.8853 (t-170) REVERT: D 130 LYS cc_start: 0.9440 (mmmm) cc_final: 0.9217 (mmmm) REVERT: E 130 LYS cc_start: 0.9466 (mmmm) cc_final: 0.9243 (mmmm) REVERT: E 231 HIS cc_start: 0.9058 (t-90) cc_final: 0.8853 (t-170) REVERT: F 130 LYS cc_start: 0.9387 (mmmm) cc_final: 0.9151 (mmmm) REVERT: G 130 LYS cc_start: 0.9425 (mmmm) cc_final: 0.9178 (mmmm) REVERT: H 130 LYS cc_start: 0.9439 (mmmm) cc_final: 0.9203 (mmmm) REVERT: I 130 LYS cc_start: 0.9434 (mmmm) cc_final: 0.9209 (mmmm) REVERT: J 130 LYS cc_start: 0.9464 (mmmm) cc_final: 0.9236 (mmmm) REVERT: J 231 HIS cc_start: 0.9059 (t-90) cc_final: 0.8828 (t-170) outliers start: 44 outliers final: 24 residues processed: 180 average time/residue: 1.4594 time to fit residues: 301.3724 Evaluate side-chains 174 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 2.637 ------------------------------------------------------------------------------- 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 C residue 133 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 153 MET 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 133 VAL 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 I residue 250 ILE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 250 ILE 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: 40.0000 chunk 231 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 225 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.100066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.059948 restraints weight = 60079.531| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 4.73 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24740 Z= 0.112 Angle : 0.530 6.860 33650 Z= 0.269 Chirality : 0.039 0.148 3680 Planarity : 0.004 0.046 4460 Dihedral : 4.113 14.686 3380 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.27 % Allowed : 10.79 % 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: 1.50 (0.16), residues: 3120 helix: 3.04 (0.15), residues: 1300 sheet: -0.28 (0.21), residues: 640 loop : -0.62 (0.20), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 237 HIS 0.003 0.001 HIS G 179 PHE 0.010 0.001 PHE C 161 TYR 0.005 0.001 TYR A 54 ARG 0.002 0.000 ARG C 160 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 1300) hydrogen bonds : angle 4.43837 ( 3690) covalent geometry : bond 0.00255 (24740) covalent geometry : angle 0.52966 (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 196 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 2.674 Fit side-chains REVERT: A 130 LYS cc_start: 0.9408 (mmmm) cc_final: 0.9188 (mmmm) REVERT: A 231 HIS cc_start: 0.9062 (t-90) cc_final: 0.8794 (t-170) REVERT: A 252 GLU cc_start: 0.8336 (mp0) cc_final: 0.7998 (mp0) REVERT: B 130 LYS cc_start: 0.9430 (mmmm) cc_final: 0.8757 (mppt) REVERT: C 130 LYS cc_start: 0.9314 (mmmm) cc_final: 0.8787 (mppt) REVERT: C 153 MET cc_start: 0.9273 (mmp) cc_final: 0.9035 (mmm) REVERT: C 231 HIS cc_start: 0.9068 (t-90) cc_final: 0.8827 (t-170) REVERT: C 252 GLU cc_start: 0.8528 (mp0) cc_final: 0.8299 (mp0) REVERT: D 130 LYS cc_start: 0.9452 (mmmm) cc_final: 0.9232 (mmmm) REVERT: D 231 HIS cc_start: 0.9003 (t-90) cc_final: 0.8789 (t-170) REVERT: E 130 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9257 (mmmm) REVERT: E 231 HIS cc_start: 0.9060 (t-90) cc_final: 0.8823 (t-170) REVERT: F 130 LYS cc_start: 0.9408 (mmmm) cc_final: 0.9172 (mmmm) REVERT: F 231 HIS cc_start: 0.9036 (t-90) cc_final: 0.8801 (t-170) REVERT: G 130 LYS cc_start: 0.9422 (mmmm) cc_final: 0.9183 (mmmm) REVERT: G 231 HIS cc_start: 0.9038 (t-90) cc_final: 0.8761 (t-170) REVERT: H 130 LYS cc_start: 0.9444 (mmmm) cc_final: 0.9206 (mmmm) REVERT: H 231 HIS cc_start: 0.9081 (t-90) cc_final: 0.8854 (t-170) REVERT: I 130 LYS cc_start: 0.9431 (mmmm) cc_final: 0.9220 (mmmm) REVERT: I 231 HIS cc_start: 0.9036 (t-90) cc_final: 0.8802 (t-170) REVERT: J 130 LYS cc_start: 0.9462 (mmmm) cc_final: 0.9241 (mmmm) REVERT: J 231 HIS cc_start: 0.9077 (t-90) cc_final: 0.8843 (t-170) outliers start: 32 outliers final: 18 residues processed: 189 average time/residue: 1.4418 time to fit residues: 313.0164 Evaluate side-chains 187 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 2.673 ------------------------------------------------------------------------------- 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 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 250 ILE Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 250 ILE 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 143 THR Chi-restraints excluded: chain J residue 250 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 39 optimal weight: 0.3980 chunk 179 optimal weight: 0.9990 chunk 250 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 253 optimal weight: 0.0670 chunk 261 optimal weight: 0.0050 chunk 106 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 279 optimal weight: 9.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.102038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.062198 restraints weight = 60187.685| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 4.71 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24740 Z= 0.093 Angle : 0.510 7.210 33650 Z= 0.255 Chirality : 0.038 0.149 3680 Planarity : 0.004 0.045 4460 Dihedral : 3.881 14.967 3380 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.99 % Allowed : 11.07 % 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: 1.50 (0.16), residues: 3120 helix: 3.01 (0.14), residues: 1310 sheet: -0.42 (0.21), residues: 640 loop : -0.53 (0.20), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 237 HIS 0.004 0.001 HIS G 179 PHE 0.010 0.001 PHE C 161 TYR 0.006 0.001 TYR F 54 ARG 0.002 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.02680 ( 1300) hydrogen bonds : angle 4.23779 ( 3690) covalent geometry : bond 0.00211 (24740) covalent geometry : angle 0.51047 (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 204 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 2.597 Fit side-chains REVERT: A 130 LYS cc_start: 0.9446 (mmmm) cc_final: 0.9228 (mmmm) REVERT: A 231 HIS cc_start: 0.8934 (t-90) cc_final: 0.8732 (t-170) REVERT: A 252 GLU cc_start: 0.8393 (mp0) cc_final: 0.8074 (mp0) REVERT: B 130 LYS cc_start: 0.9461 (mmmm) cc_final: 0.8792 (mppt) REVERT: B 153 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.9032 (mmm) REVERT: B 231 HIS cc_start: 0.8940 (t-90) cc_final: 0.8735 (t-170) REVERT: C 130 LYS cc_start: 0.9250 (mmmm) cc_final: 0.8744 (mppt) REVERT: C 252 GLU cc_start: 0.8529 (mp0) cc_final: 0.8284 (mp0) REVERT: D 130 LYS cc_start: 0.9484 (mmmm) cc_final: 0.9204 (mmmm) REVERT: E 130 LYS cc_start: 0.9452 (mmmm) cc_final: 0.9245 (mmmm) REVERT: F 130 LYS cc_start: 0.9448 (mmmm) cc_final: 0.9218 (mmmm) REVERT: G 130 LYS cc_start: 0.9460 (mmmm) cc_final: 0.8809 (mppt) REVERT: G 231 HIS cc_start: 0.8911 (t-90) cc_final: 0.8707 (t-170) REVERT: H 130 LYS cc_start: 0.9440 (mmmm) cc_final: 0.8803 (mppt) REVERT: I 130 LYS cc_start: 0.9459 (mmmm) cc_final: 0.8835 (mppt) REVERT: J 130 LYS cc_start: 0.9460 (mmmm) cc_final: 0.9245 (mmmm) outliers start: 25 outliers final: 10 residues processed: 198 average time/residue: 1.4323 time to fit residues: 323.8257 Evaluate side-chains 185 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain H residue 143 THR 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 114 optimal weight: 40.0000 chunk 168 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 chunk 52 optimal weight: 40.0000 chunk 41 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 300 optimal weight: 40.0000 chunk 86 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 231 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.097722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.057134 restraints weight = 60743.915| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 4.74 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 24740 Z= 0.268 Angle : 0.604 7.060 33650 Z= 0.310 Chirality : 0.041 0.143 3680 Planarity : 0.005 0.058 4460 Dihedral : 4.191 15.615 3380 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.63 % Allowed : 11.83 % 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: 1.48 (0.16), residues: 3120 helix: 3.08 (0.14), residues: 1300 sheet: -0.27 (0.21), residues: 640 loop : -0.72 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 237 HIS 0.004 0.001 HIS A 179 PHE 0.012 0.001 PHE F 58 TYR 0.007 0.001 TYR A 54 ARG 0.002 0.000 ARG C 152 Details of bonding type rmsd hydrogen bonds : bond 0.04352 ( 1300) hydrogen bonds : angle 4.69262 ( 3690) covalent geometry : bond 0.00616 (24740) covalent geometry : angle 0.60403 (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 173 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 2.799 Fit side-chains REVERT: A 130 LYS cc_start: 0.9498 (mmmm) cc_final: 0.9281 (mmmm) REVERT: A 231 HIS cc_start: 0.9029 (t-90) cc_final: 0.8803 (t-170) REVERT: B 130 LYS cc_start: 0.9506 (mmmm) cc_final: 0.9264 (mmmm) REVERT: C 252 GLU cc_start: 0.8574 (mp0) cc_final: 0.8307 (mp0) REVERT: D 130 LYS cc_start: 0.9528 (mmmm) cc_final: 0.9254 (mmmm) REVERT: E 130 LYS cc_start: 0.9516 (mmmm) cc_final: 0.9302 (mmmm) REVERT: F 130 LYS cc_start: 0.9496 (mmmm) cc_final: 0.9265 (mmmm) REVERT: G 130 LYS cc_start: 0.9507 (mmmm) cc_final: 0.9278 (mmmm) REVERT: H 130 LYS cc_start: 0.9512 (mmmm) cc_final: 0.9274 (mmmm) REVERT: I 130 LYS cc_start: 0.9513 (mmmm) cc_final: 0.9243 (mmmm) REVERT: J 130 LYS cc_start: 0.9513 (mmmm) cc_final: 0.9291 (mmmm) outliers start: 16 outliers final: 8 residues processed: 170 average time/residue: 1.6724 time to fit residues: 319.9946 Evaluate side-chains 162 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain H residue 143 THR 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: 0.0980 chunk 269 optimal weight: 40.0000 chunk 139 optimal weight: 1.9990 chunk 221 optimal weight: 0.0000 chunk 114 optimal weight: 40.0000 chunk 279 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 274 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 291 optimal weight: 0.7980 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.100181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.060167 restraints weight = 59824.745| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 4.68 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24740 Z= 0.104 Angle : 0.525 7.084 33650 Z= 0.265 Chirality : 0.038 0.146 3680 Planarity : 0.004 0.048 4460 Dihedral : 4.025 14.515 3380 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.75 % Allowed : 11.90 % Favored : 87.34 % 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: 1.54 (0.16), residues: 3120 helix: 3.09 (0.14), residues: 1300 sheet: -0.31 (0.21), residues: 640 loop : -0.58 (0.20), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 237 HIS 0.005 0.001 HIS A 179 PHE 0.012 0.001 PHE C 161 TYR 0.009 0.001 TYR J 54 ARG 0.002 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 1300) hydrogen bonds : angle 4.35326 ( 3690) covalent geometry : bond 0.00241 (24740) covalent geometry : angle 0.52459 (33650) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12533.73 seconds wall clock time: 218 minutes 8.38 seconds (13088.38 seconds total)