Starting phenix.real_space_refine on Mon Aug 25 00:09:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k04_36757/08_2025/8k04_36757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k04_36757/08_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_36757/08_2025/8k04_36757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k04_36757/08_2025/8k04_36757.map" model { file = "/net/cci-nas-00/data/ceres_data/8k04_36757/08_2025/8k04_36757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k04_36757/08_2025/8k04_36757.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.50, per 1000 atoms: 0.23 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: 2.28 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.07 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: 4.77 Time building geometry restraints manager: 2.89 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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: 5.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.260 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 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:8.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.270 ------------------------------------------------------------------------------- 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 : 10.56 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 196 TYR 0.010 0.001 TYR E 109 PHE 0.010 0.002 PHE D 58 TRP 0.017 0.002 TRP J 237 HIS 0.006 0.001 HIS A 2 Details of bonding type rmsd covalent geometry : bond 0.01098 (24740) covalent geometry : angle 0.77572 (33650) hydrogen bonds : bond 0.14276 ( 1300) hydrogen bonds : angle 7.18000 ( 3690) *********************** 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 : 0.789 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 1.0195 time to fit residues: 187.4210 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 : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 50.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.100006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.059814 restraints weight = 60439.233| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 4.75 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24740 Z= 0.110 Angle : 0.554 5.205 33650 Z= 0.285 Chirality : 0.040 0.165 3680 Planarity : 0.004 0.045 4460 Dihedral : 4.598 16.586 3380 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.63 % Allowed : 5.20 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.16), residues: 3120 helix: 2.59 (0.14), residues: 1300 sheet: -0.55 (0.20), residues: 640 loop : -0.97 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 160 TYR 0.011 0.001 TYR E 54 PHE 0.011 0.001 PHE J 161 TRP 0.016 0.001 TRP I 237 HIS 0.003 0.001 HIS D 10 Details of bonding type rmsd covalent geometry : bond 0.00234 (24740) covalent geometry : angle 0.55438 (33650) hydrogen bonds : bond 0.03743 ( 1300) hydrogen bonds : angle 5.09861 ( 3690) *********************** 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 183 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 1.036 Fit side-chains REVERT: A 231 HIS cc_start: 0.9043 (t-90) cc_final: 0.8766 (t-170) REVERT: C 130 LYS cc_start: 0.9286 (mmmm) cc_final: 0.9044 (mmmm) REVERT: C 153 MET cc_start: 0.9251 (mmp) cc_final: 0.9042 (mmm) REVERT: C 231 HIS cc_start: 0.9053 (t-90) cc_final: 0.8839 (t-170) REVERT: D 231 HIS cc_start: 0.9055 (t-90) cc_final: 0.8840 (t-170) REVERT: D 252 GLU cc_start: 0.8183 (mp0) cc_final: 0.7819 (mp0) REVERT: E 231 HIS cc_start: 0.9042 (t-90) cc_final: 0.8824 (t-170) REVERT: F 252 GLU cc_start: 0.8264 (mp0) cc_final: 0.7916 (mp0) REVERT: H 231 HIS cc_start: 0.9059 (t-90) cc_final: 0.8839 (t-170) REVERT: H 252 GLU cc_start: 0.8203 (mp0) cc_final: 0.7846 (mp0) REVERT: I 252 GLU cc_start: 0.8199 (mp0) cc_final: 0.7828 (mp0) REVERT: J 231 HIS cc_start: 0.9028 (t-90) cc_final: 0.8808 (t-170) REVERT: J 252 GLU cc_start: 0.8198 (mp0) cc_final: 0.7990 (mp0) outliers start: 16 outliers final: 1 residues processed: 171 average time/residue: 0.7776 time to fit residues: 151.1267 Evaluate side-chains 139 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 138 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.099034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.058340 restraints weight = 60630.538| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 4.78 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 24740 Z= 0.160 Angle : 0.528 5.219 33650 Z= 0.271 Chirality : 0.040 0.149 3680 Planarity : 0.004 0.046 4460 Dihedral : 4.425 15.090 3380 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.79 % Allowed : 7.70 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.16), residues: 3120 helix: 2.73 (0.14), residues: 1300 sheet: -0.41 (0.21), residues: 640 loop : -0.91 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 152 TYR 0.007 0.001 TYR E 54 PHE 0.008 0.001 PHE D 58 TRP 0.013 0.001 TRP H 237 HIS 0.003 0.001 HIS G 10 Details of bonding type rmsd covalent geometry : bond 0.00365 (24740) covalent geometry : angle 0.52846 (33650) hydrogen bonds : bond 0.03921 ( 1300) hydrogen bonds : angle 4.85996 ( 3690) *********************** 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 187 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.976 Fit side-chains REVERT: A 231 HIS cc_start: 0.9033 (t-90) cc_final: 0.8791 (t-170) REVERT: A 252 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8627 (mp0) REVERT: C 130 LYS cc_start: 0.9368 (mmmm) cc_final: 0.9102 (mmmm) REVERT: C 153 MET cc_start: 0.9289 (mmp) cc_final: 0.9069 (mmm) REVERT: D 231 HIS cc_start: 0.9051 (t-90) cc_final: 0.8835 (t-170) REVERT: F 130 LYS cc_start: 0.9224 (mmmm) cc_final: 0.8996 (mmmm) outliers start: 20 outliers final: 9 residues processed: 184 average time/residue: 0.7598 time to fit residues: 158.8543 Evaluate side-chains 144 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C 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 H residue 158 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain J residue 38 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 99 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 168 optimal weight: 0.0770 chunk 290 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 20 optimal weight: 50.0000 chunk 114 optimal weight: 50.0000 chunk 14 optimal weight: 1.9990 chunk 144 optimal weight: 50.0000 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.099156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.058447 restraints weight = 60716.455| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 4.79 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 24740 Z= 0.168 Angle : 0.546 5.397 33650 Z= 0.279 Chirality : 0.040 0.148 3680 Planarity : 0.004 0.046 4460 Dihedral : 4.332 14.421 3380 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.75 % Allowed : 7.98 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.16), residues: 3120 helix: 2.82 (0.14), residues: 1300 sheet: -0.36 (0.21), residues: 640 loop : -0.75 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 152 TYR 0.006 0.001 TYR A 54 PHE 0.009 0.001 PHE I 58 TRP 0.013 0.001 TRP I 237 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd covalent geometry : bond 0.00385 (24740) covalent geometry : angle 0.54589 (33650) hydrogen bonds : bond 0.03770 ( 1300) hydrogen bonds : angle 4.76881 ( 3690) *********************** 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 196 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 0.844 Fit side-chains REVERT: A 231 HIS cc_start: 0.9067 (t-90) cc_final: 0.8816 (t-170) REVERT: B 252 GLU cc_start: 0.8420 (mp0) cc_final: 0.8203 (mp0) REVERT: C 130 LYS cc_start: 0.9422 (mmmm) cc_final: 0.9174 (mmmm) REVERT: C 153 MET cc_start: 0.9292 (mmp) cc_final: 0.9059 (mmm) REVERT: D 231 HIS cc_start: 0.9095 (t-90) cc_final: 0.8864 (t-170) REVERT: E 252 GLU cc_start: 0.8376 (mp0) cc_final: 0.7990 (mp0) REVERT: H 252 GLU cc_start: 0.8424 (mp0) cc_final: 0.8054 (mp0) outliers start: 44 outliers final: 23 residues processed: 187 average time/residue: 0.7646 time to fit residues: 162.0213 Evaluate side-chains 161 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 158 ILE 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 158 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 250 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 45 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 143 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 232 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.099663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.058980 restraints weight = 60348.341| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 4.77 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24740 Z= 0.137 Angle : 0.525 5.701 33650 Z= 0.266 Chirality : 0.039 0.148 3680 Planarity : 0.004 0.047 4460 Dihedral : 4.211 14.763 3380 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.67 % Allowed : 8.25 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.16), residues: 3120 helix: 2.94 (0.14), residues: 1300 sheet: -0.35 (0.21), residues: 640 loop : -0.67 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 160 TYR 0.006 0.001 TYR A 54 PHE 0.008 0.001 PHE C 161 TRP 0.013 0.001 TRP C 237 HIS 0.003 0.001 HIS B 179 Details of bonding type rmsd covalent geometry : bond 0.00314 (24740) covalent geometry : angle 0.52479 (33650) hydrogen bonds : bond 0.03464 ( 1300) hydrogen bonds : angle 4.56872 ( 3690) *********************** 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 198 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 1.067 Fit side-chains REVERT: A 231 HIS cc_start: 0.9017 (t-90) cc_final: 0.8769 (t-170) REVERT: C 130 LYS cc_start: 0.9421 (mmmm) cc_final: 0.9199 (mmmm) REVERT: C 153 MET cc_start: 0.9275 (mmp) cc_final: 0.9048 (mmm) REVERT: C 231 HIS cc_start: 0.9072 (t-90) cc_final: 0.8859 (t-170) REVERT: D 231 HIS cc_start: 0.9021 (t-90) cc_final: 0.8815 (t-170) REVERT: D 252 GLU cc_start: 0.8618 (mp0) cc_final: 0.8271 (mp0) REVERT: E 252 GLU cc_start: 0.8418 (mp0) cc_final: 0.8072 (mp0) REVERT: G 153 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.9031 (mmm) REVERT: I 252 GLU cc_start: 0.8608 (mp0) cc_final: 0.8260 (mp0) outliers start: 42 outliers final: 25 residues processed: 181 average time/residue: 0.6601 time to fit residues: 137.3464 Evaluate side-chains 171 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 158 ILE 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 153 MET Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 250 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 186 optimal weight: 10.0000 chunk 114 optimal weight: 40.0000 chunk 44 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 296 optimal weight: 1.9990 chunk 251 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 191 optimal weight: 0.1980 chunk 219 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.098746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.058253 restraints weight = 60236.181| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 4.75 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24740 Z= 0.183 Angle : 0.548 6.100 33650 Z= 0.280 Chirality : 0.040 0.144 3680 Planarity : 0.004 0.051 4460 Dihedral : 4.230 14.922 3380 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.06 % Allowed : 8.33 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.16), residues: 3120 helix: 2.98 (0.14), residues: 1300 sheet: -0.36 (0.21), residues: 640 loop : -0.66 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 152 TYR 0.006 0.001 TYR F 109 PHE 0.010 0.001 PHE I 58 TRP 0.012 0.001 TRP I 237 HIS 0.003 0.001 HIS J 179 Details of bonding type rmsd covalent geometry : bond 0.00421 (24740) covalent geometry : angle 0.54752 (33650) hydrogen bonds : bond 0.03807 ( 1300) hydrogen bonds : angle 4.64004 ( 3690) *********************** 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 195 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 143 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 130 LYS cc_start: 0.9435 (mmmm) cc_final: 0.9199 (mmmm) REVERT: A 231 HIS cc_start: 0.9081 (t-90) cc_final: 0.8816 (t-170) REVERT: B 130 LYS cc_start: 0.9427 (mmmm) cc_final: 0.9179 (mmmm) REVERT: B 252 GLU cc_start: 0.8526 (mp0) cc_final: 0.8233 (mp0) REVERT: C 130 LYS cc_start: 0.9482 (mmmm) cc_final: 0.9268 (mmmm) REVERT: C 231 HIS cc_start: 0.9102 (t-90) cc_final: 0.8875 (t-170) REVERT: D 231 HIS cc_start: 0.9075 (t-90) cc_final: 0.8847 (t-170) REVERT: E 130 LYS cc_start: 0.9456 (mmmm) cc_final: 0.9223 (mmmm) REVERT: F 231 HIS cc_start: 0.9075 (t-90) cc_final: 0.8826 (t-170) REVERT: G 130 LYS cc_start: 0.9416 (mmmm) cc_final: 0.9171 (mmmm) REVERT: I 130 LYS cc_start: 0.9441 (mmmm) cc_final: 0.9201 (mmmm) REVERT: J 130 LYS cc_start: 0.9448 (mmmm) cc_final: 0.9208 (mmmm) REVERT: J 252 GLU cc_start: 0.8612 (mp0) cc_final: 0.8270 (mp0) outliers start: 52 outliers final: 26 residues processed: 181 average time/residue: 0.6567 time to fit residues: 135.8758 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 : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain 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 I residue 250 ILE 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 309 optimal weight: 10.0000 chunk 304 optimal weight: 0.4980 chunk 92 optimal weight: 0.4980 chunk 140 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 111 optimal weight: 50.0000 chunk 255 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 267 optimal weight: 50.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.099056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.059060 restraints weight = 60171.210| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 4.70 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24740 Z= 0.142 Angle : 0.529 6.493 33650 Z= 0.268 Chirality : 0.039 0.143 3680 Planarity : 0.004 0.045 4460 Dihedral : 4.140 15.088 3380 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.63 % Allowed : 9.76 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.16), residues: 3120 helix: 3.02 (0.14), residues: 1300 sheet: -0.33 (0.21), residues: 640 loop : -0.60 (0.20), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 160 TYR 0.006 0.001 TYR D 109 PHE 0.008 0.001 PHE F 161 TRP 0.013 0.001 TRP H 237 HIS 0.003 0.001 HIS F 179 Details of bonding type rmsd covalent geometry : bond 0.00327 (24740) covalent geometry : angle 0.52906 (33650) hydrogen bonds : bond 0.03453 ( 1300) hydrogen bonds : angle 4.50604 ( 3690) *********************** 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 198 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.884 Fit side-chains REVERT: A 130 LYS cc_start: 0.9469 (mmmm) cc_final: 0.9247 (mmmm) REVERT: A 231 HIS cc_start: 0.9020 (t-90) cc_final: 0.8764 (t-170) REVERT: B 130 LYS cc_start: 0.9453 (mmmm) cc_final: 0.9209 (mmmm) REVERT: C 130 LYS cc_start: 0.9474 (mmmm) cc_final: 0.9265 (mmmm) REVERT: C 252 GLU cc_start: 0.8355 (mp0) cc_final: 0.7977 (mp0) REVERT: D 130 LYS cc_start: 0.9458 (mmmm) cc_final: 0.9232 (mmmm) REVERT: E 130 LYS cc_start: 0.9463 (mmmm) cc_final: 0.9232 (mmmm) REVERT: E 252 GLU cc_start: 0.8651 (mp0) cc_final: 0.8307 (mp0) REVERT: F 130 LYS cc_start: 0.9432 (mmmm) cc_final: 0.9209 (mmmm) REVERT: F 231 HIS cc_start: 0.9022 (t-90) cc_final: 0.8803 (t-170) REVERT: G 130 LYS cc_start: 0.9449 (mmmm) cc_final: 0.9206 (mmmm) REVERT: H 130 LYS cc_start: 0.9439 (mmmm) cc_final: 0.9202 (mmmm) REVERT: I 130 LYS cc_start: 0.9463 (mmmm) cc_final: 0.9236 (mmmm) REVERT: J 130 LYS cc_start: 0.9453 (mmmm) cc_final: 0.9220 (mmmm) outliers start: 41 outliers final: 23 residues processed: 186 average time/residue: 0.6397 time to fit residues: 137.0132 Evaluate side-chains 175 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 133 VAL 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 38 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 143 THR 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 160 optimal weight: 0.0050 chunk 274 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 224 optimal weight: 20.0000 chunk 51 optimal weight: 40.0000 chunk 240 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 228 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.098591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.058861 restraints weight = 60102.750| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 4.63 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24740 Z= 0.165 Angle : 0.541 6.489 33650 Z= 0.277 Chirality : 0.040 0.144 3680 Planarity : 0.004 0.045 4460 Dihedral : 4.128 14.788 3380 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.63 % Allowed : 10.00 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.16), residues: 3120 helix: 3.02 (0.14), residues: 1300 sheet: -0.34 (0.21), residues: 640 loop : -0.62 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 249 TYR 0.006 0.001 TYR E 54 PHE 0.009 0.001 PHE J 58 TRP 0.013 0.001 TRP H 237 HIS 0.003 0.001 HIS F 179 Details of bonding type rmsd covalent geometry : bond 0.00380 (24740) covalent geometry : angle 0.54142 (33650) hydrogen bonds : bond 0.03652 ( 1300) hydrogen bonds : angle 4.55887 ( 3690) *********************** 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 192 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.966 Fit side-chains REVERT: A 130 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9249 (mmmm) REVERT: A 231 HIS cc_start: 0.9063 (t-90) cc_final: 0.8797 (t-170) REVERT: B 130 LYS cc_start: 0.9464 (mmmm) cc_final: 0.9222 (mmmm) REVERT: C 130 LYS cc_start: 0.9486 (mmmm) cc_final: 0.9278 (mmmm) REVERT: C 252 GLU cc_start: 0.8385 (mp0) cc_final: 0.8099 (mp0) REVERT: D 130 LYS cc_start: 0.9476 (mmmm) cc_final: 0.9248 (mmmm) REVERT: E 130 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9243 (mmmm) REVERT: F 130 LYS cc_start: 0.9442 (mmmm) cc_final: 0.9216 (mmmm) REVERT: F 231 HIS cc_start: 0.9047 (t-90) cc_final: 0.8808 (t-170) REVERT: G 130 LYS cc_start: 0.9464 (mmmm) cc_final: 0.9225 (mmmm) REVERT: H 130 LYS cc_start: 0.9446 (mmmm) cc_final: 0.8789 (mppt) REVERT: H 231 HIS cc_start: 0.9096 (t-90) cc_final: 0.8876 (t-170) REVERT: I 130 LYS cc_start: 0.9477 (mmmm) cc_final: 0.9261 (mmmm) REVERT: J 130 LYS cc_start: 0.9460 (mmmm) cc_final: 0.9230 (mmmm) outliers start: 41 outliers final: 20 residues processed: 181 average time/residue: 0.7095 time to fit residues: 146.4375 Evaluate side-chains 174 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain E residue 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 133 VAL 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 217 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 138 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 190 optimal weight: 0.0770 chunk 147 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 282 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.3742 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.100587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.060619 restraints weight = 60154.353| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 4.71 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2317 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= 0.102 Angle : 0.521 6.608 33650 Z= 0.262 Chirality : 0.038 0.148 3680 Planarity : 0.004 0.044 4460 Dihedral : 3.987 14.751 3380 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.03 % Allowed : 10.56 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.16), residues: 3120 helix: 3.05 (0.14), residues: 1300 sheet: -0.38 (0.21), residues: 640 loop : -0.54 (0.20), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 152 TYR 0.006 0.001 TYR E 54 PHE 0.010 0.001 PHE F 161 TRP 0.014 0.001 TRP J 237 HIS 0.004 0.001 HIS G 179 Details of bonding type rmsd covalent geometry : bond 0.00236 (24740) covalent geometry : angle 0.52093 (33650) hydrogen bonds : bond 0.02965 ( 1300) hydrogen bonds : angle 4.34390 ( 3690) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 231 HIS cc_start: 0.8963 (t-90) cc_final: 0.8722 (t-170) REVERT: B 130 LYS cc_start: 0.9481 (mmmm) cc_final: 0.9255 (mmmm) REVERT: C 231 HIS cc_start: 0.9061 (t-90) cc_final: 0.8840 (t-170) REVERT: C 252 GLU cc_start: 0.8407 (mp0) cc_final: 0.8093 (mp0) REVERT: D 130 LYS cc_start: 0.9488 (mmmm) cc_final: 0.9276 (mmmm) REVERT: E 130 LYS cc_start: 0.9495 (mmmm) cc_final: 0.9280 (mmmm) REVERT: F 130 LYS cc_start: 0.9480 (mmmm) cc_final: 0.8905 (mppt) REVERT: F 231 HIS cc_start: 0.8965 (t-90) cc_final: 0.8751 (t-170) REVERT: G 130 LYS cc_start: 0.9475 (mmmm) cc_final: 0.9248 (mmmm) REVERT: H 130 LYS cc_start: 0.9458 (mmmm) cc_final: 0.8822 (mppt) REVERT: I 130 LYS cc_start: 0.9486 (mmmm) cc_final: 0.9222 (mmmm) REVERT: J 130 LYS cc_start: 0.9481 (mmmm) cc_final: 0.9264 (mmmm) outliers start: 26 outliers final: 12 residues processed: 190 average time/residue: 0.6920 time to fit residues: 149.9371 Evaluate side-chains 179 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 99 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 250 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 115 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 270 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 265 optimal weight: 9.9990 chunk 287 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 230 optimal weight: 2.9990 chunk 208 optimal weight: 40.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 231 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.098269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.058012 restraints weight = 60590.681| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 4.72 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24740 Z= 0.212 Angle : 0.577 6.621 33650 Z= 0.296 Chirality : 0.040 0.145 3680 Planarity : 0.004 0.045 4460 Dihedral : 4.137 14.752 3380 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.67 % Allowed : 11.35 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.16), residues: 3120 helix: 3.07 (0.14), residues: 1300 sheet: -0.32 (0.21), residues: 640 loop : -0.62 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 152 TYR 0.006 0.001 TYR D 109 PHE 0.010 0.001 PHE B 58 TRP 0.012 0.001 TRP J 237 HIS 0.004 0.001 HIS F 179 Details of bonding type rmsd covalent geometry : bond 0.00488 (24740) covalent geometry : angle 0.57730 (33650) hydrogen bonds : bond 0.04008 ( 1300) hydrogen bonds : angle 4.60403 ( 3690) ********************** 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 172 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.976 Fit side-chains REVERT: A 231 HIS cc_start: 0.9023 (t-90) cc_final: 0.8778 (t-170) REVERT: B 130 LYS cc_start: 0.9512 (mmmm) cc_final: 0.9282 (mmmm) REVERT: C 231 HIS cc_start: 0.9054 (t-90) cc_final: 0.8848 (t-170) REVERT: D 130 LYS cc_start: 0.9524 (mmmm) cc_final: 0.8909 (mppt) REVERT: E 130 LYS cc_start: 0.9516 (mmmm) cc_final: 0.9297 (mmmm) REVERT: F 130 LYS cc_start: 0.9516 (mmmm) cc_final: 0.8891 (mppt) REVERT: F 231 HIS cc_start: 0.9020 (t-90) cc_final: 0.8807 (t-170) REVERT: G 130 LYS cc_start: 0.9509 (mmmm) cc_final: 0.9280 (mmmm) REVERT: G 252 GLU cc_start: 0.8665 (mp0) cc_final: 0.8385 (mp0) REVERT: H 130 LYS cc_start: 0.9484 (mmmm) cc_final: 0.8820 (mppt) REVERT: I 130 LYS cc_start: 0.9523 (mmmm) cc_final: 0.9260 (mmmm) REVERT: J 130 LYS cc_start: 0.9492 (mmmm) cc_final: 0.9273 (mmmm) outliers start: 17 outliers final: 10 residues processed: 169 average time/residue: 0.7233 time to fit residues: 138.4891 Evaluate side-chains 164 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 C residue 250 ILE 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 Chi-restraints excluded: chain J residue 250 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 259 optimal weight: 10.0000 chunk 220 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 chunk 291 optimal weight: 0.9980 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.099808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.059757 restraints weight = 59977.523| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 4.70 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24740 Z= 0.123 Angle : 0.531 6.789 33650 Z= 0.269 Chirality : 0.039 0.146 3680 Planarity : 0.004 0.045 4460 Dihedral : 4.034 14.705 3380 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.87 % Allowed : 11.23 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.16), residues: 3120 helix: 3.10 (0.14), residues: 1300 sheet: -0.35 (0.21), residues: 640 loop : -0.55 (0.20), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 152 TYR 0.008 0.001 TYR E 54 PHE 0.010 0.001 PHE C 161 TRP 0.013 0.001 TRP D 237 HIS 0.004 0.001 HIS G 179 Details of bonding type rmsd covalent geometry : bond 0.00286 (24740) covalent geometry : angle 0.53116 (33650) hydrogen bonds : bond 0.03183 ( 1300) hydrogen bonds : angle 4.37464 ( 3690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5887.75 seconds wall clock time: 101 minutes 38.63 seconds (6098.63 seconds total)