Starting phenix.real_space_refine on Tue Aug 26 21:14:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sr2_40718/08_2025/8sr2_40718_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sr2_40718/08_2025/8sr2_40718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sr2_40718/08_2025/8sr2_40718_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sr2_40718/08_2025/8sr2_40718_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sr2_40718/08_2025/8sr2_40718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sr2_40718/08_2025/8sr2_40718.map" } resolution = 2.36 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19403 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians Cu 12 5.60 5 P 36 5.49 5 S 93 5.16 5 Cl 3 4.86 5 C 15030 2.51 5 N 3417 2.21 5 O 4294 1.98 5 H 76 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s 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: 22961 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "B" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "E" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3036 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "I" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "J" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1976 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "G" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 2029 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "K" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 158 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 359 Unusual residues: {' CL': 1, ' CU': 2, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 5} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 158 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "G" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 359 Unusual residues: {' CL': 1, ' CU': 2, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 5} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "K" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 317 Unusual residues: {' CL': 1, ' CU': 2, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "I" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "K" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 4.54, per 1000 atoms: 0.20 Number of scatterers: 22961 At special positions: 0 Unit cell: (106.92, 107.455, 120.285, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cu 12 28.99 Cl 3 17.00 S 93 16.00 P 36 15.00 O 4294 8.00 N 3417 7.00 C 15030 6.00 H 76 1.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 853.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 19 sheets defined 50.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 184 through 208 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 231 through 257 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 10 through 43 Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.792A pdb=" N TRP B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 55 Processing helix chain 'B' and resid 58 through 69 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 69 through 84 removed outlier: 3.897A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 107 Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 124 through 137 removed outlier: 3.501A pdb=" N LEU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 165 removed outlier: 3.934A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Proline residue: B 158 - end of helix Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 180 through 188 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 211 through 239 removed outlier: 3.818A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 72 removed outlier: 3.772A pdb=" N PHE C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 89 Processing helix chain 'C' and resid 89 through 114 Processing helix chain 'C' and resid 123 through 150 Processing helix chain 'C' and resid 150 through 160 removed outlier: 3.509A pdb=" N TRP C 159 " --> pdb=" O GLN C 155 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 198 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 220 Processing helix chain 'C' and resid 223 through 233 removed outlier: 3.600A pdb=" N ASN C 227 " --> pdb=" O ASN C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 254 removed outlier: 3.807A pdb=" N LEU C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 208 Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 231 through 257 Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'I' and resid 39 through 45 Processing helix chain 'I' and resid 162 through 166 Processing helix chain 'I' and resid 184 through 208 Processing helix chain 'I' and resid 212 through 221 Processing helix chain 'I' and resid 231 through 257 Processing helix chain 'I' and resid 337 through 339 No H-bonds generated for 'chain 'I' and resid 337 through 339' Processing helix chain 'I' and resid 369 through 374 Processing helix chain 'J' and resid 10 through 43 Processing helix chain 'J' and resid 45 through 51 removed outlier: 3.792A pdb=" N TRP J 51 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 55 Processing helix chain 'J' and resid 58 through 69 Proline residue: J 65 - end of helix Processing helix chain 'J' and resid 69 through 84 removed outlier: 3.898A pdb=" N GLU J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 107 Processing helix chain 'J' and resid 115 through 120 Processing helix chain 'J' and resid 124 through 137 removed outlier: 3.501A pdb=" N LEU J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 165 removed outlier: 3.934A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET J 150 " --> pdb=" O ILE J 146 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) Proline residue: J 158 - end of helix Proline residue: J 162 - end of helix Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 180 through 188 Processing helix chain 'J' and resid 194 through 198 Processing helix chain 'J' and resid 211 through 239 removed outlier: 3.818A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 43 Processing helix chain 'F' and resid 45 through 51 removed outlier: 3.792A pdb=" N TRP F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 55 Processing helix chain 'F' and resid 58 through 69 Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 69 through 84 removed outlier: 3.897A pdb=" N GLU F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 107 Processing helix chain 'F' and resid 115 through 120 Processing helix chain 'F' and resid 124 through 137 removed outlier: 3.501A pdb=" N LEU F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 165 removed outlier: 3.934A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET F 150 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Proline residue: F 162 - end of helix Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 180 through 188 Processing helix chain 'F' and resid 194 through 198 Processing helix chain 'F' and resid 211 through 239 removed outlier: 3.818A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 72 removed outlier: 3.772A pdb=" N PHE G 53 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 89 Processing helix chain 'G' and resid 89 through 114 Processing helix chain 'G' and resid 123 through 150 Processing helix chain 'G' and resid 150 through 160 removed outlier: 3.509A pdb=" N TRP G 159 " --> pdb=" O GLN G 155 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS G 160 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 198 Processing helix chain 'G' and resid 207 through 216 Processing helix chain 'G' and resid 217 through 220 Processing helix chain 'G' and resid 223 through 233 removed outlier: 3.600A pdb=" N ASN G 227 " --> pdb=" O ASN G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 254 removed outlier: 3.808A pdb=" N LEU G 254 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 270 Processing helix chain 'K' and resid 49 through 72 removed outlier: 3.772A pdb=" N PHE K 53 " --> pdb=" O LYS K 49 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 89 Processing helix chain 'K' and resid 89 through 114 Processing helix chain 'K' and resid 123 through 150 Processing helix chain 'K' and resid 150 through 160 removed outlier: 3.509A pdb=" N TRP K 159 " --> pdb=" O GLN K 155 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS K 160 " --> pdb=" O ASP K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 198 Processing helix chain 'K' and resid 208 through 216 Processing helix chain 'K' and resid 217 through 220 Processing helix chain 'K' and resid 223 through 233 removed outlier: 3.600A pdb=" N ASN K 227 " --> pdb=" O ASN K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 254 removed outlier: 3.808A pdb=" N LEU K 254 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 270 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54 removed outlier: 4.302A pdb=" N LEU A 52 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS A 68 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TRP A 54 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU A 66 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A 108 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 342 removed outlier: 6.402A pdb=" N ARG A 323 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU A 314 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE A 394 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N SER A 283 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ASP A 406 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LYS A 285 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLU A 287 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 9.734A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N SER A 412 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYR A 291 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N THR A 305 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL A 286 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR A 303 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP A 288 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A 292 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA A 297 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 170 through 173 Processing sheet with id=AA7, first strand: chain 'E' and resid 47 through 54 removed outlier: 4.301A pdb=" N LEU E 52 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS E 68 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TRP E 54 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU E 66 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN E 108 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 58 through 60 Processing sheet with id=AA9, first strand: chain 'E' and resid 87 through 89 Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AB2, first strand: chain 'E' and resid 341 through 342 removed outlier: 6.403A pdb=" N ARG E 323 " --> pdb=" O ALA E 342 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU E 314 " --> pdb=" O PHE E 394 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE E 394 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N SER E 283 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N ASP E 406 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N LYS E 285 " --> pdb=" O ASP E 406 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLU E 287 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 9.734A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL E 284 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N THR E 305 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL E 286 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR E 303 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP E 288 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG E 292 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ALA E 297 " --> pdb=" O ARG E 292 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 47 through 54 removed outlier: 4.301A pdb=" N LEU I 52 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TRP I 54 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU I 66 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN I 108 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 58 through 60 Processing sheet with id=AB5, first strand: chain 'I' and resid 87 through 89 Processing sheet with id=AB6, first strand: chain 'I' and resid 169 through 171 Processing sheet with id=AB7, first strand: chain 'I' and resid 341 through 342 removed outlier: 6.402A pdb=" N ARG I 323 " --> pdb=" O ALA I 342 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU I 314 " --> pdb=" O PHE I 394 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE I 394 " --> pdb=" O LEU I 314 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N SER I 283 " --> pdb=" O GLN I 404 " (cutoff:3.500A) removed outlier: 11.282A pdb=" N ASP I 406 " --> pdb=" O SER I 283 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LYS I 285 " --> pdb=" O ASP I 406 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLU I 287 " --> pdb=" O PRO I 408 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N SER I 412 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TYR I 291 " --> pdb=" O SER I 412 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR I 305 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL I 286 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR I 303 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP I 288 " --> pdb=" O LYS I 301 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG I 292 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA I 297 " --> pdb=" O ARG I 292 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 170 through 173 Processing sheet with id=AB9, first strand: chain 'J' and resid 243 through 244 Processing sheet with id=AC1, first strand: chain 'F' and resid 170 through 173 1063 hydrogen bonds defined for protein. 3105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.15: 76 1.15 - 1.46: 12678 1.46 - 1.78: 10265 1.78 - 2.09: 180 2.09 - 2.40: 3 Bond restraints: 23202 Sorted by residual: bond pdb=" C ILE K 220 " pdb=" N LEU K 221 " ideal model delta sigma weight residual 1.331 2.400 -1.069 2.07e-02 2.33e+03 2.67e+03 bond pdb=" C ILE C 220 " pdb=" N LEU C 221 " ideal model delta sigma weight residual 1.331 2.400 -1.069 2.07e-02 2.33e+03 2.67e+03 bond pdb=" C ILE G 220 " pdb=" N LEU G 221 " ideal model delta sigma weight residual 1.331 2.399 -1.068 2.07e-02 2.33e+03 2.66e+03 bond pdb=" C LEU K 221 " pdb=" N PRO K 222 " ideal model delta sigma weight residual 1.334 1.703 -0.369 2.34e-02 1.83e+03 2.49e+02 bond pdb=" C LEU C 221 " pdb=" N PRO C 222 " ideal model delta sigma weight residual 1.334 1.703 -0.369 2.34e-02 1.83e+03 2.49e+02 ... (remaining 23197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.06: 31388 9.06 - 18.11: 61 18.11 - 27.17: 3 27.17 - 36.23: 6 36.23 - 45.28: 9 Bond angle restraints: 31467 Sorted by residual: angle pdb=" O LEU K 221 " pdb=" C LEU K 221 " pdb=" N PRO K 222 " ideal model delta sigma weight residual 121.32 76.04 45.28 1.15e+00 7.56e-01 1.55e+03 angle pdb=" O LEU C 221 " pdb=" C LEU C 221 " pdb=" N PRO C 222 " ideal model delta sigma weight residual 121.32 76.07 45.25 1.15e+00 7.56e-01 1.55e+03 angle pdb=" O LEU G 221 " pdb=" C LEU G 221 " pdb=" N PRO G 222 " ideal model delta sigma weight residual 121.32 76.10 45.22 1.15e+00 7.56e-01 1.55e+03 angle pdb=" O ILE K 220 " pdb=" C ILE K 220 " pdb=" N LEU K 221 " ideal model delta sigma weight residual 121.94 85.11 36.83 1.03e+00 9.43e-01 1.28e+03 angle pdb=" O ILE G 220 " pdb=" C ILE G 220 " pdb=" N LEU G 221 " ideal model delta sigma weight residual 121.94 85.12 36.82 1.03e+00 9.43e-01 1.28e+03 ... (remaining 31462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.60: 12304 34.60 - 69.20: 1133 69.20 - 103.81: 93 103.81 - 138.41: 6 138.41 - 173.01: 45 Dihedral angle restraints: 13581 sinusoidal: 6109 harmonic: 7472 Sorted by residual: dihedral pdb=" CA ALA B 7 " pdb=" C ALA B 7 " pdb=" N VAL B 8 " pdb=" CA VAL B 8 " ideal model delta harmonic sigma weight residual 180.00 79.33 100.67 0 5.00e+00 4.00e-02 4.05e+02 dihedral pdb=" CA ALA J 7 " pdb=" C ALA J 7 " pdb=" N VAL J 8 " pdb=" CA VAL J 8 " ideal model delta harmonic sigma weight residual 180.00 79.35 100.65 0 5.00e+00 4.00e-02 4.05e+02 dihedral pdb=" CA ALA F 7 " pdb=" C ALA F 7 " pdb=" N VAL F 8 " pdb=" CA VAL F 8 " ideal model delta harmonic sigma weight residual 180.00 79.37 100.63 0 5.00e+00 4.00e-02 4.05e+02 ... (remaining 13578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2836 0.093 - 0.187: 298 0.187 - 0.280: 57 0.280 - 0.373: 10 0.373 - 0.467: 6 Chirality restraints: 3207 Sorted by residual: chirality pdb=" CA PHE G 201 " pdb=" N PHE G 201 " pdb=" C PHE G 201 " pdb=" CB PHE G 201 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CA PHE C 201 " pdb=" N PHE C 201 " pdb=" C PHE C 201 " pdb=" CB PHE C 201 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA PHE K 201 " pdb=" N PHE K 201 " pdb=" C PHE K 201 " pdb=" CB PHE K 201 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.32e+00 ... (remaining 3204 not shown) Planarity restraints: 3738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU K 221 " -0.163 2.00e-02 2.50e+03 2.33e-01 5.44e+02 pdb=" C LEU K 221 " 0.400 2.00e-02 2.50e+03 pdb=" O LEU K 221 " -0.154 2.00e-02 2.50e+03 pdb=" N PRO K 222 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 221 " -0.163 2.00e-02 2.50e+03 2.33e-01 5.44e+02 pdb=" C LEU C 221 " 0.400 2.00e-02 2.50e+03 pdb=" O LEU C 221 " -0.154 2.00e-02 2.50e+03 pdb=" N PRO C 222 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 221 " -0.163 2.00e-02 2.50e+03 2.33e-01 5.43e+02 pdb=" C LEU G 221 " 0.400 2.00e-02 2.50e+03 pdb=" O LEU G 221 " -0.154 2.00e-02 2.50e+03 pdb=" N PRO G 222 " -0.083 2.00e-02 2.50e+03 ... (remaining 3735 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 33 2.06 - 2.69: 1431 2.69 - 3.33: 28377 3.33 - 3.96: 53637 3.96 - 4.60: 78235 Nonbonded interactions: 161713 Sorted by model distance: nonbonded pdb=" HA MET G 236 " pdb=" HE3 MET G 236 " model vdw 1.421 2.440 nonbonded pdb=" O GLY E 147 " pdb=" CD1 LEU J 205 " model vdw 1.592 3.100 nonbonded pdb=" HH2 TRP G 234 " pdb=" HG2 PRO G 243 " model vdw 1.616 2.270 nonbonded pdb=" CD1 LEU B 205 " pdb=" O GLY I 147 " model vdw 1.644 3.100 nonbonded pdb=" O GLY A 147 " pdb=" CD1 LEU F 205 " model vdw 1.665 3.100 ... (remaining 161708 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 33 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2)) or resid 83 through \ 144 or (resid 145 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name OE1 or name NE2)) or (resid 146 through 148 and (name N or \ name CA or name C or name O )) or resid 149 through 503)) selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 7 through 244 or (resid 245 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 246 throu \ gh 247 or resid 304 through 306)) selection = (chain 'F' and (resid 7 through 244 or (resid 245 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 246 throu \ gh 247 or resid 304 through 306)) selection = (chain 'J' and (resid 7 through 247 or resid 304 through 306)) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 303 or resid 308 or resid 312)) selection = (chain 'G' and (resid 45 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or (resid 234 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or \ name CZ2 or name CZ3 or name CH2)) or (resid 235 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE \ 2 or name CZ )) or (resid 236 and (name N or name CA or name C or name O or name \ CB or name CG or name SD or name CE )) or (resid 237 through 238 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or nam \ e OE2)) or resid 239 through 242 or (resid 243 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or resid 244 through 245 or (resid \ 246 and (name N or name CA or name C or name O or name CB or name CG or name CD \ 1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resid 247 thro \ ugh 280 or resid 303 or resid 308 or resid 312)) selection = (chain 'K' and (resid 45 through 280 or resid 303 or resid 308 or resid 312)) } 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: 12.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.130 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 17.590 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 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 : 0.017 1.069 23129 Z= 1.100 Angle : 1.492 45.285 31291 Z= 0.938 Chirality : 0.064 0.467 3207 Planarity : 0.010 0.245 3731 Dihedral : 25.577 173.010 8787 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 38.17 Ramachandran Plot: Outliers : 1.41 % Allowed : 8.50 % Favored : 90.09 % Rotamer: Outliers : 12.85 % Allowed : 15.18 % Favored : 71.97 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 2.22 % Twisted General : 0.25 % 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: -0.97 (0.16), residues: 2553 helix: -0.39 (0.15), residues: 1176 sheet: 1.20 (0.29), residues: 348 loop : -1.52 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 57 TYR 0.023 0.001 TYR C 184 PHE 0.013 0.001 PHE C 248 TRP 0.017 0.001 TRP F 152 HIS 0.017 0.002 HIS G 160 Details of bonding type rmsd covalent geometry : bond 0.01528 (23126) covalent geometry : angle 1.49199 (31291) hydrogen bonds : bond 0.17547 ( 1063) hydrogen bonds : angle 7.61428 ( 3105) Misc. bond : bond 0.68952 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 281 poor density : 583 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 175 ILE cc_start: 0.6474 (mm) cc_final: 0.6272 (mm) REVERT: C 218 PHE cc_start: 0.6532 (OUTLIER) cc_final: 0.6195 (t80) REVERT: C 240 PHE cc_start: 0.5725 (OUTLIER) cc_final: 0.5074 (t80) REVERT: J 62 THR cc_start: 0.6974 (m) cc_final: 0.6759 (m) REVERT: G 175 ILE cc_start: 0.6828 (mm) cc_final: 0.6586 (mm) REVERT: G 218 PHE cc_start: 0.6513 (OUTLIER) cc_final: 0.6250 (t80) REVERT: G 240 PHE cc_start: 0.6041 (OUTLIER) cc_final: 0.5254 (t80) REVERT: K 158 THR cc_start: 0.6661 (OUTLIER) cc_final: 0.6356 (t) REVERT: K 189 PHE cc_start: 0.7406 (m-10) cc_final: 0.7205 (m-80) REVERT: K 218 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.6154 (OUTLIER) REVERT: K 240 PHE cc_start: 0.5931 (OUTLIER) cc_final: 0.5050 (t80) outliers start: 281 outliers final: 52 residues processed: 803 average time/residue: 0.5593 time to fit residues: 514.3349 Evaluate side-chains 415 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 357 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 363 ASP Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain J residue 206 ARG Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 218 PHE Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 201 PHE Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 218 PHE Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 245 HIS Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 ASN A 176 GLN B 76 GLN ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN E 168 ASN E 176 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 ASN I 176 GLN F 187 ASN G 161 GLN ** K 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 161 GLN ** K 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.186395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.161686 restraints weight = 31228.586| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.39 r_work: 0.3913 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23129 Z= 0.214 Angle : 0.705 8.421 31291 Z= 0.367 Chirality : 0.047 0.207 3207 Planarity : 0.006 0.087 3731 Dihedral : 25.550 179.300 4249 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 36.49 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.90 % Favored : 93.71 % Rotamer: Outliers : 7.13 % Allowed : 23.09 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.12 (0.17), residues: 2559 helix: 0.73 (0.15), residues: 1197 sheet: 0.78 (0.28), residues: 387 loop : -0.96 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 299 TYR 0.025 0.002 TYR G 88 PHE 0.024 0.002 PHE K 132 TRP 0.021 0.002 TRP C 234 HIS 0.006 0.002 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00469 (23126) covalent geometry : angle 0.70506 (31291) hydrogen bonds : bond 0.05287 ( 1063) hydrogen bonds : angle 5.49054 ( 3105) Misc. bond : bond 0.00239 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 420 time to evaluate : 0.606 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 132 ARG cc_start: 0.7074 (mmm-85) cc_final: 0.6852 (mtm-85) REVERT: A 318 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.6319 (t80) REVERT: A 359 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8067 (p) REVERT: A 401 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7871 (mt0) REVERT: B 68 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7674 (mp) REVERT: B 237 TRP cc_start: 0.6877 (t60) cc_final: 0.6470 (t60) REVERT: C 240 PHE cc_start: 0.5935 (OUTLIER) cc_final: 0.5001 (t80) REVERT: E 318 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7146 (t80) REVERT: E 359 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8090 (p) REVERT: I 318 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.5593 (t80) REVERT: J 68 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7621 (mp) REVERT: J 201 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.6140 (tm-30) REVERT: J 237 TRP cc_start: 0.6894 (t60) cc_final: 0.6566 (t60) REVERT: F 68 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7661 (mp) REVERT: F 237 TRP cc_start: 0.6801 (t60) cc_final: 0.6298 (t60) REVERT: G 236 MET cc_start: 0.5812 (mmm) cc_final: 0.5393 (mpm) REVERT: G 240 PHE cc_start: 0.6197 (OUTLIER) cc_final: 0.5129 (t80) REVERT: G 268 SER cc_start: 0.7374 (OUTLIER) cc_final: 0.7167 (p) REVERT: K 240 PHE cc_start: 0.6024 (OUTLIER) cc_final: 0.4642 (t80) REVERT: K 268 SER cc_start: 0.7194 (OUTLIER) cc_final: 0.6989 (p) outliers start: 156 outliers final: 72 residues processed: 529 average time/residue: 0.4998 time to fit residues: 308.0065 Evaluate side-chains 426 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 339 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain B residue 11 HIS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 318 TYR Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain J residue 11 HIS Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 201 GLU Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain F residue 11 HIS Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 143 TRP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 143 TRP Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 269 PHE Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 210 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 238 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN J 40 HIS J 76 GLN J 245 GLN F 40 HIS ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN ** K 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.185486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.161275 restraints weight = 31451.484| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 1.36 r_work: 0.3896 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23129 Z= 0.171 Angle : 0.580 7.569 31291 Z= 0.309 Chirality : 0.043 0.148 3207 Planarity : 0.004 0.048 3731 Dihedral : 24.036 178.891 4188 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 38.98 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.14 % Favored : 93.59 % Rotamer: Outliers : 6.68 % Allowed : 25.51 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.61 (0.17), residues: 2559 helix: 1.33 (0.15), residues: 1200 sheet: 0.57 (0.28), residues: 393 loop : -0.80 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 206 TYR 0.017 0.002 TYR F 196 PHE 0.017 0.002 PHE F 31 TRP 0.018 0.002 TRP F 231 HIS 0.003 0.001 HIS I 137 Details of bonding type rmsd covalent geometry : bond 0.00370 (23126) covalent geometry : angle 0.58019 (31291) hydrogen bonds : bond 0.05247 ( 1063) hydrogen bonds : angle 5.15596 ( 3105) Misc. bond : bond 0.00106 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 371 time to evaluate : 0.748 Fit side-chains TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 299 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6862 (tmt-80) REVERT: B 50 PHE cc_start: 0.7827 (m-10) cc_final: 0.7621 (m-10) REVERT: B 68 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7638 (mp) REVERT: B 237 TRP cc_start: 0.6741 (t60) cc_final: 0.6333 (t60) REVERT: C 228 GLU cc_start: 0.5730 (OUTLIER) cc_final: 0.5300 (mp0) REVERT: C 240 PHE cc_start: 0.5925 (OUTLIER) cc_final: 0.4779 (t80) REVERT: E 299 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.7028 (tmt-80) REVERT: I 299 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7165 (tmt-80) REVERT: J 43 LEU cc_start: 0.6622 (mt) cc_final: 0.6261 (pp) REVERT: J 68 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7668 (mp) REVERT: J 201 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.6150 (tm-30) REVERT: J 237 TRP cc_start: 0.6765 (t60) cc_final: 0.6455 (t60) REVERT: F 43 LEU cc_start: 0.6611 (mt) cc_final: 0.6373 (pp) REVERT: F 68 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7635 (mp) REVERT: F 237 TRP cc_start: 0.6684 (t60) cc_final: 0.6245 (t60) REVERT: G 48 LYS cc_start: 0.6202 (OUTLIER) cc_final: 0.5999 (mptt) REVERT: G 146 TYR cc_start: 0.6547 (t80) cc_final: 0.5954 (t80) REVERT: G 228 GLU cc_start: 0.5956 (OUTLIER) cc_final: 0.5563 (mp0) REVERT: K 48 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.5793 (mptt) REVERT: K 74 TRP cc_start: 0.4351 (OUTLIER) cc_final: 0.0977 (t60) REVERT: K 228 GLU cc_start: 0.5971 (OUTLIER) cc_final: 0.5559 (mp0) REVERT: K 240 PHE cc_start: 0.5992 (OUTLIER) cc_final: 0.4596 (t80) REVERT: K 268 SER cc_start: 0.7223 (OUTLIER) cc_final: 0.7013 (p) outliers start: 146 outliers final: 78 residues processed: 478 average time/residue: 0.4862 time to fit residues: 272.6665 Evaluate side-chains 432 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 338 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 299 ARG Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 299 ARG Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 201 GLU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 143 TRP Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 143 TRP Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 269 PHE Chi-restraints excluded: chain K residue 274 LEU Chi-restraints excluded: chain K residue 278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 179 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 250 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN C 173 HIS ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN ** I 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 ASN J 240 ASN F 174 ASN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.184189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.160058 restraints weight = 31596.691| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.39 r_work: 0.3893 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 23129 Z= 0.216 Angle : 0.660 9.811 31291 Z= 0.349 Chirality : 0.046 0.146 3207 Planarity : 0.005 0.064 3731 Dihedral : 22.252 178.347 4176 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 40.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.10 % Favored : 93.67 % Rotamer: Outliers : 8.73 % Allowed : 23.87 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.36 (0.17), residues: 2559 helix: 1.29 (0.15), residues: 1191 sheet: -0.00 (0.27), residues: 414 loop : -0.95 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 125 TYR 0.024 0.002 TYR J 196 PHE 0.023 0.002 PHE F 31 TRP 0.026 0.002 TRP F 231 HIS 0.007 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00483 (23126) covalent geometry : angle 0.66035 (31291) hydrogen bonds : bond 0.05899 ( 1063) hydrogen bonds : angle 5.28260 ( 3105) Misc. bond : bond 0.00063 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 349 time to evaluate : 0.749 Fit side-chains TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 217 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7937 (mp) REVERT: A 233 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7252 (mtp85) REVERT: A 288 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7807 (p0) REVERT: A 299 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6960 (tmt-80) REVERT: A 318 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7271 (t80) REVERT: B 68 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7672 (mp) REVERT: B 237 TRP cc_start: 0.6464 (t60) cc_final: 0.6084 (t60) REVERT: C 74 TRP cc_start: 0.4571 (OUTLIER) cc_final: 0.1089 (t60) REVERT: C 223 ASN cc_start: 0.4550 (OUTLIER) cc_final: 0.3898 (t0) REVERT: C 228 GLU cc_start: 0.5727 (OUTLIER) cc_final: 0.5222 (mp0) REVERT: E 217 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7879 (mp) REVERT: E 288 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7698 (p0) REVERT: E 299 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7041 (tmt-80) REVERT: E 318 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.5809 (t80) REVERT: E 360 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7538 (ptp90) REVERT: E 414 MET cc_start: 0.6673 (mtt) cc_final: 0.6260 (mtm) REVERT: I 100 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7606 (ttp-110) REVERT: I 145 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7962 (tp40) REVERT: I 217 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8004 (mp) REVERT: I 299 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.7084 (tmt-80) REVERT: I 318 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.5823 (t80) REVERT: J 68 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7663 (mp) REVERT: J 206 ARG cc_start: 0.6740 (OUTLIER) cc_final: 0.6524 (mtp85) REVERT: J 237 TRP cc_start: 0.6512 (t60) cc_final: 0.6281 (t60) REVERT: F 68 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7679 (mp) REVERT: F 237 TRP cc_start: 0.6479 (t60) cc_final: 0.6096 (t60) REVERT: G 146 TYR cc_start: 0.6565 (t80) cc_final: 0.5880 (t80) REVERT: G 228 GLU cc_start: 0.5915 (OUTLIER) cc_final: 0.5431 (mp0) REVERT: K 74 TRP cc_start: 0.4607 (OUTLIER) cc_final: 0.1248 (t60) REVERT: K 228 GLU cc_start: 0.6111 (OUTLIER) cc_final: 0.5650 (mp0) REVERT: K 278 LEU cc_start: 0.4852 (OUTLIER) cc_final: 0.4339 (mt) outliers start: 191 outliers final: 96 residues processed: 486 average time/residue: 0.4909 time to fit residues: 279.0200 Evaluate side-chains 437 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 315 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 299 ARG Chi-restraints excluded: chain E residue 318 TYR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 100 ARG Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 237 MET Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 299 ARG Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 206 ARG Chi-restraints excluded: chain J residue 242 ARG Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 143 TRP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 143 TRP Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 185 ILE Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 274 LEU Chi-restraints excluded: chain K residue 278 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 47 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 232 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 231 optimal weight: 0.0980 chunk 101 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN J 11 HIS ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 ASN F 174 ASN ** K 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.187232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.163475 restraints weight = 31297.590| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.41 r_work: 0.3939 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23129 Z= 0.105 Angle : 0.489 6.675 31291 Z= 0.258 Chirality : 0.040 0.139 3207 Planarity : 0.003 0.046 3731 Dihedral : 20.859 174.675 4171 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 40.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.81 % Favored : 94.96 % Rotamer: Outliers : 5.53 % Allowed : 27.57 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.78 (0.17), residues: 2559 helix: 1.69 (0.15), residues: 1206 sheet: 0.13 (0.26), residues: 411 loop : -0.82 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 242 TYR 0.017 0.001 TYR K 184 PHE 0.018 0.001 PHE C 218 TRP 0.012 0.001 TRP F 231 HIS 0.003 0.001 HIS J 11 Details of bonding type rmsd covalent geometry : bond 0.00215 (23126) covalent geometry : angle 0.48905 (31291) hydrogen bonds : bond 0.04473 ( 1063) hydrogen bonds : angle 4.78856 ( 3105) Misc. bond : bond 0.00006 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 337 time to evaluate : 0.981 Fit side-chains TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 217 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7873 (mp) REVERT: A 400 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8065 (ptt-90) REVERT: B 68 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7680 (mp) REVERT: B 237 TRP cc_start: 0.6502 (t60) cc_final: 0.6136 (t60) REVERT: C 74 TRP cc_start: 0.4462 (OUTLIER) cc_final: 0.1060 (t60) REVERT: E 400 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8246 (ptt90) REVERT: E 414 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.6239 (mtm) REVERT: I 233 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7002 (mtp85) REVERT: I 400 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7346 (ptt-90) REVERT: J 68 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7692 (mp) REVERT: J 237 TRP cc_start: 0.6541 (t60) cc_final: 0.6327 (t60) REVERT: F 68 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7648 (mp) REVERT: F 237 TRP cc_start: 0.6427 (t60) cc_final: 0.6018 (t60) REVERT: K 74 TRP cc_start: 0.4518 (OUTLIER) cc_final: 0.1269 (t60) REVERT: K 240 PHE cc_start: 0.6070 (OUTLIER) cc_final: 0.4755 (t80) REVERT: K 265 THR cc_start: 0.6747 (p) cc_final: 0.6543 (m) REVERT: K 268 SER cc_start: 0.7089 (t) cc_final: 0.6887 (p) outliers start: 121 outliers final: 67 residues processed: 428 average time/residue: 0.4787 time to fit residues: 240.8871 Evaluate side-chains 398 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 319 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 400 ARG Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 143 TRP Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 143 TRP Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 184 TYR Chi-restraints excluded: chain K residue 185 ILE Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 269 PHE Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 38 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 22 optimal weight: 0.0030 chunk 107 optimal weight: 0.0030 chunk 62 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 117 optimal weight: 0.0980 chunk 185 optimal weight: 9.9990 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN J 11 HIS ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 ASN F 11 HIS ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN F 187 ASN ** K 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.188860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.165061 restraints weight = 31554.535| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.42 r_work: 0.3963 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3838 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23129 Z= 0.089 Angle : 0.461 6.475 31291 Z= 0.240 Chirality : 0.039 0.143 3207 Planarity : 0.003 0.044 3731 Dihedral : 19.042 167.642 4169 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 40.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.39 % Favored : 94.37 % Rotamer: Outliers : 4.62 % Allowed : 29.13 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 1.08 (0.17), residues: 2559 helix: 1.98 (0.15), residues: 1209 sheet: 0.21 (0.26), residues: 411 loop : -0.71 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 100 TYR 0.022 0.001 TYR K 184 PHE 0.018 0.001 PHE C 218 TRP 0.011 0.001 TRP F 152 HIS 0.004 0.000 HIS J 11 Details of bonding type rmsd covalent geometry : bond 0.00185 (23126) covalent geometry : angle 0.46075 (31291) hydrogen bonds : bond 0.03932 ( 1063) hydrogen bonds : angle 4.46661 ( 3105) Misc. bond : bond 0.00044 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 343 time to evaluate : 0.557 Fit side-chains TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: B 68 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7611 (mp) REVERT: B 83 TYR cc_start: 0.6804 (m-10) cc_final: 0.6471 (m-10) REVERT: B 237 TRP cc_start: 0.6476 (t60) cc_final: 0.6167 (t60) REVERT: C 74 TRP cc_start: 0.4402 (OUTLIER) cc_final: 0.1096 (t60) REVERT: E 414 MET cc_start: 0.6606 (mtt) cc_final: 0.6269 (mtm) REVERT: I 93 MET cc_start: 0.7077 (ptt) cc_final: 0.6847 (pmm) REVERT: I 233 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.7038 (mtp85) REVERT: J 68 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7669 (mp) REVERT: J 201 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.6017 (tm-30) REVERT: J 237 TRP cc_start: 0.6554 (t60) cc_final: 0.6336 (t60) REVERT: F 68 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7587 (mp) REVERT: K 240 PHE cc_start: 0.6035 (OUTLIER) cc_final: 0.4774 (t80) outliers start: 101 outliers final: 53 residues processed: 406 average time/residue: 0.4538 time to fit residues: 217.7598 Evaluate side-chains 387 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 327 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 206 TRP Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 206 TRP Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 249 MET Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 201 GLU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 185 ILE Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 269 PHE Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 249 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 169 optimal weight: 0.5980 chunk 232 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 225 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN E 168 ASN E 176 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN I 176 GLN J 11 HIS ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 ASN F 11 HIS ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN F 187 ASN ** K 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.187984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.163867 restraints weight = 31497.112| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.43 r_work: 0.3947 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23129 Z= 0.109 Angle : 0.479 5.828 31291 Z= 0.251 Chirality : 0.040 0.141 3207 Planarity : 0.003 0.046 3731 Dihedral : 18.317 160.346 4164 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 40.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.00 % Favored : 94.84 % Rotamer: Outliers : 5.12 % Allowed : 28.72 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 1.09 (0.17), residues: 2559 helix: 1.96 (0.15), residues: 1209 sheet: 0.23 (0.26), residues: 411 loop : -0.66 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 58 TYR 0.016 0.001 TYR G 184 PHE 0.020 0.001 PHE C 218 TRP 0.018 0.001 TRP K 234 HIS 0.003 0.001 HIS J 11 Details of bonding type rmsd covalent geometry : bond 0.00234 (23126) covalent geometry : angle 0.47935 (31291) hydrogen bonds : bond 0.04218 ( 1063) hydrogen bonds : angle 4.53026 ( 3105) Misc. bond : bond 0.00022 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 327 time to evaluate : 0.629 Fit side-chains TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 120 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7523 (mptp) REVERT: B 68 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7645 (mp) REVERT: B 237 TRP cc_start: 0.6480 (t60) cc_final: 0.6141 (t60) REVERT: C 74 TRP cc_start: 0.4468 (OUTLIER) cc_final: 0.1178 (t60) REVERT: E 217 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7799 (mp) REVERT: E 360 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7451 (ptp90) REVERT: E 414 MET cc_start: 0.6574 (mtt) cc_final: 0.6245 (mtm) REVERT: I 145 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8077 (tp40) REVERT: I 233 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.7142 (mtp85) REVERT: I 400 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7398 (ptt-90) REVERT: J 62 THR cc_start: 0.7872 (m) cc_final: 0.7644 (m) REVERT: J 68 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7637 (mp) REVERT: J 201 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.6200 (tm-30) REVERT: F 68 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7618 (mp) REVERT: K 74 TRP cc_start: 0.4490 (OUTLIER) cc_final: 0.1296 (t60) REVERT: K 233 PHE cc_start: 0.4181 (t80) cc_final: 0.3563 (t80) REVERT: K 240 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.4997 (t80) outliers start: 112 outliers final: 66 residues processed: 399 average time/residue: 0.4729 time to fit residues: 222.5826 Evaluate side-chains 404 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 325 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 206 TRP Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 206 TRP Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 237 MET Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 400 ARG Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 178 MET Chi-restraints excluded: chain J residue 201 GLU Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 143 TRP Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 185 ILE Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 2 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 122 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN I 176 GLN I 306 ASN J 11 HIS ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 ASN F 11 HIS ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** K 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.185477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.161663 restraints weight = 31230.961| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.36 r_work: 0.3920 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3793 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23129 Z= 0.189 Angle : 0.604 8.215 31291 Z= 0.321 Chirality : 0.044 0.176 3207 Planarity : 0.005 0.049 3731 Dihedral : 17.875 158.341 4160 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 41.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.45 % Favored : 93.40 % Rotamer: Outliers : 5.26 % Allowed : 28.62 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.69 (0.17), residues: 2559 helix: 1.60 (0.15), residues: 1212 sheet: 0.11 (0.26), residues: 411 loop : -0.88 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 58 TYR 0.026 0.002 TYR J 196 PHE 0.026 0.002 PHE C 218 TRP 0.022 0.002 TRP F 231 HIS 0.004 0.001 HIS F 168 Details of bonding type rmsd covalent geometry : bond 0.00420 (23126) covalent geometry : angle 0.60419 (31291) hydrogen bonds : bond 0.05492 ( 1063) hydrogen bonds : angle 4.99498 ( 3105) Misc. bond : bond 0.00018 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 327 time to evaluate : 0.899 Fit side-chains TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 120 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7513 (mptp) REVERT: A 400 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8160 (ptt-90) REVERT: B 68 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7667 (mp) REVERT: B 227 ILE cc_start: 0.8508 (mm) cc_final: 0.8290 (mp) REVERT: B 237 TRP cc_start: 0.6465 (t60) cc_final: 0.6121 (t60) REVERT: C 74 TRP cc_start: 0.4667 (OUTLIER) cc_final: 0.1356 (t60) REVERT: E 251 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.7020 (ttt) REVERT: E 360 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7518 (ptp90) REVERT: E 414 MET cc_start: 0.6597 (mtt) cc_final: 0.6275 (mtm) REVERT: I 145 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7890 (tp40) REVERT: I 233 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7258 (mtp85) REVERT: I 400 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7481 (ptt-90) REVERT: J 68 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7686 (mp) REVERT: J 227 ILE cc_start: 0.8459 (mm) cc_final: 0.8246 (mp) REVERT: F 68 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7676 (mp) REVERT: F 237 TRP cc_start: 0.6415 (t60) cc_final: 0.6014 (t60) REVERT: G 146 TYR cc_start: 0.6617 (t80) cc_final: 0.6021 (t80) REVERT: K 74 TRP cc_start: 0.4679 (OUTLIER) cc_final: 0.3865 (p-90) REVERT: K 240 PHE cc_start: 0.6137 (OUTLIER) cc_final: 0.5149 (t80) outliers start: 115 outliers final: 71 residues processed: 407 average time/residue: 0.4417 time to fit residues: 213.1149 Evaluate side-chains 404 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 320 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 237 MET Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 MET Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 400 ARG Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 143 TRP Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 218 PHE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 143 TRP Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 185 ILE Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 218 PHE Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 263 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 32 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 222 optimal weight: 0.6980 chunk 227 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 232 optimal weight: 0.0370 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN I 176 GLN J 11 HIS ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 ASN F 11 HIS ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** K 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.188631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.164619 restraints weight = 31482.864| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 1.42 r_work: 0.3946 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23129 Z= 0.099 Angle : 0.484 5.961 31291 Z= 0.254 Chirality : 0.040 0.144 3207 Planarity : 0.003 0.046 3731 Dihedral : 17.120 160.410 4160 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 40.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Rotamer: Outliers : 3.34 % Allowed : 30.68 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.99 (0.17), residues: 2559 helix: 1.89 (0.15), residues: 1209 sheet: 0.26 (0.28), residues: 375 loop : -0.75 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 58 TYR 0.018 0.001 TYR G 184 PHE 0.027 0.001 PHE C 218 TRP 0.014 0.001 TRP K 234 HIS 0.004 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00207 (23126) covalent geometry : angle 0.48386 (31291) hydrogen bonds : bond 0.04298 ( 1063) hydrogen bonds : angle 4.61814 ( 3105) Misc. bond : bond 0.00022 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 330 time to evaluate : 0.756 Fit side-chains TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 120 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7535 (mptp) REVERT: A 400 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8156 (ptt-90) REVERT: B 68 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7696 (mp) REVERT: B 237 TRP cc_start: 0.6381 (t60) cc_final: 0.6032 (t60) REVERT: C 74 TRP cc_start: 0.4620 (OUTLIER) cc_final: 0.1362 (t60) REVERT: E 414 MET cc_start: 0.6633 (mtt) cc_final: 0.6308 (mtm) REVERT: I 93 MET cc_start: 0.7068 (ptt) cc_final: 0.6823 (pmm) REVERT: I 233 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7167 (mtp85) REVERT: I 400 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7548 (ptt-90) REVERT: J 68 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7672 (mp) REVERT: F 68 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7659 (mp) REVERT: K 240 PHE cc_start: 0.6077 (OUTLIER) cc_final: 0.5004 (t80) outliers start: 73 outliers final: 48 residues processed: 380 average time/residue: 0.4778 time to fit residues: 214.5946 Evaluate side-chains 380 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 323 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 206 TRP Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 400 ARG Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 218 PHE Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 184 TYR Chi-restraints excluded: chain K residue 185 ILE Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 199 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 99 optimal weight: 0.0670 chunk 67 optimal weight: 0.9980 chunk 191 optimal weight: 0.3980 chunk 38 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN J 11 HIS ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 ASN F 11 HIS ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** K 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.187147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.163284 restraints weight = 31240.781| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.36 r_work: 0.3943 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23129 Z= 0.102 Angle : 0.482 6.041 31291 Z= 0.252 Chirality : 0.040 0.142 3207 Planarity : 0.003 0.046 3731 Dihedral : 16.666 162.878 4160 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 40.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.74 % Favored : 94.14 % Rotamer: Outliers : 3.48 % Allowed : 30.73 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 1.08 (0.17), residues: 2559 helix: 2.01 (0.15), residues: 1200 sheet: 0.30 (0.28), residues: 375 loop : -0.74 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 58 TYR 0.018 0.001 TYR G 184 PHE 0.028 0.001 PHE C 218 TRP 0.021 0.001 TRP G 234 HIS 0.004 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00217 (23126) covalent geometry : angle 0.48167 (31291) hydrogen bonds : bond 0.04270 ( 1063) hydrogen bonds : angle 4.57603 ( 3105) Misc. bond : bond 0.00027 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 324 time to evaluate : 0.709 Fit side-chains TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 120 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7565 (mptp) REVERT: A 400 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8192 (ptt-90) REVERT: B 68 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7621 (mp) REVERT: B 237 TRP cc_start: 0.6396 (t60) cc_final: 0.6059 (t60) REVERT: C 74 TRP cc_start: 0.4648 (OUTLIER) cc_final: 0.1433 (t60) REVERT: E 360 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.7386 (ptp90) REVERT: E 414 MET cc_start: 0.6672 (mtt) cc_final: 0.6349 (mtm) REVERT: I 93 MET cc_start: 0.7116 (ptt) cc_final: 0.6878 (pmm) REVERT: I 233 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7205 (mtp85) REVERT: I 400 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7604 (ptt-90) REVERT: J 62 THR cc_start: 0.7905 (m) cc_final: 0.7672 (m) REVERT: J 68 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7640 (mp) REVERT: J 206 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.5517 (ptm160) REVERT: F 68 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7633 (mp) REVERT: K 240 PHE cc_start: 0.6068 (OUTLIER) cc_final: 0.5018 (t80) outliers start: 76 outliers final: 55 residues processed: 374 average time/residue: 0.4535 time to fit residues: 199.9699 Evaluate side-chains 388 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 322 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 206 TRP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 206 TRP Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 400 ARG Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 206 ARG Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 185 ILE Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 218 PHE Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN J 11 HIS ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 ASN F 11 HIS ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** K 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.182489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.157639 restraints weight = 31444.907| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.40 r_work: 0.3881 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.6449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 23129 Z= 0.296 Angle : 0.723 8.596 31291 Z= 0.386 Chirality : 0.048 0.199 3207 Planarity : 0.005 0.057 3731 Dihedral : 17.020 163.105 4160 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 42.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.96 % Favored : 92.93 % Rotamer: Outliers : 4.25 % Allowed : 30.09 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.28 (0.17), residues: 2559 helix: 1.23 (0.15), residues: 1205 sheet: 0.11 (0.27), residues: 375 loop : -1.06 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 104 TYR 0.027 0.003 TYR F 113 PHE 0.030 0.002 PHE B 31 TRP 0.028 0.003 TRP F 231 HIS 0.006 0.002 HIS F 168 Details of bonding type rmsd covalent geometry : bond 0.00666 (23126) covalent geometry : angle 0.72298 (31291) hydrogen bonds : bond 0.06504 ( 1063) hydrogen bonds : angle 5.37556 ( 3105) Misc. bond : bond 0.00007 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8540.29 seconds wall clock time: 145 minutes 52.66 seconds (8752.66 seconds total)