Starting phenix.real_space_refine on Wed Apr 17 13:48:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr2_40718/04_2024/8sr2_40718_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr2_40718/04_2024/8sr2_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr2_40718/04_2024/8sr2_40718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr2_40718/04_2024/8sr2_40718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr2_40718/04_2024/8sr2_40718_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr2_40718/04_2024/8sr2_40718_trim_updated.pdb" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Residue "C GLU 228": "OE1" <-> "OE2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "K GLU 228": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/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: 11.79, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 10.47 Conformation dependent library (CDL) restraints added in 3.6 seconds 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... running ksdssp... Secondary structure from input PDB file: 84 helices and 24 sheets defined 45.1% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 185 through 207 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 232 through 256 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 369 through 373 removed outlier: 3.731A pdb=" N VAL A 373 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 42 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 59 through 83 Proline residue: B 65 - end of helix removed outlier: 4.641A pdb=" N THR B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Proline residue: B 72 - end of helix removed outlier: 3.897A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 106 Processing helix chain 'B' and resid 116 through 119 No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing helix chain 'B' and resid 125 through 136 removed outlier: 3.501A pdb=" N LEU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 168 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 Proline residue: B 166 - end of helix Processing helix chain 'B' and resid 180 through 187 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 212 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 50 through 71 removed outlier: 3.836A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 88 No H-bonds generated for 'chain 'C' and resid 85 through 88' Processing helix chain 'C' and resid 90 through 113 Processing helix chain 'C' and resid 124 through 149 Processing helix chain 'C' and resid 151 through 159 removed outlier: 3.509A pdb=" N TRP C 159 " --> pdb=" O GLN C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 197 Processing helix chain 'C' and resid 208 through 215 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.770A pdb=" N ASN C 227 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU C 228 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR C 232 " --> pdb=" O TRP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 269 removed outlier: 3.807A pdb=" N LEU C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU C 256 " --> pdb=" O GLY C 252 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N MET C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 44 Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 185 through 207 Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'E' and resid 232 through 256 Processing helix chain 'E' and resid 338 through 340 No H-bonds generated for 'chain 'E' and resid 338 through 340' Processing helix chain 'E' and resid 369 through 373 removed outlier: 3.733A pdb=" N VAL E 373 " --> pdb=" O ALA E 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 44 Processing helix chain 'I' and resid 163 through 165 No H-bonds generated for 'chain 'I' and resid 163 through 165' Processing helix chain 'I' and resid 185 through 207 Processing helix chain 'I' and resid 213 through 220 Processing helix chain 'I' and resid 232 through 256 Processing helix chain 'I' and resid 338 through 340 No H-bonds generated for 'chain 'I' and resid 338 through 340' Processing helix chain 'I' and resid 369 through 373 removed outlier: 3.731A pdb=" N VAL I 373 " --> pdb=" O ALA I 370 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 42 Processing helix chain 'J' and resid 46 through 50 Processing helix chain 'J' and resid 52 through 54 No H-bonds generated for 'chain 'J' and resid 52 through 54' Processing helix chain 'J' and resid 59 through 83 Proline residue: J 65 - end of helix removed outlier: 4.641A pdb=" N THR J 70 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N PHE J 71 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Proline residue: J 72 - end of helix removed outlier: 3.898A pdb=" N GLU J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 106 Processing helix chain 'J' and resid 116 through 119 No H-bonds generated for 'chain 'J' and resid 116 through 119' Processing helix chain 'J' and resid 125 through 136 removed outlier: 3.501A pdb=" N LEU J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 168 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 Proline residue: J 166 - end of helix Processing helix chain 'J' and resid 180 through 187 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'J' and resid 212 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 11 through 42 Processing helix chain 'F' and resid 46 through 50 Processing helix chain 'F' and resid 52 through 54 No H-bonds generated for 'chain 'F' and resid 52 through 54' Processing helix chain 'F' and resid 59 through 83 Proline residue: F 65 - end of helix removed outlier: 4.641A pdb=" N THR F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix removed outlier: 3.897A pdb=" N GLU F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 106 Processing helix chain 'F' and resid 116 through 119 No H-bonds generated for 'chain 'F' and resid 116 through 119' Processing helix chain 'F' and resid 125 through 136 removed outlier: 3.501A pdb=" N LEU F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 168 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 Proline residue: F 166 - end of helix Processing helix chain 'F' and resid 180 through 187 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 212 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 50 through 71 removed outlier: 3.836A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 88 No H-bonds generated for 'chain 'G' and resid 85 through 88' Processing helix chain 'G' and resid 90 through 113 Processing helix chain 'G' and resid 124 through 149 Processing helix chain 'G' and resid 151 through 159 removed outlier: 3.509A pdb=" N TRP G 159 " --> pdb=" O GLN G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 197 Processing helix chain 'G' and resid 208 through 215 Processing helix chain 'G' and resid 217 through 219 No H-bonds generated for 'chain 'G' and resid 217 through 219' Processing helix chain 'G' and resid 223 through 232 removed outlier: 3.769A pdb=" N ASN G 227 " --> pdb=" O VAL G 224 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU G 228 " --> pdb=" O GLY G 225 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR G 232 " --> pdb=" O TRP G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 269 removed outlier: 3.808A pdb=" N LEU G 254 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA G 255 " --> pdb=" O PHE G 251 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU G 256 " --> pdb=" O GLY G 252 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA G 257 " --> pdb=" O TRP G 253 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N MET G 259 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY G 260 " --> pdb=" O LEU G 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 71 removed outlier: 3.835A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 88 No H-bonds generated for 'chain 'K' and resid 85 through 88' Processing helix chain 'K' and resid 90 through 113 Processing helix chain 'K' and resid 124 through 149 Processing helix chain 'K' and resid 151 through 159 removed outlier: 3.509A pdb=" N TRP K 159 " --> pdb=" O GLN K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 197 Processing helix chain 'K' and resid 208 through 215 Processing helix chain 'K' and resid 217 through 219 No H-bonds generated for 'chain 'K' and resid 217 through 219' Processing helix chain 'K' and resid 223 through 232 removed outlier: 3.769A pdb=" N ASN K 227 " --> pdb=" O VAL K 224 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU K 228 " --> pdb=" O GLY K 225 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR K 232 " --> pdb=" O TRP K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 269 removed outlier: 3.808A pdb=" N LEU K 254 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA K 255 " --> pdb=" O PHE K 251 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU K 256 " --> pdb=" O GLY K 252 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA K 257 " --> pdb=" O TRP K 253 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N MET K 259 " --> pdb=" O ALA K 255 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY K 260 " --> pdb=" O LEU K 256 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 47 through 50 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) Processing sheet with id= B, first strand: chain 'A' and resid 58 through 60 removed outlier: 8.449A pdb=" N VAL A 59 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR A 158 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 87 through 89 Processing sheet with id= D, first strand: chain 'A' and resid 169 through 171 Processing sheet with id= E, first strand: chain 'A' and resid 282 through 286 Processing sheet with id= F, first strand: chain 'A' and resid 298 through 300 Processing sheet with id= G, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.608A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 390 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 170 through 173 Processing sheet with id= I, first strand: chain 'E' and resid 47 through 50 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) Processing sheet with id= J, first strand: chain 'E' and resid 58 through 60 removed outlier: 8.447A pdb=" N VAL E 59 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR E 158 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 87 through 89 Processing sheet with id= L, first strand: chain 'E' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'E' and resid 282 through 286 Processing sheet with id= N, first strand: chain 'E' and resid 298 through 300 Processing sheet with id= O, first strand: chain 'E' and resid 323 through 325 removed outlier: 6.606A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU E 390 " --> pdb=" O PHE E 317 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 47 through 50 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) Processing sheet with id= Q, first strand: chain 'I' and resid 58 through 60 removed outlier: 8.451A pdb=" N VAL I 59 " --> pdb=" O TRP I 156 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR I 158 " --> pdb=" O VAL I 59 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 87 through 89 Processing sheet with id= S, first strand: chain 'I' and resid 169 through 171 Processing sheet with id= T, first strand: chain 'I' and resid 282 through 286 Processing sheet with id= U, first strand: chain 'I' and resid 298 through 300 Processing sheet with id= V, first strand: chain 'I' and resid 323 through 325 removed outlier: 6.606A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU I 390 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 170 through 173 Processing sheet with id= X, first strand: chain 'F' and resid 170 through 173 921 hydrogen bonds defined for protein. 2700 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: 6.85 Time building geometry restraints manager: 11.07 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: 76.04 - 91.24: 9 91.24 - 106.45: 811 106.45 - 121.66: 25694 121.66 - 136.87: 4947 136.87 - 152.08: 6 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: 1447 2.69 - 3.33: 28504 3.33 - 3.96: 53849 3.96 - 4.60: 78451 Nonbonded interactions: 162284 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 162279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 414 or resid 501 through 50 \ 3)) 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: 7.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.600 Extract box with map and model: 27.670 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 59.270 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.770 ------------------------------------------------------------------------------- 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 : 0.015 1.069 23126 Z= 0.968 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (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 TRP 0.017 0.001 TRP F 152 HIS 0.017 0.002 HIS G 160 PHE 0.013 0.001 PHE C 248 TYR 0.023 0.001 TYR C 184 ARG 0.005 0.000 ARG J 57 *********************** 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 fitting. rotamer outliers: 281 poor density : 583 time to evaluate : 2.605 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: 0.6194 (t80) REVERT: C 240 PHE cc_start: 0.5725 (OUTLIER) cc_final: 0.5075 (t80) REVERT: J 62 THR cc_start: 0.6974 (m) cc_final: 0.6764 (m) REVERT: G 175 ILE cc_start: 0.6828 (mm) cc_final: 0.6563 (mm) REVERT: G 218 PHE cc_start: 0.6513 (OUTLIER) cc_final: 0.6249 (t80) REVERT: G 240 PHE cc_start: 0.6041 (OUTLIER) cc_final: 0.5255 (t80) REVERT: K 158 THR cc_start: 0.6661 (OUTLIER) cc_final: 0.6358 (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: 0.6156 (OUTLIER) REVERT: K 240 PHE cc_start: 0.5931 (OUTLIER) cc_final: 0.5053 (t80) outliers start: 281 outliers final: 53 residues processed: 803 average time/residue: 1.3538 time to fit residues: 1243.1904 Evaluate side-chains 419 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 360 time to evaluate : 2.637 ------------------------------------------------------------------------------- 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 105 ILE 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 215 optimal weight: 0.9980 chunk 193 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 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 J 76 GLN ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23126 Z= 0.214 Angle : 0.594 8.100 31291 Z= 0.305 Chirality : 0.043 0.183 3207 Planarity : 0.005 0.094 3731 Dihedral : 25.589 179.380 4251 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 38.08 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.24 % Favored : 94.22 % Rotamer: Outliers : 6.77 % Allowed : 23.18 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2559 helix: 0.90 (0.15), residues: 1191 sheet: 1.21 (0.28), residues: 372 loop : -0.97 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 64 HIS 0.005 0.001 HIS F 40 PHE 0.020 0.002 PHE K 132 TYR 0.018 0.002 TYR F 113 ARG 0.006 0.001 ARG A 299 *********************** 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 552 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 404 time to evaluate : 2.710 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: A 359 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7789 (p) REVERT: A 401 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7395 (mt0) REVERT: B 68 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7336 (mp) REVERT: B 237 TRP cc_start: 0.6423 (t60) cc_final: 0.6021 (t60) REVERT: C 78 LEU cc_start: 0.4837 (OUTLIER) cc_final: 0.4617 (mm) REVERT: C 236 MET cc_start: 0.5199 (mpm) cc_final: 0.4819 (mpm) REVERT: C 240 PHE cc_start: 0.5823 (OUTLIER) cc_final: 0.5128 (t80) REVERT: E 359 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7746 (p) REVERT: I 132 ARG cc_start: 0.6778 (mmm-85) cc_final: 0.6550 (mtm-85) REVERT: J 68 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7383 (mp) REVERT: J 237 TRP cc_start: 0.6366 (t60) cc_final: 0.5968 (t60) REVERT: F 68 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7343 (mp) REVERT: F 237 TRP cc_start: 0.6314 (t60) cc_final: 0.5890 (t60) REVERT: G 78 LEU cc_start: 0.5373 (OUTLIER) cc_final: 0.5123 (mm) REVERT: G 198 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.4773 (mpp-170) REVERT: G 240 PHE cc_start: 0.6036 (OUTLIER) cc_final: 0.5024 (t80) REVERT: K 78 LEU cc_start: 0.5316 (OUTLIER) cc_final: 0.5065 (mm) REVERT: K 198 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.4109 (mpp-170) REVERT: K 240 PHE cc_start: 0.5955 (OUTLIER) cc_final: 0.4796 (t80) outliers start: 148 outliers final: 76 residues processed: 512 average time/residue: 1.2181 time to fit residues: 723.5442 Evaluate side-chains 433 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 343 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR 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 97 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 251 MET 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 138 SER Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 262 ILE 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 64 THR Chi-restraints excluded: chain I residue 135 ASP Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain J residue 11 HIS Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain J residue 201 GLU Chi-restraints excluded: chain J residue 206 ARG 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 138 SER Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 78 LEU 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 198 ARG Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE 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 78 LEU 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 198 ARG 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 128 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 230 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 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 145 GLN A 176 GLN B 76 GLN B 168 HIS C 118 ASN ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN J 168 HIS F 76 GLN F 168 HIS ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 23126 Z= 0.464 Angle : 0.795 12.856 31291 Z= 0.423 Chirality : 0.050 0.186 3207 Planarity : 0.006 0.074 3731 Dihedral : 24.477 179.859 4195 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 47.26 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.88 % Favored : 92.73 % Rotamer: Outliers : 8.96 % Allowed : 22.04 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2559 helix: 0.70 (0.15), residues: 1170 sheet: 0.47 (0.28), residues: 390 loop : -1.12 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP J 231 HIS 0.008 0.002 HIS A 48 PHE 0.025 0.003 PHE B 31 TYR 0.038 0.003 TYR J 83 ARG 0.008 0.001 ARG F 58 *********************** 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 591 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 395 time to evaluate : 2.552 Fit side-chains TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 163 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7327 (ttp) REVERT: A 299 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6543 (tmt-80) REVERT: A 318 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7302 (t80) REVERT: B 68 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7380 (mp) REVERT: B 83 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.6639 (m-10) REVERT: B 160 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.6923 (m-40) REVERT: B 237 TRP cc_start: 0.5996 (t60) cc_final: 0.5585 (t60) REVERT: C 115 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.6267 (ptt-90) REVERT: C 228 GLU cc_start: 0.5647 (OUTLIER) cc_final: 0.5121 (mp0) REVERT: E 120 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7260 (mmmt) REVERT: E 163 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7465 (ttp) REVERT: E 318 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.5889 (t80) REVERT: E 360 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7231 (ptp90) REVERT: I 150 ILE cc_start: 0.8083 (mp) cc_final: 0.7858 (mm) REVERT: I 163 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7471 (ttp) REVERT: I 299 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6674 (tmt-80) REVERT: J 68 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7422 (mp) REVERT: J 83 TYR cc_start: 0.7090 (OUTLIER) cc_final: 0.6539 (m-10) REVERT: J 156 PHE cc_start: 0.6284 (t80) cc_final: 0.5727 (t80) REVERT: J 201 GLU cc_start: 0.5977 (tt0) cc_final: 0.5773 (tm-30) REVERT: J 237 TRP cc_start: 0.5977 (t60) cc_final: 0.5702 (t60) REVERT: F 68 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7428 (mp) REVERT: F 83 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6534 (m-10) REVERT: F 156 PHE cc_start: 0.6281 (t80) cc_final: 0.5736 (t80) REVERT: F 237 TRP cc_start: 0.5966 (t60) cc_final: 0.5635 (t60) REVERT: G 49 LYS cc_start: 0.6788 (OUTLIER) cc_final: 0.6548 (pmtt) REVERT: G 74 TRP cc_start: 0.4714 (OUTLIER) cc_final: 0.4034 (p-90) REVERT: G 146 TYR cc_start: 0.6008 (t80) cc_final: 0.5267 (t80) REVERT: G 228 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.5354 (mp0) REVERT: K 146 TYR cc_start: 0.5976 (t80) cc_final: 0.5470 (t80) REVERT: K 228 GLU cc_start: 0.5808 (OUTLIER) cc_final: 0.5239 (mp0) REVERT: K 240 PHE cc_start: 0.5976 (OUTLIER) cc_final: 0.5013 (t80) outliers start: 196 outliers final: 100 residues processed: 544 average time/residue: 1.1406 time to fit residues: 728.2569 Evaluate side-chains 467 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 344 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR 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 75 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 163 MET 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 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 361 THR Chi-restraints excluded: chain A residue 403 VAL 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 83 TYR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 160 ASN 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 115 ARG 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 228 GLU Chi-restraints excluded: chain C residue 265 THR 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 64 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 237 MET 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 360 ARG Chi-restraints excluded: chain E residue 395 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 135 ASP Chi-restraints excluded: chain I residue 163 MET Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 299 ARG Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 ASP Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 83 TYR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 138 SER 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 245 GLN Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 138 SER 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 G residue 49 LYS Chi-restraints excluded: chain G residue 52 THR 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 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 226 LEU Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 265 THR 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 52 THR Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 143 TRP 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 240 PHE Chi-restraints excluded: chain K residue 265 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 246 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 220 optimal weight: 0.0470 chunk 66 optimal weight: 3.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN B 76 GLN B 174 ASN ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN E 176 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN I 176 GLN J 76 GLN J 174 ASN F 76 GLN F 174 ASN ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23126 Z= 0.162 Angle : 0.520 7.127 31291 Z= 0.271 Chirality : 0.041 0.134 3207 Planarity : 0.004 0.049 3731 Dihedral : 22.838 179.890 4180 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 43.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.57 % Favored : 95.12 % Rotamer: Outliers : 6.58 % Allowed : 25.70 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2559 helix: 1.48 (0.16), residues: 1176 sheet: 0.43 (0.27), residues: 393 loop : -0.97 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 231 HIS 0.004 0.001 HIS I 137 PHE 0.015 0.001 PHE F 31 TYR 0.015 0.001 TYR C 62 ARG 0.010 0.000 ARG J 206 *********************** 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 490 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 346 time to evaluate : 2.439 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 163 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7488 (ttp) REVERT: A 299 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6620 (tmt-80) REVERT: B 68 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7389 (mp) REVERT: B 83 TYR cc_start: 0.6651 (m-80) cc_final: 0.6281 (m-10) REVERT: B 237 TRP cc_start: 0.5961 (t60) cc_final: 0.5601 (t60) REVERT: C 228 GLU cc_start: 0.5364 (OUTLIER) cc_final: 0.4873 (mp0) REVERT: E 163 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7475 (ttp) REVERT: I 150 ILE cc_start: 0.7963 (mp) cc_final: 0.7720 (mm) REVERT: I 163 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7379 (ttp) REVERT: I 299 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6756 (tmt-80) REVERT: J 83 TYR cc_start: 0.6569 (m-80) cc_final: 0.6330 (m-80) REVERT: J 237 TRP cc_start: 0.6009 (t60) cc_final: 0.5768 (t60) REVERT: F 68 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7346 (mp) REVERT: F 237 TRP cc_start: 0.5927 (t60) cc_final: 0.5524 (t60) REVERT: G 49 LYS cc_start: 0.6665 (OUTLIER) cc_final: 0.6441 (pmtt) REVERT: G 228 GLU cc_start: 0.5733 (OUTLIER) cc_final: 0.5308 (mp0) REVERT: K 240 PHE cc_start: 0.6033 (OUTLIER) cc_final: 0.4988 (t80) outliers start: 144 outliers final: 79 residues processed: 456 average time/residue: 1.0872 time to fit residues: 582.5992 Evaluate side-chains 414 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 324 time to evaluate : 1.815 ------------------------------------------------------------------------------- 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 135 ASP Chi-restraints excluded: chain A residue 163 MET 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 348 VAL Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 97 ILE 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 226 LEU Chi-restraints excluded: chain C residue 228 GLU 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 46 THR Chi-restraints excluded------------------------------------------------------------------------------- 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 176 GLN ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** 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 176 GLN ** E 306 ASN ** 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 11 HIS J 76 GLN J 174 ASN F 11 HIS F 76 GLN F 174 ASN ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 23126 Z= 0.433 Angle : 0.737 7.251 31291 Z= 0.391 Chirality : 0.048 0.177 3207 Planarity : 0.006 0.064 3731 Dihedral : 21.833 178.754 4180 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 48.59 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.50 % Favored : 92.26 % Rotamer: Outliers : 9.14 % Allowed : 24.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2559 helix: 0.81 (0.15), residues: 1185 sheet: 0.10 (0.27), residues: 390 loop : -1.38 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP F 231 HIS 0.009 0.002 HIS A 48 PHE 0.030 0.002 PHE F 31 TYR 0.033 0.003 TYR B 83 ARG 0.034 0.001 ARG B 242 *********************** 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 528 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 328 time to evaluate : 2.224 Fit side-chains TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 100 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7832 (ttp-110) REVERT: A 163 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7462 (ttp) REVERT: A 299 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6662 (tmt-80) REVERT: A 400 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7755 (ptt-90) REVERT: B 68 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7403 (mp) REVERT: B 83 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.6505 (m-10) REVERT: B 160 ASN cc_start: 0.7280 (OUTLIER) cc_final: 0.6906 (m-40) REVERT: B 237 TRP cc_start: 0.5875 (t60) cc_final: 0.5502 (t60) REVERT: C 228 GLU cc_start: 0.5422 (OUTLIER) cc_final: 0.4849 (mp0) REVERT: C 240 PHE cc_start: 0.5970 (OUTLIER) cc_final: 0.4998 (t80) REVERT: E 89 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8206 (tp) REVERT: E 120 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7376 (mmpt) REVERT: E 163 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7630 (ttp) REVERT: E 360 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7249 (ptp90) REVERT: I 120 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7223 (mmmt) REVERT: I 163 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7708 (ttp) REVERT: I 299 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6760 (tmt-80) REVERT: I 318 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.6027 (t80) REVERT: I 400 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7184 (ptt-90) REVERT: F 68 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7455 (mp) REVERT: F 83 TYR cc_start: 0.7099 (OUTLIER) cc_final: 0.6334 (m-10) REVERT: F 237 TRP cc_start: 0.5879 (t60) cc_final: 0.5646 (t60) REVERT: G 49 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6782 (pmtt) REVERT: G 146 TYR cc_start: 0.6050 (t80) cc_final: 0.5292 (t80) REVERT: G 227 ASN cc_start: 0.4076 (OUTLIER) cc_final: 0.3658 (p0) REVERT: G 228 GLU cc_start: 0.5645 (OUTLIER) cc_final: 0.5229 (mp0) REVERT: G 240 PHE cc_start: 0.6035 (OUTLIER) cc_final: 0.4923 (t80) REVERT: K 146 TYR cc_start: 0.6049 (t80) cc_final: 0.5394 (t80) REVERT: K 226 LEU cc_start: 0.5089 (OUTLIER) cc_final: 0.4752 (tp) REVERT: K 240 PHE cc_start: 0.6033 (OUTLIER) cc_final: 0.5150 (t80) REVERT: K 278 LEU cc_start: 0.5658 (OUTLIER) cc_final: 0.5390 (mp) outliers start: 200 outliers final: 114 residues processed: 478 average time/residue: 1.0585 time to fit residues: 593.8172 Evaluate side-chains 463 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 322 time to evaluate : 2.400 ------------------------------------------------------------------------------- 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 75 GLU Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 160 ASN 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 57 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 THR 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 226 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 265 THR 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 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 299 ARG 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 E residue 395 ASP Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain I residue 135 ASP Chi-restraints excluded: chain I residue 163 MET Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 213 ILE 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 299 ARG Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 395 ASP Chi-restraints excluded: chain I residue 400 ARG Chi-restraints excluded: chain I residue 401 GLN Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 87 TRP Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 138 SER 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 G residue 49 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 103 THR 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 218 PHE Chi-restraints excluded: chain G residue 227 ASN Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 265 THR 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 57 ILE Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 103 THR 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 240 PHE Chi-restraints excluded: chain K residue 265 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 10.0000 chunk 221 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 176 GLN B 11 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN I 176 GLN J 11 HIS F 11 HIS F 76 GLN F 174 ASN ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23126 Z= 0.229 Angle : 0.549 5.479 31291 Z= 0.290 Chirality : 0.042 0.148 3207 Planarity : 0.004 0.048 3731 Dihedral : 20.494 167.476 4176 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 46.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.65 % Favored : 95.15 % Rotamer: Outliers : 7.41 % Allowed : 26.66 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2559 helix: 1.30 (0.15), residues: 1190 sheet: 0.09 (0.26), residues: 393 loop : -1.23 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 231 HIS 0.003 0.001 HIS A 139 PHE 0.021 0.001 PHE F 31 TYR 0.016 0.001 TYR B 196 ARG 0.003 0.000 ARG I 100 *********************** 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 492 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 330 time to evaluate : 2.376 Fit side-chains TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 120 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7491 (mptp) REVERT: A 163 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7472 (ttp) REVERT: A 400 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7741 (ptt-90) REVERT: B 83 TYR cc_start: 0.6645 (m-80) cc_final: 0.6167 (m-10) REVERT: B 160 ASN cc_start: 0.7281 (OUTLIER) cc_final: 0.6900 (m-40) REVERT: B 237 TRP cc_start: 0.5840 (t60) cc_final: 0.5532 (t60) REVERT: C 228 GLU cc_start: 0.5270 (OUTLIER) cc_final: 0.4829 (mp0) REVERT: E 89 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8217 (tp) REVERT: E 163 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7664 (ttp) REVERT: E 251 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6478 (ttt) REVERT: E 360 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7174 (ptp90) REVERT: I 163 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7560 (ttp) REVERT: J 206 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.5935 (ptm160) REVERT: F 68 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7488 (mp) REVERT: F 227 ILE cc_start: 0.8049 (mm) cc_final: 0.7822 (mp) REVERT: F 237 TRP cc_start: 0.5862 (t60) cc_final: 0.5539 (t60) REVERT: K 146 TYR cc_start: 0.6194 (t80) cc_final: 0.5537 (t80) REVERT: K 240 PHE cc_start: 0.6029 (OUTLIER) cc_final: 0.5222 (t80) outliers start: 162 outliers final: 104 residues processed: 449 average time/residue: 1.0197 time to fit residues: 536.7076 Evaluate side-chains 434 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 317 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 87 TRP 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 160 ASN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 174 ASN 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 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 164 VAL 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 226 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 265 THR 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 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 170 VAL 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 348 VAL Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 135 ASP Chi-restraints excluded: chain I residue 163 MET Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 206 TRP Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 246 ILE Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 ASP Chi-restraints excluded: chain I residue 401 GLN Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain J residue 87 TRP Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 174 ASN Chi-restraints excluded: chain J residue 206 ARG Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 87 TRP 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 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 214 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 265 THR 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 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 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 265 THR Chi-restraints excluded: chain K residue 268 SER 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 237 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 176 GLN ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 HIS ** B 103 ASN ** 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 176 GLN ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN ** I 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 HIS ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 ASN F 11 HIS F 174 ASN ** K 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 23126 Z= 0.571 Angle : 0.809 7.892 31291 Z= 0.434 Chirality : 0.051 0.189 3207 Planarity : 0.006 0.074 3731 Dihedral : 20.400 159.759 4173 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 49.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.01 % Favored : 91.75 % Rotamer: Outliers : 9.92 % Allowed : 24.69 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2559 helix: 0.59 (0.15), residues: 1158 sheet: -0.28 (0.26), residues: 390 loop : -1.58 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP F 231 HIS 0.007 0.002 HIS E 48 PHE 0.033 0.003 PHE B 31 TYR 0.034 0.003 TYR B 83 ARG 0.007 0.001 ARG B 58 *********************** 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 560 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 343 time to evaluate : 2.346 Fit side-chains TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 120 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7560 (mptp) REVERT: A 318 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7655 (t80) REVERT: A 400 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7690 (ptt-90) REVERT: B 160 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.6955 (m-40) REVERT: B 237 TRP cc_start: 0.5871 (t60) cc_final: 0.5537 (t60) REVERT: C 126 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: C 223 ASN cc_start: 0.4491 (OUTLIER) cc_final: 0.4096 (t0) REVERT: C 228 GLU cc_start: 0.5529 (OUTLIER) cc_final: 0.4945 (mp0) REVERT: E 89 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8220 (tp) REVERT: E 120 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7368 (mmpt) REVERT: E 163 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7779 (ttp) REVERT: E 251 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6534 (ttt) REVERT: E 318 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.6220 (t80) REVERT: E 360 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7304 (ptp90) REVERT: I 163 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7783 (ttp) REVERT: J 81 GLU cc_start: 0.7729 (tp30) cc_final: 0.7153 (tp30) REVERT: J 83 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6523 (m-10) REVERT: J 206 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6257 (ptm160) REVERT: F 68 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7429 (mp) REVERT: F 160 ASN cc_start: 0.7313 (OUTLIER) cc_final: 0.6898 (m110) REVERT: F 227 ILE cc_start: 0.8125 (mm) cc_final: 0.7896 (mp) REVERT: G 146 TYR cc_start: 0.6039 (t80) cc_final: 0.5208 (t80) REVERT: K 126 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: K 146 TYR cc_start: 0.6016 (t80) cc_final: 0.5296 (t80) REVERT: K 226 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.4867 (tp) REVERT: K 240 PHE cc_start: 0.6087 (OUTLIER) cc_final: 0.5409 (t80) outliers start: 217 outliers final: 124 residues processed: 512 average time/residue: 1.0086 time to fit residues: 612.3257 Evaluate side-chains 480 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 335 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 256 SER 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 395 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 87 TRP 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 160 ASN 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 57 ILE Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 126 GLU 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 164 VAL 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 232 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 265 THR 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 64 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 213 ILE 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 299 ARG Chi-restraints excluded: chain E residue 318 TYR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 135 ASP Chi-restraints excluded: chain I residue 163 MET Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 ASP Chi-restraints excluded: chain I residue 400 ARG Chi-restraints excluded: chain I residue 401 GLN Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 83 TYR Chi-restraints excluded: chain J residue 87 TRP 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 164 ILE Chi-restraints excluded: chain J residue 174 ASN Chi-restraints excluded: chain J residue 206 ARG Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 87 TRP 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 160 ASN 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 52 THR Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 143 TRP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 164 VAL 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 263 THR Chi-restraints excluded: chain G residue 265 THR 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 57 ILE Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 143 TRP 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 240 PHE Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 22 optimal weight: 0.0470 chunk 193 optimal weight: 0.5980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: