Starting phenix.real_space_refine on Sat Feb 24 19:08:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oyi_17287/02_2024/8oyi_17287_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oyi_17287/02_2024/8oyi_17287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oyi_17287/02_2024/8oyi_17287.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oyi_17287/02_2024/8oyi_17287.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oyi_17287/02_2024/8oyi_17287_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oyi_17287/02_2024/8oyi_17287_trim_updated.pdb" } resolution = 2.19 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= 0.003 sd= 0.033 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 20898 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: 7 Type Number sf(0) Gaussians Cu 9 5.60 5 P 36 5.49 5 S 93 5.16 5 C 15036 2.51 5 N 3417 2.21 5 O 4249 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 406": "OD1" <-> "OD2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "K GLU 228": "OE1" <-> "OE2" Residue "K GLU 237": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22849 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: "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: "J" 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: "E" 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: "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: "G" 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: "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: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 242 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 279 Unusual residues: {' CU': 1, 'D10': 1, 'ETF': 1, 'HXG': 2, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "F" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 242 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "J" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 242 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: "G" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 279 Unusual residues: {' CU': 1, 'D10': 1, 'ETF': 1, 'HXG': 2, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "K" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 279 Unusual residues: {' CU': 1, 'D10': 1, 'ETF': 1, 'HXG': 2, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "I" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "K" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 12.16, per 1000 atoms: 0.53 Number of scatterers: 22849 At special positions: 0 Unit cell: (107.407, 106.878, 119.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cu 9 28.99 S 93 16.00 P 36 15.00 F 9 9.00 O 4249 8.00 N 3417 7.00 C 15036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=0, symmetry=0 Time building additional restraints: 10.51 Conformation dependent library (CDL) restraints added in 3.7 seconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 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: 81 helices and 24 sheets defined 47.5% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 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 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.631A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 44 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 59 through 83 Proline residue: B 65 - end of helix removed outlier: 4.442A pdb=" N THR B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Proline residue: B 72 - end of helix removed outlier: 3.956A 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 Processing helix chain 'B' and resid 141 through 168 removed outlier: 4.110A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.064A 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 238 removed outlier: 3.764A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 72 removed outlier: 3.906A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 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 162 Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 208 through 232 Proline residue: C 217 - end of helix removed outlier: 3.580A pdb=" N ILE C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Proline residue: C 222 - end of helix removed outlier: 4.663A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 269 removed outlier: 4.984A pdb=" N GLY C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE C 250 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 251 " --> pdb=" O PHE C 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 44 Processing helix chain 'F' and resid 46 through 50 Processing helix chain 'F' and resid 59 through 83 Proline residue: F 65 - end of helix removed outlier: 4.441A pdb=" N THR F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix removed outlier: 3.958A 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 Processing helix chain 'F' and resid 141 through 168 removed outlier: 4.109A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 5.064A 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 238 removed outlier: 3.764A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 44 Processing helix chain 'J' and resid 46 through 50 Processing helix chain 'J' and resid 59 through 83 Proline residue: J 65 - end of helix removed outlier: 4.442A pdb=" N THR J 70 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE J 71 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Proline residue: J 72 - end of helix removed outlier: 3.959A 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 Processing helix chain 'J' and resid 141 through 168 removed outlier: 4.110A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) removed outlier: 5.064A 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 238 removed outlier: 3.763A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (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 Processing helix chain 'E' and resid 377 through 381 removed outlier: 3.631A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (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 Processing helix chain 'I' and resid 377 through 381 removed outlier: 3.632A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 72 removed outlier: 3.906A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 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 162 Processing helix chain 'G' and resid 171 through 176 Processing helix chain 'G' and resid 182 through 198 Processing helix chain 'G' and resid 208 through 232 Proline residue: G 217 - end of helix removed outlier: 3.580A pdb=" N ILE G 220 " --> pdb=" O GLY G 216 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Proline residue: G 222 - end of helix removed outlier: 4.662A pdb=" N GLY G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU G 226 " --> pdb=" O PRO G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 269 removed outlier: 4.983A pdb=" N GLY G 247 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE G 250 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE G 251 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 72 removed outlier: 3.906A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 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 162 Processing helix chain 'K' and resid 171 through 176 Processing helix chain 'K' and resid 182 through 198 Processing helix chain 'K' and resid 208 through 232 Proline residue: K 217 - end of helix removed outlier: 3.579A pdb=" N ILE K 220 " --> pdb=" O GLY K 216 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Proline residue: K 222 - end of helix removed outlier: 4.663A pdb=" N GLY K 225 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU K 226 " --> pdb=" O PRO K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 269 removed outlier: 4.984A pdb=" N GLY K 247 " --> pdb=" O LEU K 244 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE K 250 " --> pdb=" O GLY K 247 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE K 251 " --> pdb=" O PHE K 248 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.730A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.744A 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: 8.377A pdb=" N VAL A 59 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR A 158 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 141 through 144 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 removed outlier: 6.453A pdb=" N ILE A 410 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.554A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.449A 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 'F' and resid 170 through 173 Processing sheet with id= J, first strand: chain 'J' and resid 170 through 173 Processing sheet with id= K, first strand: chain 'E' and resid 47 through 50 removed outlier: 6.731A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 58 through 60 removed outlier: 8.378A pdb=" N VAL E 59 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR E 158 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 141 through 144 Processing sheet with id= N, first strand: chain 'E' and resid 169 through 171 Processing sheet with id= O, first strand: chain 'E' and resid 282 through 286 Processing sheet with id= P, first strand: chain 'E' and resid 298 through 300 removed outlier: 6.452A pdb=" N ILE E 410 " --> pdb=" O TYR E 291 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 323 through 325 removed outlier: 6.554A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU E 390 " --> pdb=" O PHE E 317 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 47 through 50 removed outlier: 6.729A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 58 through 60 removed outlier: 8.377A pdb=" N VAL I 59 " --> pdb=" O TRP I 156 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR I 158 " --> pdb=" O VAL I 59 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 141 through 144 Processing sheet with id= U, first strand: chain 'I' and resid 169 through 171 Processing sheet with id= V, first strand: chain 'I' and resid 282 through 286 Processing sheet with id= W, first strand: chain 'I' and resid 298 through 300 removed outlier: 6.454A pdb=" N ILE I 410 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 323 through 325 removed outlier: 6.554A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU I 390 " --> pdb=" O PHE I 317 " (cutoff:3.500A) 1008 hydrogen bonds defined for protein. 2781 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: 7.85 Time building geometry restraints manager: 10.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3350 1.32 - 1.44: 6774 1.44 - 1.57: 12699 1.57 - 1.69: 139 1.69 - 1.81: 180 Bond restraints: 23142 Sorted by residual: bond pdb=" CB PLC C 302 " pdb=" O3 PLC C 302 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" CB PLC G 302 " pdb=" O3 PLC G 302 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" CB PLC K 302 " pdb=" O3 PLC K 302 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" C9 P1O B 307 " pdb=" O5 P1O B 307 " ideal model delta sigma weight residual 1.331 1.456 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CB PLC F 301 " pdb=" O3 PLC F 301 " ideal model delta sigma weight residual 1.327 1.452 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 23137 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.83: 586 105.83 - 113.01: 12405 113.01 - 120.18: 8573 120.18 - 127.35: 9362 127.35 - 134.52: 388 Bond angle restraints: 31314 Sorted by residual: angle pdb=" N HIS C 231 " pdb=" CA HIS C 231 " pdb=" C HIS C 231 " ideal model delta sigma weight residual 112.12 104.45 7.67 1.34e+00 5.57e-01 3.27e+01 angle pdb=" N HIS G 231 " pdb=" CA HIS G 231 " pdb=" C HIS G 231 " ideal model delta sigma weight residual 112.12 104.46 7.66 1.34e+00 5.57e-01 3.27e+01 angle pdb=" N HIS K 231 " pdb=" CA HIS K 231 " pdb=" C HIS K 231 " ideal model delta sigma weight residual 112.12 104.47 7.65 1.34e+00 5.57e-01 3.26e+01 angle pdb=" C PHE K 177 " pdb=" CA PHE K 177 " pdb=" CB PHE K 177 " ideal model delta sigma weight residual 110.79 101.36 9.43 1.66e+00 3.63e-01 3.23e+01 angle pdb=" C PHE C 177 " pdb=" CA PHE C 177 " pdb=" CB PHE C 177 " ideal model delta sigma weight residual 110.79 101.40 9.39 1.66e+00 3.63e-01 3.20e+01 ... (remaining 31309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 12602 34.43 - 68.86: 799 68.86 - 103.29: 99 103.29 - 137.73: 36 137.73 - 172.16: 12 Dihedral angle restraints: 13548 sinusoidal: 6096 harmonic: 7452 Sorted by residual: dihedral pdb=" O2 PLC F 301 " pdb=" C1 PLC F 301 " pdb=" C2 PLC F 301 " pdb=" O3P PLC F 301 " ideal model delta sinusoidal sigma weight residual -55.71 116.45 -172.16 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O2 PLC J 308 " pdb=" C1 PLC J 308 " pdb=" C2 PLC J 308 " pdb=" O3P PLC J 308 " ideal model delta sinusoidal sigma weight residual -55.71 116.44 -172.15 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O2 PLC B 308 " pdb=" C1 PLC B 308 " pdb=" C2 PLC B 308 " pdb=" O3P PLC B 308 " ideal model delta sinusoidal sigma weight residual -55.71 116.41 -172.12 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 13545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2371 0.052 - 0.103: 633 0.103 - 0.155: 142 0.155 - 0.207: 40 0.207 - 0.258: 21 Chirality restraints: 3207 Sorted by residual: chirality pdb=" CA HIS K 173 " pdb=" N HIS K 173 " pdb=" C HIS K 173 " pdb=" CB HIS K 173 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA HIS C 173 " pdb=" N HIS C 173 " pdb=" C HIS C 173 " pdb=" CB HIS C 173 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA HIS G 173 " pdb=" N HIS G 173 " pdb=" C HIS G 173 " pdb=" CB HIS G 173 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 3204 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS K 245 " 0.027 2.00e-02 2.50e+03 3.57e-02 1.91e+01 pdb=" CG HIS K 245 " 0.004 2.00e-02 2.50e+03 pdb=" ND1 HIS K 245 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS K 245 " -0.057 2.00e-02 2.50e+03 pdb=" CE1 HIS K 245 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS K 245 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 245 " 0.027 2.00e-02 2.50e+03 3.56e-02 1.90e+01 pdb=" CG HIS G 245 " 0.004 2.00e-02 2.50e+03 pdb=" ND1 HIS G 245 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS G 245 " -0.057 2.00e-02 2.50e+03 pdb=" CE1 HIS G 245 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS G 245 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 245 " -0.027 2.00e-02 2.50e+03 3.55e-02 1.90e+01 pdb=" CG HIS C 245 " -0.004 2.00e-02 2.50e+03 pdb=" ND1 HIS C 245 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS C 245 " 0.057 2.00e-02 2.50e+03 pdb=" CE1 HIS C 245 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS C 245 " -0.055 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 248 2.55 - 3.13: 18451 3.13 - 3.72: 40064 3.72 - 4.31: 59776 4.31 - 4.90: 95105 Nonbonded interactions: 213644 Sorted by model distance: nonbonded pdb=" NE2 HIS C 245 " pdb="CU CU C 301 " model vdw 1.958 2.320 nonbonded pdb=" NE2 HIS K 245 " pdb="CU CU K 301 " model vdw 1.958 2.320 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 301 " model vdw 1.959 2.320 nonbonded pdb=" ND1 HIS I 33 " pdb="CU CU I 502 " model vdw 1.967 2.320 nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU A 501 " model vdw 1.967 2.320 ... (remaining 213639 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' and (resid 33 through 414 or resid 502)) selection = (chain 'E' and (resid 33 through 414 or resid 502)) selection = (chain 'I' and (resid 33 through 414 or resid 502)) } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 305 through 306)) selection = (chain 'F' and (resid 7 through 247 or resid 305 through 306)) selection = (chain 'J' and (resid 7 through 247 or resid 305 through 306)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.020 Extract box with map and model: 27.740 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 62.200 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.190 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:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 0.009 0.126 23142 Z= 0.523 Angle : 1.051 10.641 31314 Z= 0.529 Chirality : 0.054 0.258 3207 Planarity : 0.005 0.036 3732 Dihedral : 22.696 172.158 8790 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.82 % Allowed : 5.55 % Favored : 93.63 % Rotamer: Outliers : 4.53 % Allowed : 17.19 % Favored : 78.28 % Cbeta Deviations : 0.13 % 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: 0.59 (0.17), residues: 2559 helix: 0.98 (0.15), residues: 1203 sheet: 1.30 (0.28), residues: 357 loop : -0.62 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 202 HIS 0.046 0.004 HIS K 245 PHE 0.053 0.002 PHE K 248 TYR 0.040 0.002 TYR G 178 ARG 0.005 0.001 ARG E 375 *********************** REFINEMENT MACRO_CYCLE 1 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 487 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 388 time to evaluate : 2.479 Fit side-chains REVERT: B 39 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8062 (tp) REVERT: C 57 ILE cc_start: 0.8272 (tp) cc_final: 0.7985 (tp) REVERT: C 240 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: F 39 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8134 (tp) REVERT: G 57 ILE cc_start: 0.8299 (tp) cc_final: 0.8097 (tp) REVERT: G 74 TRP cc_start: 0.6111 (OUTLIER) cc_final: 0.5888 (m-90) REVERT: G 240 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.6738 (m-80) REVERT: K 240 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.6994 (m-80) outliers start: 99 outliers final: 27 residues processed: 459 average time/residue: 1.4576 time to fit residues: 758.8867 Evaluate side-chains 301 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 268 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 207 SER Chi-restraints excluded: chain K residue 231 HIS Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 B 16 GLN F 187 ASN J 240 ASN E 38 GLN E 108 GLN E 168 ASN E 176 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23142 Z= 0.280 Angle : 0.675 9.556 31314 Z= 0.344 Chirality : 0.048 0.301 3207 Planarity : 0.005 0.041 3732 Dihedral : 22.323 175.019 4208 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.53 % Favored : 95.15 % Rotamer: Outliers : 4.66 % Allowed : 16.14 % Favored : 79.20 % 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: 0.92 (0.14), residues: 1218 sheet: 1.17 (0.27), residues: 354 loop : -0.46 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 206 HIS 0.005 0.001 HIS A 192 PHE 0.019 0.002 PHE K 177 TYR 0.015 0.002 TYR K 184 ARG 0.005 0.001 ARG F 57 *********************** 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 364 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 262 time to evaluate : 2.431 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8358 (mtm180) REVERT: B 39 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8169 (tp) REVERT: C 154 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: C 196 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8026 (tttm) REVERT: E 45 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.6374 (mtp85) REVERT: E 112 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8442 (mtt180) REVERT: E 276 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6662 (mt-10) REVERT: I 112 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8359 (mtm180) REVERT: I 316 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7625 (tm-30) REVERT: I 344 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.7220 (m-30) REVERT: G 154 GLU cc_start: 0.7602 (tt0) cc_final: 0.7254 (tp30) REVERT: G 240 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7066 (m-80) REVERT: K 101 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8277 (mp) outliers start: 102 outliers final: 41 residues processed: 337 average time/residue: 1.4774 time to fit residues: 564.2550 Evaluate side-chains 298 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 245 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 344 ASP Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 231 optimal weight: 0.5980 chunk 250 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN F 187 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN E 176 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23142 Z= 0.311 Angle : 0.656 6.424 31314 Z= 0.342 Chirality : 0.048 0.230 3207 Planarity : 0.005 0.044 3732 Dihedral : 21.163 179.138 4186 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.77 % Favored : 95.00 % Rotamer: Outliers : 4.80 % Allowed : 16.46 % Favored : 78.74 % 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: 0.43 (0.16), residues: 2559 helix: 0.78 (0.14), residues: 1224 sheet: 1.00 (0.27), residues: 354 loop : -0.50 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 206 HIS 0.006 0.001 HIS A 192 PHE 0.018 0.002 PHE J 31 TYR 0.018 0.002 TYR K 184 ARG 0.006 0.001 ARG C 115 *********************** 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 359 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 254 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8501 (mtt180) REVERT: A 163 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.6885 (ttt) REVERT: B 22 ASP cc_start: 0.7899 (m-30) cc_final: 0.7659 (m-30) REVERT: B 39 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8147 (tp) REVERT: E 112 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8484 (mtt180) REVERT: E 276 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6811 (mt-10) REVERT: E 404 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6920 (tt0) REVERT: I 45 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.6347 (mtp85) REVERT: I 112 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8429 (mtt180) REVERT: I 227 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.5837 (mp) REVERT: I 292 ARG cc_start: 0.7351 (mtp85) cc_final: 0.6986 (mtp85) REVERT: I 316 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: G 154 GLU cc_start: 0.7608 (tt0) cc_final: 0.7136 (tp30) REVERT: G 196 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8126 (tttm) REVERT: K 101 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8221 (mp) REVERT: K 196 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8499 (tttm) outliers start: 105 outliers final: 37 residues processed: 326 average time/residue: 1.5264 time to fit residues: 561.5859 Evaluate side-chains 288 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 238 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 196 LYS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 196 LYS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 232 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 220 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN E 108 GLN E 176 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23142 Z= 0.232 Angle : 0.604 6.724 31314 Z= 0.313 Chirality : 0.046 0.227 3207 Planarity : 0.005 0.043 3732 Dihedral : 20.505 179.738 4176 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.85 % Favored : 94.92 % Rotamer: Outliers : 4.89 % Allowed : 16.64 % Favored : 78.46 % 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: 0.45 (0.16), residues: 2559 helix: 0.83 (0.14), residues: 1224 sheet: 0.63 (0.27), residues: 375 loop : -0.39 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 206 HIS 0.004 0.001 HIS A 192 PHE 0.017 0.002 PHE J 31 TYR 0.017 0.002 TYR K 184 ARG 0.005 0.000 ARG A 313 *********************** 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 352 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 245 time to evaluate : 2.582 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.6214 (mtp85) REVERT: A 112 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8429 (mtt180) REVERT: A 163 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.6875 (ttt) REVERT: A 331 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7799 (mtmm) REVERT: B 22 ASP cc_start: 0.7835 (m-30) cc_final: 0.7620 (m-30) REVERT: C 196 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7835 (tttm) REVERT: J 47 ASP cc_start: 0.7709 (m-30) cc_final: 0.7477 (m-30) REVERT: J 198 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8085 (ttp-170) REVERT: J 201 GLU cc_start: 0.8016 (tt0) cc_final: 0.7790 (tt0) REVERT: E 145 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.6723 (tp40) REVERT: E 276 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6725 (mt-10) REVERT: I 112 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8354 (mtm180) REVERT: I 209 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.6083 (mtp85) REVERT: I 227 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.5680 (mp) REVERT: I 292 ARG cc_start: 0.7323 (mtp85) cc_final: 0.6951 (mtp85) REVERT: I 316 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: I 344 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: G 101 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8397 (mp) REVERT: G 154 GLU cc_start: 0.7509 (tt0) cc_final: 0.7085 (tp30) REVERT: G 196 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.7791 (tttm) REVERT: G 240 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7160 (m-80) REVERT: K 101 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8219 (mp) outliers start: 107 outliers final: 40 residues processed: 321 average time/residue: 1.5873 time to fit residues: 573.1361 Evaluate side-chains 293 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 236 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 209 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 344 ASP Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 196 LYS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 chunk 221 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN C 155 GLN E 108 GLN E 176 GLN I 176 GLN K 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23142 Z= 0.196 Angle : 0.579 10.357 31314 Z= 0.298 Chirality : 0.045 0.217 3207 Planarity : 0.004 0.043 3732 Dihedral : 19.724 175.593 4174 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.57 % Favored : 95.19 % Rotamer: Outliers : 3.80 % Allowed : 17.83 % Favored : 78.37 % 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: 0.54 (0.16), residues: 2559 helix: 0.84 (0.14), residues: 1236 sheet: 0.69 (0.25), residues: 396 loop : -0.30 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 206 HIS 0.003 0.001 HIS J 11 PHE 0.016 0.001 PHE F 31 TYR 0.017 0.001 TYR K 184 ARG 0.003 0.000 ARG J 57 *********************** 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 329 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 246 time to evaluate : 2.841 Fit side-chains REVERT: A 45 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.6162 (mtp85) REVERT: A 112 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8407 (mtt180) REVERT: B 22 ASP cc_start: 0.7795 (m-30) cc_final: 0.7585 (m-30) REVERT: C 101 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8274 (mp) REVERT: C 196 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.7808 (tttm) REVERT: J 47 ASP cc_start: 0.7687 (m-30) cc_final: 0.7448 (m-30) REVERT: J 198 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7989 (ttp-170) REVERT: J 201 GLU cc_start: 0.8010 (tt0) cc_final: 0.7782 (tt0) REVERT: E 45 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.6189 (mtp85) REVERT: E 276 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6694 (mt-10) REVERT: I 45 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.6160 (mtp85) REVERT: I 209 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.6099 (mtp85) REVERT: I 292 ARG cc_start: 0.7307 (mtp85) cc_final: 0.6928 (mtp85) REVERT: I 316 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: G 101 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8402 (mp) REVERT: G 196 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7760 (tttm) REVERT: G 240 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: K 101 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8202 (mp) outliers start: 83 outliers final: 35 residues processed: 307 average time/residue: 1.5324 time to fit residues: 532.6198 Evaluate side-chains 283 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 234 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 209 ARG Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 196 LYS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 246 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN G 155 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23142 Z= 0.310 Angle : 0.637 8.660 31314 Z= 0.332 Chirality : 0.048 0.218 3207 Planarity : 0.005 0.044 3732 Dihedral : 19.728 173.261 4174 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.65 % Favored : 95.12 % Rotamer: Outliers : 4.12 % Allowed : 17.56 % Favored : 78.33 % 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: 0.43 (0.16), residues: 2559 helix: 0.76 (0.14), residues: 1224 sheet: 0.92 (0.27), residues: 351 loop : -0.44 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 206 HIS 0.006 0.001 HIS A 192 PHE 0.019 0.002 PHE F 31 TYR 0.019 0.002 TYR J 188 ARG 0.005 0.001 ARG B 57 *********************** 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 328 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 238 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.6335 (mtp85) REVERT: A 112 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8494 (mtt180) REVERT: A 145 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.6608 (tp40) REVERT: A 331 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7784 (mtmm) REVERT: B 22 ASP cc_start: 0.7850 (m-30) cc_final: 0.7635 (m-30) REVERT: C 101 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8237 (mp) REVERT: C 196 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7837 (tttm) REVERT: J 47 ASP cc_start: 0.7685 (m-30) cc_final: 0.7450 (m-30) REVERT: J 198 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8069 (ttp-170) REVERT: J 201 GLU cc_start: 0.8039 (tt0) cc_final: 0.7807 (tt0) REVERT: E 112 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8525 (mtt180) REVERT: E 145 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: I 45 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6348 (mtp85) REVERT: I 209 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.6197 (mtp85) REVERT: I 292 ARG cc_start: 0.7316 (mtp85) cc_final: 0.6930 (mtp85) REVERT: I 316 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: I 406 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7118 (p0) REVERT: G 101 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8400 (mp) REVERT: G 196 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.7948 (tttm) REVERT: G 240 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7216 (m-80) REVERT: K 101 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8211 (mp) REVERT: K 196 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.7733 (ttmm) outliers start: 90 outliers final: 46 residues processed: 311 average time/residue: 1.4981 time to fit residues: 527.2555 Evaluate side-chains 299 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 235 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 209 ARG Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 196 LYS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 196 LYS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 140 optimal weight: 0.4980 chunk 180 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 245 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN E 108 GLN E 176 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23142 Z= 0.244 Angle : 0.606 10.910 31314 Z= 0.314 Chirality : 0.046 0.203 3207 Planarity : 0.005 0.044 3732 Dihedral : 19.416 169.850 4174 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.57 % Favored : 95.19 % Rotamer: Outliers : 3.98 % Allowed : 17.74 % Favored : 78.28 % 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: 0.49 (0.16), residues: 2559 helix: 0.80 (0.14), residues: 1227 sheet: 1.03 (0.28), residues: 321 loop : -0.39 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 206 HIS 0.004 0.001 HIS E 192 PHE 0.017 0.002 PHE J 31 TYR 0.017 0.002 TYR K 184 ARG 0.004 0.000 ARG B 57 *********************** 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 327 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 240 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.6236 (mtp85) REVERT: A 112 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8446 (mtt180) REVERT: A 145 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.6613 (tp40) REVERT: A 163 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.5985 (tpt) REVERT: A 331 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7782 (mtmm) REVERT: B 22 ASP cc_start: 0.7823 (m-30) cc_final: 0.7596 (m-30) REVERT: C 101 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8219 (mp) REVERT: F 22 ASP cc_start: 0.7705 (m-30) cc_final: 0.7472 (m-30) REVERT: J 47 ASP cc_start: 0.7705 (m-30) cc_final: 0.7458 (m-30) REVERT: J 198 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8097 (ttp-170) REVERT: J 201 GLU cc_start: 0.8022 (tt0) cc_final: 0.7788 (tt0) REVERT: E 112 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8500 (mtt180) REVERT: I 112 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8426 (mtt180) REVERT: I 209 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.6168 (mtp85) REVERT: I 292 ARG cc_start: 0.7301 (mtp85) cc_final: 0.6907 (mtp85) REVERT: I 316 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: I 344 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: G 101 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8427 (mp) REVERT: G 196 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.7775 (tttm) REVERT: G 240 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7228 (m-80) REVERT: K 101 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8218 (mp) outliers start: 87 outliers final: 45 residues processed: 308 average time/residue: 1.5393 time to fit residues: 542.7919 Evaluate side-chains 294 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 233 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 209 ARG Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 344 ASP Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 196 LYS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 22 optimal weight: 0.0470 chunk 193 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN C 155 GLN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN I 176 GLN G 155 GLN K 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23142 Z= 0.169 Angle : 0.572 11.657 31314 Z= 0.293 Chirality : 0.044 0.188 3207 Planarity : 0.004 0.042 3732 Dihedral : 18.967 167.341 4174 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.53 % Favored : 95.23 % Rotamer: Outliers : 3.16 % Allowed : 18.52 % Favored : 78.33 % 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 (0.16), residues: 2559 helix: 0.89 (0.14), residues: 1230 sheet: 0.76 (0.26), residues: 366 loop : -0.28 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 206 HIS 0.002 0.001 HIS I 139 PHE 0.015 0.001 PHE J 31 TYR 0.017 0.001 TYR K 184 ARG 0.004 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 241 time to evaluate : 2.697 Fit side-chains REVERT: A 45 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.6115 (mtp85) REVERT: A 331 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7750 (mtmm) REVERT: B 22 ASP cc_start: 0.7750 (m-30) cc_final: 0.7511 (m-30) REVERT: C 57 ILE cc_start: 0.8480 (tp) cc_final: 0.8196 (tp) REVERT: C 101 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8254 (mp) REVERT: J 47 ASP cc_start: 0.7707 (m-30) cc_final: 0.7460 (m-30) REVERT: J 198 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8127 (ttp-170) REVERT: J 201 GLU cc_start: 0.8004 (tt0) cc_final: 0.7774 (tt0) REVERT: E 45 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.6169 (mtp85) REVERT: I 45 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.6166 (mtp85) REVERT: I 112 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8379 (mtt180) REVERT: I 292 ARG cc_start: 0.7265 (mtp85) cc_final: 0.6870 (mtp85) REVERT: I 316 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: I 406 ASP cc_start: 0.7233 (p0) cc_final: 0.7014 (p0) REVERT: G 101 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8411 (mp) REVERT: G 196 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.7680 (tttm) REVERT: G 240 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7271 (m-80) REVERT: K 101 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8204 (mp) REVERT: K 196 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7748 (tttm) outliers start: 69 outliers final: 34 residues processed: 298 average time/residue: 1.5601 time to fit residues: 524.2336 Evaluate side-chains 279 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 232 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 196 LYS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 196 LYS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 7.9990 chunk 235 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 229 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 216 optimal weight: 0.0470 chunk 228 optimal weight: 6.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- 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 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN E 108 GLN E 176 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23142 Z= 0.327 Angle : 0.649 11.850 31314 Z= 0.338 Chirality : 0.048 0.199 3207 Planarity : 0.005 0.044 3732 Dihedral : 19.151 175.324 4172 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.61 % Favored : 95.15 % Rotamer: Outliers : 3.20 % Allowed : 18.98 % Favored : 77.82 % 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: 0.43 (0.16), residues: 2559 helix: 0.76 (0.14), residues: 1224 sheet: 1.25 (0.29), residues: 294 loop : -0.48 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 206 HIS 0.006 0.001 HIS A 192 PHE 0.019 0.002 PHE F 31 TYR 0.021 0.002 TYR J 188 ARG 0.004 0.001 ARG J 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 232 time to evaluate : 2.627 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.6289 (mtp85) REVERT: A 163 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.5947 (tpt) REVERT: A 331 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7786 (mtmm) REVERT: B 22 ASP cc_start: 0.7846 (m-30) cc_final: 0.7615 (m-30) REVERT: C 101 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8214 (mp) REVERT: J 47 ASP cc_start: 0.7704 (m-30) cc_final: 0.7460 (m-30) REVERT: J 198 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8194 (ttp-170) REVERT: E 112 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8514 (mtt180) REVERT: I 112 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8473 (mtt180) REVERT: I 292 ARG cc_start: 0.7301 (mtp85) cc_final: 0.6901 (mtp85) REVERT: I 316 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: G 101 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8419 (mp) REVERT: G 196 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.7945 (tttm) REVERT: G 240 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: K 101 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8216 (mp) REVERT: K 196 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.7723 (ttmm) outliers start: 70 outliers final: 40 residues processed: 289 average time/residue: 1.5051 time to fit residues: 492.1445 Evaluate side-chains 282 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 229 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 196 LYS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 196 LYS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 0.6980 chunk 242 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 254 optimal weight: 2.9990 chunk 233 optimal weight: 0.7980 chunk 202 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN E 108 GLN E 176 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN K 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23142 Z= 0.254 Angle : 0.618 13.299 31314 Z= 0.319 Chirality : 0.046 0.189 3207 Planarity : 0.005 0.044 3732 Dihedral : 18.934 179.244 4172 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.69 % Favored : 95.08 % Rotamer: Outliers : 2.93 % Allowed : 19.16 % Favored : 77.91 % 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: 0.45 (0.16), residues: 2559 helix: 0.77 (0.14), residues: 1227 sheet: 1.27 (0.29), residues: 294 loop : -0.47 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 206 HIS 0.004 0.001 HIS E 192 PHE 0.017 0.002 PHE F 31 TYR 0.018 0.002 TYR K 184 ARG 0.004 0.000 ARG B 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 234 time to evaluate : 2.529 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.6258 (mtp85) REVERT: A 163 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.5971 (tpt) REVERT: A 331 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7761 (mtmm) REVERT: B 22 ASP cc_start: 0.7826 (m-30) cc_final: 0.7594 (m-30) REVERT: J 47 ASP cc_start: 0.7704 (m-30) cc_final: 0.7451 (m-30) REVERT: J 198 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8154 (ttp-170) REVERT: E 112 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8487 (mtt180) REVERT: I 112 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8445 (mtt180) REVERT: I 292 ARG cc_start: 0.7294 (mtp85) cc_final: 0.6884 (mtp85) REVERT: I 316 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: G 196 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.7766 (tttm) REVERT: G 240 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7228 (m-80) REVERT: K 101 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8229 (mp) REVERT: K 196 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7563 (ttmm) outliers start: 64 outliers final: 36 residues processed: 286 average time/residue: 1.5700 time to fit residues: 506.9175 Evaluate side-chains 280 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 233 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 196 LYS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 196 LYS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 208 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN C 155 GLN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.143206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116402 restraints weight = 24700.001| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.42 r_work: 0.3377 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.227 23142 Z= 0.300 Angle : 0.769 59.174 31314 Z= 0.423 Chirality : 0.048 0.618 3207 Planarity : 0.005 0.044 3732 Dihedral : 18.934 179.255 4172 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.73 % Favored : 95.04 % Rotamer: Outliers : 2.51 % Allowed : 19.34 % Favored : 78.14 % Cbeta Deviations : 0.04 % 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: 0.45 (0.16), residues: 2559 helix: 0.77 (0.14), residues: 1227 sheet: 1.27 (0.29), residues: 294 loop : -0.47 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 206 HIS 0.004 0.001 HIS E 192 PHE 0.017 0.002 PHE F 31 TYR 0.018 0.002 TYR K 184 ARG 0.003 0.000 ARG B 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9305.26 seconds wall clock time: 166 minutes 32.84 seconds (9992.84 seconds total)