Starting phenix.real_space_refine on Mon Mar 25 03:01:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/03_2024/8sr1_40717_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/03_2024/8sr1_40717.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/03_2024/8sr1_40717_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/03_2024/8sr1_40717_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/03_2024/8sr1_40717_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/03_2024/8sr1_40717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/03_2024/8sr1_40717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/03_2024/8sr1_40717_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr1_40717/03_2024/8sr1_40717_trim_updated.pdb" } resolution = 2.18 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= 0.004 sd= 0.036 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 15042 2.51 5 N 3417 2.21 5 O 4248 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 ARG 165": "NH1" <-> "NH2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 165": "NH1" <-> "NH2" Residue "G PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 165": "NH1" <-> "NH2" Residue "K PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22854 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "B" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "E" Number of atoms: 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: "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: "I" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "J" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "G" Number of atoms: 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: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 323 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4, 'WIY': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: "F" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "G" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 323 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4, 'WIY': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "K" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 323 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4, 'WIY': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} 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: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} 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: "J" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "G" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 11.44, per 1000 atoms: 0.50 Number of scatterers: 22854 At special positions: 0 Unit cell: (107.936, 107.936, 120.635, 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 4248 8.00 N 3417 7.00 C 15042 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: 8.25 Conformation dependent library (CDL) restraints added in 3.4 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 47.3% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.71 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: 3.630A 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: 4.441A pdb=" N THR B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Proline residue: B 72 - end of helix removed outlier: 3.958A 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: 5.062A 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 160 Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 180 through 198 Processing helix chain 'C' and resid 208 through 231 Proline residue: C 217 - end of helix removed outlier: 3.579A pdb=" N ILE C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Proline residue: C 222 - end of helix removed outlier: 4.662A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 269 removed outlier: 4.535A pdb=" N GLY C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 248 " --> pdb=" O HIS C 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 250 " --> pdb=" O GLY C 247 " (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: 3.630A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (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: 4.440A pdb=" N THR F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 5.419A 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: 4.110A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 5.063A 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: 3.766A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (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: 3.630A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (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: 4.441A pdb=" N THR J 70 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE J 71 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Proline residue: J 72 - end of helix removed outlier: 3.957A 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: 4.108A 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: 5.063A 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: 3.765A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (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 160 Processing helix chain 'G' and resid 171 through 175 Processing helix chain 'G' and resid 180 through 198 Processing helix chain 'G' and resid 208 through 231 Proline residue: G 217 - end of helix removed outlier: 3.578A pdb=" N ILE G 220 " --> pdb=" O GLY G 216 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Proline residue: G 222 - end of helix removed outlier: 4.661A pdb=" N GLY G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU G 226 " --> pdb=" O PRO G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 269 removed outlier: 4.535A pdb=" N GLY G 247 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE G 248 " --> pdb=" O HIS G 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE G 250 " --> pdb=" O GLY G 247 " (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 160 Processing helix chain 'K' and resid 171 through 175 Processing helix chain 'K' and resid 180 through 198 Processing helix chain 'K' and resid 208 through 231 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: 4.342A pdb=" N LEU K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Proline residue: K 222 - end of helix removed outlier: 4.662A pdb=" N GLY K 225 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU K 226 " --> pdb=" O PRO K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 269 removed outlier: 4.535A pdb=" N GLY K 247 " --> pdb=" O LEU K 244 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE K 248 " --> pdb=" O HIS K 245 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE K 250 " --> pdb=" O GLY K 247 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.729A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.743A 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: 6.555A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A 390 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 170 through 173 Processing sheet with id= I, first strand: chain 'E' and resid 47 through 50 removed outlier: 6.728A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 58 through 60 removed outlier: 8.376A pdb=" N VAL E 59 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR E 158 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 141 through 144 Processing sheet with id= L, first strand: chain 'E' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'E' and resid 282 through 286 Processing sheet with id= N, first strand: chain 'E' and resid 298 through 300 removed outlier: 6.453A pdb=" N ILE E 410 " --> pdb=" O TYR E 291 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 323 through 325 removed outlier: 6.555A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU E 390 " --> pdb=" O PHE E 317 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 170 through 173 Processing sheet with id= Q, first strand: chain 'I' and resid 47 through 50 removed outlier: 6.728A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) Processing sheet with id= R, 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= S, first strand: chain 'I' and resid 141 through 144 Processing sheet with id= T, first strand: chain 'I' and resid 169 through 171 Processing sheet with id= U, first strand: chain 'I' and resid 282 through 286 Processing sheet with id= V, 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= W, first strand: chain 'I' and resid 323 through 325 removed outlier: 6.556A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.295A 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) Processing sheet with id= X, first strand: chain 'J' and resid 170 through 173 1002 hydrogen bonds defined for protein. 2763 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.67 Time building geometry restraints manager: 9.04 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: 3312 1.32 - 1.44: 6811 1.44 - 1.57: 12712 1.57 - 1.69: 133 1.69 - 1.81: 180 Bond restraints: 23148 Sorted by residual: bond pdb=" CE1 HIS C 231 " pdb=" NE2 HIS C 231 " ideal model delta sigma weight residual 1.321 1.393 -0.072 1.00e-02 1.00e+04 5.20e+01 bond pdb=" CE1 HIS G 231 " pdb=" NE2 HIS G 231 " ideal model delta sigma weight residual 1.321 1.393 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" CE1 HIS K 231 " pdb=" NE2 HIS K 231 " ideal model delta sigma weight residual 1.321 1.392 -0.071 1.00e-02 1.00e+04 5.10e+01 bond pdb=" CG HIS G 245 " pdb=" ND1 HIS G 245 " ideal model delta sigma weight residual 1.378 1.455 -0.077 1.10e-02 8.26e+03 4.95e+01 bond pdb=" CG HIS C 245 " pdb=" ND1 HIS C 245 " ideal model delta sigma weight residual 1.378 1.455 -0.077 1.10e-02 8.26e+03 4.91e+01 ... (remaining 23143 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.83: 574 105.83 - 112.94: 12360 112.94 - 120.05: 8401 120.05 - 127.16: 9567 127.16 - 134.27: 418 Bond angle restraints: 31320 Sorted by residual: angle pdb=" CA HIS K 160 " pdb=" CB HIS K 160 " pdb=" CG HIS K 160 " ideal model delta sigma weight residual 113.80 105.68 8.12 1.00e+00 1.00e+00 6.59e+01 angle pdb=" CA HIS G 160 " pdb=" CB HIS G 160 " pdb=" CG HIS G 160 " ideal model delta sigma weight residual 113.80 105.69 8.11 1.00e+00 1.00e+00 6.58e+01 angle pdb=" CA HIS C 160 " pdb=" CB HIS C 160 " pdb=" CG HIS C 160 " ideal model delta sigma weight residual 113.80 105.71 8.09 1.00e+00 1.00e+00 6.55e+01 angle pdb=" CB HIS K 173 " pdb=" CG HIS K 173 " pdb=" CD2 HIS K 173 " ideal model delta sigma weight residual 131.20 121.90 9.30 1.30e+00 5.92e-01 5.12e+01 angle pdb=" CB HIS G 173 " pdb=" CG HIS G 173 " pdb=" CD2 HIS G 173 " ideal model delta sigma weight residual 131.20 121.93 9.27 1.30e+00 5.92e-01 5.09e+01 ... (remaining 31315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 12578 34.45 - 68.89: 823 68.89 - 103.34: 104 103.34 - 137.79: 37 137.79 - 172.24: 12 Dihedral angle restraints: 13554 sinusoidal: 6102 harmonic: 7452 Sorted by residual: dihedral pdb=" CD ARG G 165 " pdb=" NE ARG G 165 " pdb=" CZ ARG G 165 " pdb=" NH1 ARG G 165 " ideal model delta sinusoidal sigma weight residual 0.00 68.33 -68.33 1 1.00e+01 1.00e-02 6.06e+01 dihedral pdb=" CD ARG C 165 " pdb=" NE ARG C 165 " pdb=" CZ ARG C 165 " pdb=" NH1 ARG C 165 " ideal model delta sinusoidal sigma weight residual 0.00 68.33 -68.33 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CD ARG K 165 " pdb=" NE ARG K 165 " pdb=" CZ ARG K 165 " pdb=" NH1 ARG K 165 " ideal model delta sinusoidal sigma weight residual 0.00 68.29 -68.29 1 1.00e+01 1.00e-02 6.05e+01 ... (remaining 13551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2337 0.049 - 0.097: 635 0.097 - 0.146: 178 0.146 - 0.194: 38 0.194 - 0.243: 19 Chirality restraints: 3207 Sorted by residual: chirality pdb=" C2 PLC G 308 " pdb=" C1 PLC G 308 " pdb=" C3 PLC G 308 " pdb=" O2 PLC G 308 " both_signs ideal model delta sigma weight residual False -2.31 -2.56 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C2 PLC C 307 " pdb=" C1 PLC C 307 " pdb=" C3 PLC C 307 " pdb=" O2 PLC C 307 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C2 PLC K 308 " pdb=" C1 PLC K 308 " pdb=" C3 PLC K 308 " pdb=" O2 PLC K 308 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3204 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 165 " -0.939 9.50e-02 1.11e+02 4.21e-01 1.09e+02 pdb=" NE ARG G 165 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG G 165 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 165 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 165 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 165 " -0.938 9.50e-02 1.11e+02 4.21e-01 1.09e+02 pdb=" NE ARG C 165 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG C 165 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 165 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 165 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 165 " -0.938 9.50e-02 1.11e+02 4.21e-01 1.09e+02 pdb=" NE ARG K 165 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG K 165 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG K 165 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K 165 " -0.015 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 149 2.42 - 3.04: 14614 3.04 - 3.66: 37938 3.66 - 4.28: 62140 4.28 - 4.90: 98901 Nonbonded interactions: 213742 Sorted by model distance: nonbonded pdb=" CA GLU K 238 " pdb=" F1 WIY K 311 " model vdw 1.795 3.420 nonbonded pdb=" CA GLU G 238 " pdb=" F1 WIY G 311 " model vdw 1.795 3.420 nonbonded pdb=" CA GLU C 238 " pdb=" F1 WIY C 310 " model vdw 1.795 3.420 nonbonded pdb=" NH2 ARG K 165 " pdb=" F2 WIY K 311 " model vdw 1.836 2.470 nonbonded pdb=" NH2 ARG C 165 " pdb=" F2 WIY C 310 " model vdw 1.836 2.470 ... (remaining 213737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 304 through 306)) selection = (chain 'F' and (resid 7 through 247 or resid 304 through 306)) selection = (chain 'J' and (resid 7 through 247 or resid 304 through 306)) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 309)) selection = (chain 'G' and (resid 45 through 280 or resid 309)) selection = (chain 'K' and (resid 45 through 280 or resid 309)) } 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: 0.680 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: 4.650 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 56.680 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.150 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:10.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 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 23148 Z= 0.544 Angle : 1.107 16.144 31320 Z= 0.573 Chirality : 0.052 0.243 3207 Planarity : 0.013 0.421 3732 Dihedral : 22.923 172.235 8796 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.02 % Favored : 93.51 % Rotamer: Outliers : 3.93 % Allowed : 17.60 % 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: 0.61 (0.17), residues: 2559 helix: 1.03 (0.15), residues: 1191 sheet: 1.30 (0.28), residues: 357 loop : -0.63 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 202 HIS 0.023 0.003 HIS K 160 PHE 0.015 0.002 PHE B 31 TYR 0.022 0.001 TYR C 184 ARG 0.022 0.001 ARG C 165 *********************** 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 448 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 362 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7769 (mmp) cc_final: 0.7483 (mmm) REVERT: B 45 MET cc_start: 0.7151 (ppp) cc_final: 0.6481 (ppp) REVERT: B 93 VAL cc_start: 0.7692 (t) cc_final: 0.7446 (p) REVERT: B 206 ARG cc_start: 0.6551 (mmm160) cc_final: 0.6174 (mtp-110) REVERT: C 90 MET cc_start: 0.6069 (mmm) cc_final: 0.5728 (mmp) REVERT: C 155 GLN cc_start: 0.7210 (tt0) cc_final: 0.6979 (tt0) REVERT: C 165 ARG cc_start: 0.3797 (OUTLIER) cc_final: 0.3233 (ttt180) REVERT: C 207 SER cc_start: 0.7747 (OUTLIER) cc_final: 0.7479 (p) REVERT: E 145 GLN cc_start: 0.7107 (tp-100) cc_final: 0.6906 (tp40) REVERT: E 248 VAL cc_start: 0.7947 (t) cc_final: 0.7740 (m) REVERT: E 256 SER cc_start: 0.7133 (OUTLIER) cc_final: 0.6811 (p) REVERT: E 272 MET cc_start: 0.7755 (mmp) cc_final: 0.7355 (mmp) REVERT: F 93 VAL cc_start: 0.7609 (t) cc_final: 0.7340 (t) REVERT: F 223 MET cc_start: 0.8089 (mmm) cc_final: 0.7755 (mmm) REVERT: I 272 MET cc_start: 0.7688 (mmp) cc_final: 0.7435 (mmp) REVERT: J 223 MET cc_start: 0.7819 (mmm) cc_final: 0.7442 (mmm) REVERT: K 90 MET cc_start: 0.5794 (mmm) cc_final: 0.5586 (mmp) REVERT: K 97 ILE cc_start: 0.7020 (mt) cc_final: 0.6793 (mm) REVERT: K 238 GLU cc_start: 0.3372 (OUTLIER) cc_final: 0.2934 (mm-30) outliers start: 86 outliers final: 24 residues processed: 438 average time/residue: 1.3733 time to fit residues: 686.5066 Evaluate side-chains 295 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 267 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 165 ARG Chi-restraints excluded: chain G residue 238 GLU 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 164 VAL Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain K residue 238 GLU 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: 4.9990 chunk 193 optimal weight: 0.5980 chunk 107 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 231 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN B 187 ASN E 168 ASN F 187 ASN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN I 176 GLN J 187 ASN G 91 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23148 Z= 0.191 Angle : 0.649 7.258 31320 Z= 0.325 Chirality : 0.046 0.328 3207 Planarity : 0.005 0.047 3732 Dihedral : 22.275 176.767 4218 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.39 % Favored : 94.37 % Rotamer: Outliers : 3.75 % Allowed : 20.03 % Favored : 76.22 % 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: 0.70 (0.17), residues: 2559 helix: 1.00 (0.15), residues: 1233 sheet: 1.02 (0.29), residues: 342 loop : -0.31 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 234 HIS 0.008 0.002 HIS G 160 PHE 0.016 0.002 PHE B 31 TYR 0.019 0.002 TYR C 184 ARG 0.009 0.001 ARG E 299 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 287 time to evaluate : 2.498 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.6700 (mmm) cc_final: 0.6488 (mmm) REVERT: B 59 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8138 (mm) REVERT: C 90 MET cc_start: 0.6190 (mmm) cc_final: 0.5856 (mmp) REVERT: C 236 MET cc_start: 0.4426 (mmp) cc_final: 0.3735 (pp-130) REVERT: C 259 MET cc_start: 0.7088 (mtm) cc_final: 0.6734 (mtm) REVERT: E 248 VAL cc_start: 0.7941 (t) cc_final: 0.7673 (p) REVERT: E 272 MET cc_start: 0.8018 (mmp) cc_final: 0.7456 (mmp) REVERT: F 223 MET cc_start: 0.8090 (mmm) cc_final: 0.7737 (mmm) REVERT: J 196 TYR cc_start: 0.6649 (p90) cc_final: 0.6387 (p90) REVERT: J 223 MET cc_start: 0.7878 (mmm) cc_final: 0.7480 (mmm) REVERT: G 227 ASN cc_start: 0.5575 (t0) cc_final: 0.5117 (t0) REVERT: G 236 MET cc_start: 0.3932 (OUTLIER) cc_final: 0.2602 (pp-130) REVERT: G 248 PHE cc_start: 0.5324 (m-80) cc_final: 0.5102 (m-80) REVERT: G 259 MET cc_start: 0.7468 (mtm) cc_final: 0.7089 (mtm) REVERT: K 90 MET cc_start: 0.5788 (mmm) cc_final: 0.5556 (mmp) REVERT: K 97 ILE cc_start: 0.6964 (mt) cc_final: 0.6627 (mm) REVERT: K 156 ASP cc_start: 0.6921 (t70) cc_final: 0.6624 (t70) REVERT: K 244 LEU cc_start: 0.3797 (OUTLIER) cc_final: 0.3516 (pp) outliers start: 82 outliers final: 29 residues processed: 354 average time/residue: 1.4196 time to fit residues: 571.4378 Evaluate side-chains 286 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 254 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 236 MET 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 164 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: 6.9990 chunk 71 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 231 optimal weight: 8.9990 chunk 250 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 230 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 168 ASN B 187 ASN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN E 168 ASN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN J 187 ASN ** K 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 276 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 23148 Z= 0.496 Angle : 0.836 9.232 31320 Z= 0.436 Chirality : 0.054 0.371 3207 Planarity : 0.006 0.050 3732 Dihedral : 21.627 179.517 4184 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.04 % Favored : 94.41 % Rotamer: Outliers : 3.70 % Allowed : 19.71 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.17), residues: 2559 helix: 0.57 (0.14), residues: 1251 sheet: 0.29 (0.26), residues: 420 loop : -0.36 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP J 231 HIS 0.014 0.003 HIS C 245 PHE 0.030 0.004 PHE B 243 TYR 0.027 0.003 TYR C 184 ARG 0.007 0.001 ARG B 206 *********************** 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 348 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 267 time to evaluate : 2.457 Fit side-chains REVERT: A 108 GLN cc_start: 0.7338 (pp30) cc_final: 0.6999 (pp30) REVERT: B 152 TRP cc_start: 0.8438 (OUTLIER) cc_final: 0.6026 (t-100) REVERT: C 90 MET cc_start: 0.6363 (mmm) cc_final: 0.5952 (mmp) REVERT: C 248 PHE cc_start: 0.6141 (m-80) cc_final: 0.5790 (m-80) REVERT: C 259 MET cc_start: 0.7743 (mtm) cc_final: 0.7378 (mtm) REVERT: E 272 MET cc_start: 0.8114 (mmp) cc_final: 0.7580 (mmp) REVERT: F 152 TRP cc_start: 0.8374 (OUTLIER) cc_final: 0.5972 (t-100) REVERT: F 212 VAL cc_start: 0.8104 (t) cc_final: 0.7790 (p) REVERT: J 100 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7461 (mt-10) REVERT: J 152 TRP cc_start: 0.8317 (OUTLIER) cc_final: 0.5676 (t-100) REVERT: J 172 GLU cc_start: 0.7363 (tm-30) cc_final: 0.7109 (tm-30) REVERT: G 248 PHE cc_start: 0.5866 (m-80) cc_final: 0.5586 (m-80) REVERT: K 156 ASP cc_start: 0.6844 (t70) cc_final: 0.6447 (t70) outliers start: 81 outliers final: 43 residues processed: 331 average time/residue: 1.3511 time to fit residues: 512.6761 Evaluate side-chains 291 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 245 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 152 TRP Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 237 MET Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 152 TRP Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 263 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 120 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 232 optimal weight: 3.9990 chunk 246 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23148 Z= 0.203 Angle : 0.630 7.665 31320 Z= 0.322 Chirality : 0.046 0.288 3207 Planarity : 0.004 0.048 3732 Dihedral : 21.015 179.635 4178 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.57 % Favored : 95.15 % Rotamer: Outliers : 2.65 % Allowed : 20.39 % Favored : 76.95 % 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 (0.17), residues: 2559 helix: 0.85 (0.15), residues: 1245 sheet: 0.68 (0.27), residues: 387 loop : -0.31 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 206 HIS 0.008 0.001 HIS K 245 PHE 0.027 0.002 PHE G 251 TYR 0.023 0.002 TYR G 184 ARG 0.005 0.001 ARG K 165 *********************** 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 322 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 264 time to evaluate : 2.591 Fit side-chains REVERT: A 108 GLN cc_start: 0.7098 (pp30) cc_final: 0.6741 (pp30) REVERT: B 59 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8002 (mm) REVERT: B 152 TRP cc_start: 0.8328 (OUTLIER) cc_final: 0.5991 (t-100) REVERT: C 90 MET cc_start: 0.6346 (mmm) cc_final: 0.5856 (mmp) REVERT: C 248 PHE cc_start: 0.6019 (m-80) cc_final: 0.5557 (m-80) REVERT: C 259 MET cc_start: 0.7454 (mtm) cc_final: 0.7227 (mtm) REVERT: E 272 MET cc_start: 0.8067 (mmp) cc_final: 0.7380 (mmp) REVERT: F 212 VAL cc_start: 0.8115 (t) cc_final: 0.7812 (p) REVERT: J 100 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7418 (mt-10) REVERT: G 69 GLU cc_start: 0.6009 (pt0) cc_final: 0.5800 (pt0) REVERT: G 96 GLU cc_start: 0.6703 (pt0) cc_final: 0.6190 (pt0) REVERT: G 100 GLU cc_start: 0.6409 (mt-10) cc_final: 0.5996 (mt-10) REVERT: G 248 PHE cc_start: 0.5797 (m-80) cc_final: 0.5440 (m-80) REVERT: K 156 ASP cc_start: 0.6858 (t70) cc_final: 0.6471 (t70) REVERT: K 176 GLU cc_start: 0.6185 (tt0) cc_final: 0.5935 (tt0) outliers start: 58 outliers final: 27 residues processed: 309 average time/residue: 1.4470 time to fit residues: 508.6514 Evaluate side-chains 271 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 242 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 381 TYR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 381 TYR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 221 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 HIS ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN I 33 HIS ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 23148 Z= 0.422 Angle : 0.769 7.327 31320 Z= 0.401 Chirality : 0.051 0.243 3207 Planarity : 0.006 0.049 3732 Dihedral : 20.935 176.839 4174 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.20 % Favored : 94.37 % Rotamer: Outliers : 3.02 % Allowed : 20.21 % Favored : 76.77 % 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: 0.33 (0.17), residues: 2559 helix: 0.66 (0.14), residues: 1251 sheet: 0.57 (0.27), residues: 372 loop : -0.38 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP J 231 HIS 0.011 0.002 HIS C 160 PHE 0.027 0.003 PHE G 251 TYR 0.027 0.003 TYR C 184 ARG 0.005 0.001 ARG I 131 *********************** 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 313 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 247 time to evaluate : 2.528 Fit side-chains REVERT: A 108 GLN cc_start: 0.7123 (pp30) cc_final: 0.6809 (pp30) REVERT: B 152 TRP cc_start: 0.8453 (OUTLIER) cc_final: 0.6063 (t-100) REVERT: C 90 MET cc_start: 0.6399 (mmm) cc_final: 0.5943 (mmp) REVERT: C 248 PHE cc_start: 0.6248 (m-80) cc_final: 0.5896 (m-80) REVERT: C 259 MET cc_start: 0.7679 (mtm) cc_final: 0.7350 (mtm) REVERT: F 152 TRP cc_start: 0.8351 (OUTLIER) cc_final: 0.5892 (t-100) REVERT: F 212 VAL cc_start: 0.8127 (t) cc_final: 0.7846 (p) REVERT: I 79 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6416 (pm20) REVERT: J 152 TRP cc_start: 0.8295 (OUTLIER) cc_final: 0.5673 (t-100) REVERT: G 248 PHE cc_start: 0.5841 (m-80) cc_final: 0.5444 (m-80) REVERT: K 156 ASP cc_start: 0.6814 (t70) cc_final: 0.6312 (t70) outliers start: 66 outliers final: 40 residues processed: 306 average time/residue: 1.3905 time to fit residues: 486.6883 Evaluate side-chains 283 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 239 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 152 TRP Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 237 MET Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 152 TRP Chi-restraints excluded: chain J residue 193 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 164 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 246 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23148 Z= 0.222 Angle : 0.648 8.187 31320 Z= 0.332 Chirality : 0.046 0.227 3207 Planarity : 0.005 0.047 3732 Dihedral : 20.427 175.127 4174 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.77 % Favored : 94.96 % Rotamer: Outliers : 2.74 % Allowed : 20.67 % Favored : 76.59 % 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: 0.53 (0.17), residues: 2559 helix: 0.89 (0.15), residues: 1224 sheet: 0.60 (0.27), residues: 387 loop : -0.32 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 206 HIS 0.008 0.001 HIS K 245 PHE 0.024 0.002 PHE G 251 TYR 0.023 0.002 TYR K 184 ARG 0.007 0.000 ARG C 129 *********************** 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 318 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 258 time to evaluate : 2.459 Fit side-chains REVERT: A 108 GLN cc_start: 0.7000 (pp30) cc_final: 0.6694 (pp30) REVERT: B 59 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8006 (mm) REVERT: B 152 TRP cc_start: 0.8348 (OUTLIER) cc_final: 0.6011 (t-100) REVERT: C 90 MET cc_start: 0.6338 (mmm) cc_final: 0.5906 (mmp) REVERT: C 259 MET cc_start: 0.7506 (mtm) cc_final: 0.7303 (mtm) REVERT: I 272 MET cc_start: 0.8103 (mmp) cc_final: 0.7277 (mpp) REVERT: J 152 TRP cc_start: 0.8265 (OUTLIER) cc_final: 0.5743 (t-100) REVERT: G 248 PHE cc_start: 0.5712 (m-80) cc_final: 0.4968 (m-80) REVERT: K 156 ASP cc_start: 0.6897 (t70) cc_final: 0.6474 (t70) REVERT: K 176 GLU cc_start: 0.6294 (tt0) cc_final: 0.5820 (tt0) outliers start: 60 outliers final: 36 residues processed: 309 average time/residue: 1.4023 time to fit residues: 494.5279 Evaluate side-chains 285 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 246 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 152 TRP 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 164 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 74 TRP Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 263 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 245 optimal weight: 0.9990 chunk 153 optimal weight: 0.0070 chunk 149 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 GLN F 16 GLN F 174 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23148 Z= 0.211 Angle : 0.637 7.994 31320 Z= 0.325 Chirality : 0.046 0.215 3207 Planarity : 0.004 0.046 3732 Dihedral : 19.808 173.070 4174 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.73 % Favored : 95.00 % Rotamer: Outliers : 2.74 % Allowed : 20.94 % Favored : 76.31 % 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: 0.66 (0.17), residues: 2559 helix: 0.94 (0.15), residues: 1233 sheet: 0.86 (0.28), residues: 339 loop : -0.24 (0.21), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 206 HIS 0.008 0.001 HIS K 245 PHE 0.022 0.002 PHE C 251 TYR 0.023 0.002 TYR K 184 ARG 0.007 0.000 ARG E 292 *********************** 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 312 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 252 time to evaluate : 2.450 Fit side-chains REVERT: A 82 ASP cc_start: 0.7319 (m-30) cc_final: 0.7050 (t0) REVERT: A 108 GLN cc_start: 0.6999 (pp30) cc_final: 0.6681 (pp30) REVERT: B 59 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8010 (mm) REVERT: B 152 TRP cc_start: 0.8349 (OUTLIER) cc_final: 0.6026 (t-100) REVERT: C 90 MET cc_start: 0.6310 (mmm) cc_final: 0.5868 (mmp) REVERT: C 243 PRO cc_start: 0.5623 (Cg_exo) cc_final: 0.5148 (Cg_endo) REVERT: F 212 VAL cc_start: 0.8048 (t) cc_final: 0.7777 (p) REVERT: I 272 MET cc_start: 0.8090 (mmp) cc_final: 0.7216 (mpp) REVERT: J 152 TRP cc_start: 0.8259 (OUTLIER) cc_final: 0.5738 (t-100) REVERT: G 248 PHE cc_start: 0.5712 (m-80) cc_final: 0.5338 (m-80) REVERT: K 156 ASP cc_start: 0.6886 (t70) cc_final: 0.6479 (t70) REVERT: K 176 GLU cc_start: 0.6165 (tt0) cc_final: 0.5871 (tt0) REVERT: K 245 HIS cc_start: 0.6379 (m90) cc_final: 0.5964 (m90) outliers start: 60 outliers final: 43 residues processed: 304 average time/residue: 1.3689 time to fit residues: 477.9813 Evaluate side-chains 290 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 244 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 381 TYR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 152 TRP Chi-restraints excluded: chain J residue 216 SER 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 164 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 74 TRP Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 263 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 22 optimal weight: 0.0870 chunk 193 optimal weight: 8.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN J 16 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23148 Z= 0.211 Angle : 0.641 8.740 31320 Z= 0.325 Chirality : 0.046 0.268 3207 Planarity : 0.004 0.047 3732 Dihedral : 19.466 171.747 4174 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.73 % Favored : 95.04 % Rotamer: Outliers : 2.56 % Allowed : 21.67 % Favored : 75.77 % 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: 0.70 (0.17), residues: 2559 helix: 1.00 (0.15), residues: 1230 sheet: 0.89 (0.28), residues: 339 loop : -0.24 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 206 HIS 0.007 0.001 HIS K 245 PHE 0.024 0.002 PHE G 251 TYR 0.022 0.002 TYR K 184 ARG 0.008 0.000 ARG C 129 *********************** 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 307 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 251 time to evaluate : 2.459 Fit side-chains REVERT: A 82 ASP cc_start: 0.7325 (m-30) cc_final: 0.7052 (t0) REVERT: A 108 GLN cc_start: 0.6972 (pp30) cc_final: 0.6675 (pp30) REVERT: B 59 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8029 (mm) REVERT: B 152 TRP cc_start: 0.8345 (OUTLIER) cc_final: 0.6028 (t-100) REVERT: C 90 MET cc_start: 0.6308 (mmm) cc_final: 0.5877 (mmp) REVERT: C 243 PRO cc_start: 0.5561 (Cg_exo) cc_final: 0.5083 (Cg_endo) REVERT: F 136 MET cc_start: 0.7536 (ttp) cc_final: 0.7219 (ttp) REVERT: F 212 VAL cc_start: 0.8035 (t) cc_final: 0.7773 (p) REVERT: I 272 MET cc_start: 0.8089 (mmp) cc_final: 0.7201 (mpp) REVERT: J 152 TRP cc_start: 0.8236 (OUTLIER) cc_final: 0.5708 (t-100) REVERT: G 248 PHE cc_start: 0.5695 (m-80) cc_final: 0.5336 (m-80) REVERT: K 156 ASP cc_start: 0.6888 (t70) cc_final: 0.6491 (t70) REVERT: K 168 ASP cc_start: 0.5123 (m-30) cc_final: 0.4917 (m-30) REVERT: K 176 GLU cc_start: 0.6178 (tt0) cc_final: 0.5869 (tt0) REVERT: K 245 HIS cc_start: 0.6392 (m90) cc_final: 0.5978 (m90) outliers start: 56 outliers final: 43 residues processed: 299 average time/residue: 1.3263 time to fit residues: 455.5160 Evaluate side-chains 294 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 248 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 152 TRP Chi-restraints excluded: chain J residue 216 SER 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 164 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 74 TRP Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 263 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 229 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 216 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 23148 Z= 0.512 Angle : 0.841 11.411 31320 Z= 0.440 Chirality : 0.054 0.303 3207 Planarity : 0.006 0.061 3732 Dihedral : 19.695 170.347 4174 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.39 % Favored : 94.18 % Rotamer: Outliers : 3.02 % Allowed : 21.26 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2559 helix: 0.60 (0.14), residues: 1251 sheet: 0.43 (0.27), residues: 375 loop : -0.31 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP J 231 HIS 0.011 0.003 HIS C 160 PHE 0.039 0.004 PHE G 251 TYR 0.031 0.003 TYR B 196 ARG 0.008 0.001 ARG E 292 *********************** 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 315 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 249 time to evaluate : 2.417 Fit side-chains REVERT: A 108 GLN cc_start: 0.6971 (pp30) cc_final: 0.6680 (pp30) REVERT: B 152 TRP cc_start: 0.8465 (OUTLIER) cc_final: 0.6082 (t-100) REVERT: B 211 ASP cc_start: 0.6504 (p0) cc_final: 0.6303 (p0) REVERT: C 90 MET cc_start: 0.6411 (mmm) cc_final: 0.5969 (mmp) REVERT: E 163 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.6947 (ttt) REVERT: F 136 MET cc_start: 0.7788 (ttp) cc_final: 0.7563 (ttp) REVERT: F 152 TRP cc_start: 0.8356 (OUTLIER) cc_final: 0.5943 (t-100) REVERT: F 212 VAL cc_start: 0.8143 (t) cc_final: 0.7860 (p) REVERT: I 79 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6448 (pm20) REVERT: J 152 TRP cc_start: 0.8295 (OUTLIER) cc_final: 0.5641 (t-100) REVERT: J 206 ARG cc_start: 0.6547 (mtp180) cc_final: 0.6215 (mtp180) REVERT: G 248 PHE cc_start: 0.5992 (m-80) cc_final: 0.5657 (m-80) REVERT: K 156 ASP cc_start: 0.6775 (t70) cc_final: 0.6311 (t70) outliers start: 66 outliers final: 45 residues processed: 304 average time/residue: 1.3292 time to fit residues: 464.3434 Evaluate side-chains 293 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 243 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 152 TRP Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 152 TRP Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 216 SER 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 164 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 52 THR Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 168 optimal weight: 0.5980 chunk 254 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN I 72 HIS J 16 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23148 Z= 0.198 Angle : 0.657 9.971 31320 Z= 0.333 Chirality : 0.046 0.212 3207 Planarity : 0.004 0.044 3732 Dihedral : 19.263 169.235 4173 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.53 % Favored : 95.15 % Rotamer: Outliers : 1.97 % Allowed : 22.68 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2559 helix: 0.90 (0.15), residues: 1230 sheet: 0.83 (0.27), residues: 363 loop : -0.33 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 206 HIS 0.010 0.001 HIS K 245 PHE 0.028 0.002 PHE G 251 TYR 0.024 0.002 TYR B 196 ARG 0.009 0.001 ARG C 129 ********************** 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 295 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 252 time to evaluate : 2.509 Fit side-chains REVERT: A 82 ASP cc_start: 0.7265 (m-30) cc_final: 0.6969 (t0) REVERT: A 108 GLN cc_start: 0.6925 (pp30) cc_final: 0.6641 (pp30) REVERT: B 59 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7974 (mm) REVERT: B 136 MET cc_start: 0.7987 (ttt) cc_final: 0.7427 (ptm) REVERT: B 152 TRP cc_start: 0.8223 (OUTLIER) cc_final: 0.5900 (t-100) REVERT: B 211 ASP cc_start: 0.6365 (p0) cc_final: 0.6151 (p0) REVERT: C 90 MET cc_start: 0.6342 (mmm) cc_final: 0.5843 (mmp) REVERT: E 79 GLU cc_start: 0.6280 (pm20) cc_final: 0.6068 (pm20) REVERT: F 136 MET cc_start: 0.7514 (ttp) cc_final: 0.7226 (ttp) REVERT: I 272 MET cc_start: 0.8085 (mmp) cc_final: 0.7199 (mpp) REVERT: J 152 TRP cc_start: 0.8228 (OUTLIER) cc_final: 0.5708 (t-100) REVERT: J 206 ARG cc_start: 0.6365 (mtp180) cc_final: 0.6121 (mtp180) REVERT: G 248 PHE cc_start: 0.5620 (m-80) cc_final: 0.4904 (m-80) REVERT: K 156 ASP cc_start: 0.6913 (t70) cc_final: 0.6537 (t70) REVERT: K 173 HIS cc_start: 0.6664 (m170) cc_final: 0.6254 (m-70) REVERT: K 176 GLU cc_start: 0.6360 (tt0) cc_final: 0.5931 (tt0) REVERT: K 245 HIS cc_start: 0.6493 (m90) cc_final: 0.6111 (m90) outliers start: 43 outliers final: 35 residues processed: 288 average time/residue: 1.3867 time to fit residues: 457.7723 Evaluate side-chains 284 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 246 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 152 TRP Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 164 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 74 TRP Chi-restraints excluded: chain K residue 164 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: 0.0570 chunk 215 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 186 optimal weight: 8.9990 chunk 29 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN J 16 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.190180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.164328 restraints weight = 27958.273| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 1.20 r_work: 0.4055 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3945 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23148 Z= 0.260 Angle : 0.689 9.912 31320 Z= 0.350 Chirality : 0.047 0.206 3207 Planarity : 0.005 0.046 3732 Dihedral : 19.071 168.040 4173 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.96 % Favored : 94.76 % Rotamer: Outliers : 2.19 % Allowed : 22.73 % Favored : 75.08 % 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: 0.59 (0.17), residues: 2559 helix: 0.89 (0.15), residues: 1233 sheet: 0.79 (0.27), residues: 363 loop : -0.30 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 206 HIS 0.009 0.002 HIS C 160 PHE 0.029 0.002 PHE G 251 TYR 0.028 0.002 TYR B 196 ARG 0.009 0.000 ARG C 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8352.56 seconds wall clock time: 148 minutes 49.03 seconds (8929.03 seconds total)