Starting phenix.real_space_refine on Sat Feb 24 11:27:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4p_25684/02_2024/7t4p_25684_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4p_25684/02_2024/7t4p_25684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4p_25684/02_2024/7t4p_25684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4p_25684/02_2024/7t4p_25684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4p_25684/02_2024/7t4p_25684_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4p_25684/02_2024/7t4p_25684_trim_updated.pdb" } resolution = 3.62 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= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19395 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: 6 Type Number sf(0) Gaussians Cu 9 5.60 5 P 30 5.49 5 S 93 5.16 5 C 14856 2.51 5 N 3411 2.21 5 O 3843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A ASP 363": "OD1" <-> "OD2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 166": "OD1" <-> "OD2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "G PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 166": "OD1" <-> "OD2" Residue "K PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 22": "OD1" <-> "OD2" Residue "F ASP 53": "OD1" <-> "OD2" Residue "J ASP 22": "OD1" <-> "OD2" Residue "J ASP 53": "OD1" <-> "OD2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 220": "OD1" <-> "OD2" Residue "E ASP 225": "OD1" <-> "OD2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 343": "OE1" <-> "OE2" Residue "E ASP 363": "OD1" <-> "OD2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "I PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 220": "OD1" <-> "OD2" Residue "I ASP 225": "OD1" <-> "OD2" Residue "I GLU 316": "OE1" <-> "OE2" Residue "I TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 343": "OE1" <-> "OE2" Residue "I ASP 363": "OD1" <-> "OD2" Residue "I ASP 368": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22242 Number of models: 1 Model: "" Number of chains: 18 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: "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: "B" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1976 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "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: "F" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1976 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1976 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "I" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "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: "C" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 285 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 1, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 194 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "G" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 285 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 1, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "K" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 243 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 1, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 12.37, per 1000 atoms: 0.56 Number of scatterers: 22242 At special positions: 0 Unit cell: (106.25, 106.722, 119, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 9 28.99 S 93 16.00 P 30 15.00 O 3843 8.00 N 3411 7.00 C 14856 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: 9.39 Conformation dependent library (CDL) restraints added in 4.6 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: 78 helices and 24 sheets defined 47.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 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 removed outlier: 4.020A pdb=" N TRP A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) 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 376 through 379 removed outlier: 3.757A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'C' and resid 50 through 72 removed outlier: 3.846A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 88 removed outlier: 3.629A pdb=" N THR C 87 " --> pdb=" O PRO C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 113 Processing helix chain 'C' and resid 124 through 149 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 180 through 198 Processing helix chain 'C' and resid 208 through 232 Proline residue: C 217 - end of helix removed outlier: 4.164A 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: 4.583A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 272 removed outlier: 4.211A pdb=" N GLY C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 250 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 271 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY C 272 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 50 removed outlier: 7.654A pdb=" N ASP B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TRP B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 83 Proline residue: B 65 - end of helix removed outlier: 4.420A pdb=" N THR B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N PHE B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Proline residue: B 72 - end of helix removed outlier: 3.729A 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 164 removed outlier: 4.116A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Proline residue: B 158 - end of helix Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 180 through 187 Processing helix chain 'B' and resid 212 through 238 removed outlier: 3.756A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 72 removed outlier: 3.847A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 88 removed outlier: 3.629A pdb=" N THR G 87 " --> pdb=" O PRO G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 113 Processing helix chain 'G' and resid 124 through 149 Processing helix chain 'G' and resid 151 through 162 Processing helix chain 'G' and resid 171 through 176 Processing helix chain 'G' and resid 180 through 198 Processing helix chain 'G' and resid 208 through 232 Proline residue: G 217 - end of helix removed outlier: 4.164A 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: 4.584A pdb=" N LEU G 226 " --> pdb=" O PRO G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 272 removed outlier: 4.211A pdb=" N GLY G 247 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE G 250 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN G 271 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY G 272 " --> pdb=" O PHE G 269 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 72 removed outlier: 3.846A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 88 removed outlier: 3.630A pdb=" N THR K 87 " --> pdb=" O PRO K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 113 Processing helix chain 'K' and resid 124 through 149 Processing helix chain 'K' and resid 151 through 162 Processing helix chain 'K' and resid 171 through 176 Processing helix chain 'K' and resid 180 through 198 Processing helix chain 'K' and resid 208 through 232 Proline residue: K 217 - end of helix removed outlier: 4.164A 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: 4.583A pdb=" N LEU K 226 " --> pdb=" O PRO K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 272 removed outlier: 4.211A pdb=" N GLY K 247 " --> pdb=" O LEU K 244 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE K 250 " --> pdb=" O GLY K 247 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN K 271 " --> pdb=" O SER K 268 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY K 272 " --> pdb=" O PHE K 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 50 removed outlier: 7.654A pdb=" N ASP F 47 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TRP F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 83 Proline residue: F 65 - end of helix removed outlier: 4.419A pdb=" N THR F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix removed outlier: 3.729A 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 164 removed outlier: 4.116A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET F 150 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Proline residue: F 162 - end of helix Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 180 through 187 Processing helix chain 'F' and resid 212 through 238 removed outlier: 3.756A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 50 removed outlier: 7.654A pdb=" N ASP J 47 " --> pdb=" O LEU J 43 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TRP J 48 " --> pdb=" O THR J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 83 Proline residue: J 65 - end of helix removed outlier: 4.420A pdb=" N THR J 70 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE J 71 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Proline residue: J 72 - end of helix removed outlier: 3.729A 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 164 removed outlier: 4.116A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET J 150 " --> pdb=" O ILE J 146 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) Proline residue: J 158 - end of helix Proline residue: J 162 - end of helix Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 180 through 187 Processing helix chain 'J' and resid 212 through 238 removed outlier: 3.756A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 44 Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 185 through 207 removed outlier: 4.020A pdb=" N TRP E 206 " --> pdb=" O TRP E 202 " (cutoff:3.500A) 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 376 through 379 removed outlier: 3.757A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 376 through 379' 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 removed outlier: 4.021A pdb=" N TRP I 206 " --> pdb=" O TRP I 202 " (cutoff:3.500A) 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 376 through 379 removed outlier: 3.757A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 376 through 379' Processing sheet with id= A, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.708A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.696A 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: 7.982A pdb=" N VAL A 59 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N THR A 158 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 87 through 89 removed outlier: 3.561A pdb=" N GLY A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) 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 removed outlier: 3.622A pdb=" N LYS A 285 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.701A 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: 6.727A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 390 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 170 through 173 Processing sheet with id= I, first strand: chain 'F' and resid 170 through 173 Processing sheet with id= J, first strand: chain 'J' and resid 170 through 173 Processing sheet with id= K, first strand: chain 'E' and resid 47 through 50 removed outlier: 6.708A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 58 through 60 removed outlier: 7.982A pdb=" N VAL E 59 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N THR E 158 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 87 through 89 removed outlier: 3.561A pdb=" N GLY E 148 " --> pdb=" O VAL E 144 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 169 through 171 Processing sheet with id= O, first strand: chain 'E' and resid 282 through 286 removed outlier: 3.622A pdb=" N LYS E 285 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 298 through 300 removed outlier: 6.701A pdb=" N ILE E 410 " --> pdb=" O TYR E 291 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 323 through 325 removed outlier: 6.728A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU E 390 " --> pdb=" O PHE E 317 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 47 through 50 removed outlier: 6.708A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 58 through 60 removed outlier: 7.983A pdb=" N VAL I 59 " --> pdb=" O TRP I 156 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR I 158 " --> pdb=" O VAL I 59 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 87 through 89 removed outlier: 3.561A pdb=" N GLY I 148 " --> pdb=" O VAL I 144 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 169 through 171 Processing sheet with id= V, first strand: chain 'I' and resid 282 through 286 removed outlier: 3.622A pdb=" N LYS I 285 " --> pdb=" O THR I 303 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 298 through 300 removed outlier: 6.702A pdb=" N ILE I 410 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 323 through 325 removed outlier: 6.727A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU I 390 " --> pdb=" O PHE I 317 " (cutoff:3.500A) 999 hydrogen bonds defined for protein. 2754 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: 6.96 Time building geometry restraints manager: 9.97 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: 3456 1.32 - 1.45: 6628 1.45 - 1.57: 12501 1.57 - 1.69: 134 1.69 - 1.81: 180 Bond restraints: 22899 Sorted by residual: bond pdb=" CB PLC G 303 " pdb=" O3 PLC G 303 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" CB PLC C 302 " pdb=" O3 PLC C 302 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" CB PLC B 305 " pdb=" O3 PLC B 305 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C19 P1O B 307 " pdb=" O7 P1O B 307 " ideal model delta sigma weight residual 1.331 1.457 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" CE1 HIS I 33 " pdb=" NE2 HIS I 33 " ideal model delta sigma weight residual 1.321 1.258 0.063 1.00e-02 1.00e+04 3.92e+01 ... (remaining 22894 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.45: 530 105.45 - 112.69: 11860 112.69 - 119.92: 8193 119.92 - 127.16: 10014 127.16 - 134.40: 420 Bond angle restraints: 31017 Sorted by residual: angle pdb=" CA PHE C 233 " pdb=" C PHE C 233 " pdb=" O PHE C 233 " ideal model delta sigma weight residual 117.94 114.33 3.61 5.80e-01 2.97e+00 3.88e+01 angle pdb=" CA PHE K 233 " pdb=" C PHE K 233 " pdb=" O PHE K 233 " ideal model delta sigma weight residual 117.94 114.33 3.61 5.80e-01 2.97e+00 3.87e+01 angle pdb=" CA PHE G 233 " pdb=" C PHE G 233 " pdb=" O PHE G 233 " ideal model delta sigma weight residual 117.94 114.36 3.58 5.80e-01 2.97e+00 3.80e+01 angle pdb=" O PHE C 233 " pdb=" C PHE C 233 " pdb=" N TRP C 234 " ideal model delta sigma weight residual 121.47 125.24 -3.77 7.50e-01 1.78e+00 2.52e+01 angle pdb=" O PHE G 233 " pdb=" C PHE G 233 " pdb=" N TRP G 234 " ideal model delta sigma weight residual 121.47 125.23 -3.76 7.50e-01 1.78e+00 2.51e+01 ... (remaining 31012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 12753 35.47 - 70.94: 489 70.94 - 106.41: 60 106.41 - 141.88: 36 141.88 - 177.35: 15 Dihedral angle restraints: 13353 sinusoidal: 5901 harmonic: 7452 Sorted by residual: dihedral pdb=" CA ARG A 45 " pdb=" C ARG A 45 " pdb=" N THR A 46 " pdb=" CA THR A 46 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ARG I 45 " pdb=" C ARG I 45 " pdb=" N THR I 46 " pdb=" CA THR I 46 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ARG E 45 " pdb=" C ARG E 45 " pdb=" N THR E 46 " pdb=" CA THR E 46 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 13350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2626 0.063 - 0.126: 508 0.126 - 0.189: 58 0.189 - 0.251: 5 0.251 - 0.314: 4 Chirality restraints: 3201 Sorted by residual: chirality pdb=" CA TRP K 234 " pdb=" N TRP K 234 " pdb=" C TRP K 234 " pdb=" CB TRP K 234 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA TRP C 234 " pdb=" N TRP C 234 " pdb=" C TRP C 234 " pdb=" CB TRP C 234 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA TRP G 234 " pdb=" N TRP G 234 " pdb=" C TRP G 234 " pdb=" CB TRP G 234 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 3198 not shown) Planarity restraints: 3717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 33 " -0.003 2.00e-02 2.50e+03 2.93e-02 1.28e+01 pdb=" CG HIS E 33 " 0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS E 33 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS E 33 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS E 33 " 0.045 2.00e-02 2.50e+03 pdb=" NE2 HIS E 33 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 33 " -0.003 2.00e-02 2.50e+03 2.92e-02 1.28e+01 pdb=" CG HIS A 33 " 0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 33 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS A 33 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS A 33 " 0.045 2.00e-02 2.50e+03 pdb=" NE2 HIS A 33 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS I 33 " 0.003 2.00e-02 2.50e+03 2.90e-02 1.26e+01 pdb=" CG HIS I 33 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS I 33 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS I 33 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS I 33 " -0.045 2.00e-02 2.50e+03 pdb=" NE2 HIS I 33 " 0.039 2.00e-02 2.50e+03 ... (remaining 3714 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 63 2.35 - 2.99: 11500 2.99 - 3.62: 34761 3.62 - 4.26: 57769 4.26 - 4.90: 96639 Nonbonded interactions: 200732 Sorted by model distance: nonbonded pdb=" NE2 HIS K 245 " pdb="CU CU K 302 " model vdw 1.709 2.320 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 302 " model vdw 1.709 2.320 nonbonded pdb=" NE2 HIS C 245 " pdb="CU CU C 301 " model vdw 1.710 2.320 nonbonded pdb=" ND1 HIS I 33 " pdb="CU CU I 502 " model vdw 1.809 2.320 nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU A 501 " model vdw 1.810 2.320 ... (remaining 200727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 414 or resid 502)) selection = (chain 'E' and (resid 33 through 414 or resid 502)) selection = (chain 'I' and (resid 33 through 414 or resid 502)) } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 304)) selection = (chain 'F' and (resid 7 through 247 or resid 304)) selection = (chain 'J' and (resid 7 through 247 or resid 304)) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 308)) selection = (chain 'G' and (resid 45 through 280 or resid 308)) selection = (chain 'K' and (resid 45 through 280 or resid 308)) } 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 group one per residue 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.270 Construct map_model_manager: 0.010 Extract box with map and model: 17.720 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 62.960 Find NCS groups from input model: 1.410 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 0.127 22899 Z= 0.573 Angle : 0.983 14.006 31017 Z= 0.497 Chirality : 0.051 0.314 3201 Planarity : 0.005 0.051 3717 Dihedral : 20.564 177.347 8595 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.14 % Favored : 93.51 % Rotamer: Outliers : 0.82 % Allowed : 1.23 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2559 helix: 0.90 (0.15), residues: 1176 sheet: -0.29 (0.30), residues: 363 loop : -0.65 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 234 HIS 0.047 0.003 HIS E 33 PHE 0.030 0.002 PHE K 235 TYR 0.026 0.002 TYR K 210 ARG 0.007 0.001 ARG A 45 *********************** 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 332 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 314 time to evaluate : 2.564 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 142 MET cc_start: 0.8330 (tpp) cc_final: 0.7931 (tpt) REVERT: A 414 MET cc_start: 0.5856 (OUTLIER) cc_final: 0.5540 (mtp) REVERT: G 210 TYR cc_start: 0.8676 (t80) cc_final: 0.8141 (t80) REVERT: G 214 VAL cc_start: 0.8349 (t) cc_final: 0.7928 (m) REVERT: G 228 GLU cc_start: 0.7078 (mp0) cc_final: 0.6709 (mp0) REVERT: K 214 VAL cc_start: 0.8422 (t) cc_final: 0.7948 (m) REVERT: E 414 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5696 (mtp) REVERT: I 142 MET cc_start: 0.8290 (tpp) cc_final: 0.7624 (tpt) REVERT: I 381 TYR cc_start: 0.6684 (t80) cc_final: 0.6344 (t80) outliers start: 18 outliers final: 9 residues processed: 319 average time/residue: 0.3396 time to fit residues: 170.3595 Evaluate side-chains 281 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 270 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 234 TRP Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 414 MET 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: 9.9990 chunk 107 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN F 160 ASN F 240 ASN J 160 ASN J 240 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22899 Z= 0.350 Angle : 0.695 7.993 31017 Z= 0.352 Chirality : 0.049 0.188 3201 Planarity : 0.005 0.059 3717 Dihedral : 21.189 166.174 3987 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.69 % Favored : 94.96 % Rotamer: Outliers : 2.01 % Allowed : 7.50 % Favored : 90.49 % 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: -0.09 (0.16), residues: 2559 helix: 0.82 (0.15), residues: 1173 sheet: -0.58 (0.28), residues: 363 loop : -0.79 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 77 HIS 0.007 0.002 HIS I 192 PHE 0.027 0.002 PHE C 92 TYR 0.041 0.002 TYR G 184 ARG 0.006 0.001 ARG A 375 *********************** 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 329 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 285 time to evaluate : 2.567 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 142 MET cc_start: 0.8315 (tpp) cc_final: 0.8064 (ttm) REVERT: A 375 ARG cc_start: 0.7881 (mtp-110) cc_final: 0.7586 (mmp80) REVERT: A 414 MET cc_start: 0.6180 (OUTLIER) cc_final: 0.5975 (mtp) REVERT: B 236 ARG cc_start: 0.8147 (mmt90) cc_final: 0.7829 (ttm-80) REVERT: G 88 TYR cc_start: 0.7817 (m-80) cc_final: 0.7499 (m-80) REVERT: K 72 TYR cc_start: 0.7995 (m-80) cc_final: 0.7593 (m-80) REVERT: J 236 ARG cc_start: 0.8143 (mmt90) cc_final: 0.7810 (ttm-80) REVERT: E 323 ARG cc_start: 0.8724 (mtp180) cc_final: 0.8471 (mtm180) REVERT: E 375 ARG cc_start: 0.7930 (mtp-110) cc_final: 0.7654 (mtp85) REVERT: E 406 ASP cc_start: 0.7942 (p0) cc_final: 0.7682 (p0) REVERT: E 414 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5905 (mtp) outliers start: 44 outliers final: 22 residues processed: 305 average time/residue: 0.3420 time to fit residues: 162.7060 Evaluate side-chains 275 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 251 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 234 TRP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 300 MET Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 288 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 250 optimal weight: 10.0000 chunk 206 optimal weight: 0.7980 chunk 230 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 186 optimal weight: 0.0980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22899 Z= 0.176 Angle : 0.564 7.398 31017 Z= 0.290 Chirality : 0.045 0.228 3201 Planarity : 0.004 0.058 3717 Dihedral : 20.252 163.982 3981 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.65 % Favored : 95.00 % Rotamer: Outliers : 1.65 % Allowed : 9.79 % Favored : 88.57 % 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: 0.26 (0.17), residues: 2559 helix: 1.16 (0.15), residues: 1161 sheet: -0.44 (0.28), residues: 363 loop : -0.65 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 237 HIS 0.003 0.001 HIS G 160 PHE 0.015 0.001 PHE B 31 TYR 0.030 0.001 TYR K 184 ARG 0.005 0.000 ARG I 313 *********************** 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 302 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 266 time to evaluate : 2.341 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 375 ARG cc_start: 0.7674 (mtp-110) cc_final: 0.7435 (mtm110) REVERT: C 169 PHE cc_start: 0.7195 (m-10) cc_final: 0.6963 (m-10) REVERT: B 141 TYR cc_start: 0.8349 (m-80) cc_final: 0.8004 (m-80) REVERT: B 160 ASN cc_start: 0.8933 (m-40) cc_final: 0.8433 (m-40) REVERT: B 236 ARG cc_start: 0.8085 (mmt90) cc_final: 0.7778 (ttm-80) REVERT: E 375 ARG cc_start: 0.7716 (mtp-110) cc_final: 0.7425 (mtp85) REVERT: E 406 ASP cc_start: 0.7856 (p0) cc_final: 0.7558 (p0) REVERT: I 62 ASN cc_start: 0.8654 (m-40) cc_final: 0.8451 (m-40) outliers start: 36 outliers final: 24 residues processed: 287 average time/residue: 0.3297 time to fit residues: 150.3868 Evaluate side-chains 262 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 238 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 234 TRP Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 300 MET Chi-restraints excluded: chain I residue 91 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 246 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 22899 Z= 0.420 Angle : 0.693 8.322 31017 Z= 0.356 Chirality : 0.050 0.220 3201 Planarity : 0.005 0.054 3717 Dihedral : 20.096 162.146 3975 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.71 % Favored : 93.94 % Rotamer: Outliers : 3.16 % Allowed : 10.93 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2559 helix: 0.76 (0.15), residues: 1155 sheet: -0.63 (0.28), residues: 348 loop : -0.95 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 77 HIS 0.009 0.002 HIS I 192 PHE 0.025 0.002 PHE B 31 TYR 0.032 0.002 TYR K 184 ARG 0.008 0.001 ARG I 375 *********************** 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 349 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 280 time to evaluate : 2.244 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 142 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7842 (ttm) REVERT: A 375 ARG cc_start: 0.7758 (mtp-110) cc_final: 0.7464 (mmp80) REVERT: B 133 THR cc_start: 0.8801 (p) cc_final: 0.8590 (p) REVERT: B 141 TYR cc_start: 0.8637 (m-80) cc_final: 0.8377 (m-80) REVERT: B 236 ARG cc_start: 0.8137 (mmt90) cc_final: 0.7923 (mmt90) REVERT: G 116 ASP cc_start: 0.7202 (t0) cc_final: 0.6931 (m-30) REVERT: K 90 MET cc_start: 0.7964 (mmm) cc_final: 0.7759 (tpp) REVERT: J 178 MET cc_start: 0.8585 (mtt) cc_final: 0.8174 (mtt) REVERT: J 236 ARG cc_start: 0.7837 (mmt90) cc_final: 0.7578 (ttm-80) REVERT: E 375 ARG cc_start: 0.7755 (mtp-110) cc_final: 0.7411 (mtp85) REVERT: E 406 ASP cc_start: 0.7942 (p0) cc_final: 0.7732 (p0) REVERT: I 227 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8766 (mt) outliers start: 69 outliers final: 41 residues processed: 322 average time/residue: 0.3147 time to fit residues: 162.9831 Evaluate side-chains 307 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 264 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 219 MET Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 359 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 221 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22899 Z= 0.209 Angle : 0.573 6.884 31017 Z= 0.296 Chirality : 0.045 0.222 3201 Planarity : 0.004 0.049 3717 Dihedral : 19.344 158.321 3971 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.53 % Favored : 95.12 % Rotamer: Outliers : 2.65 % Allowed : 12.57 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.02 (0.17), residues: 2559 helix: 1.01 (0.15), residues: 1161 sheet: -0.67 (0.27), residues: 378 loop : -0.78 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 77 HIS 0.005 0.001 HIS K 160 PHE 0.016 0.001 PHE B 31 TYR 0.026 0.001 TYR C 184 ARG 0.004 0.000 ARG I 313 *********************** 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 296 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 238 time to evaluate : 2.302 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 375 ARG cc_start: 0.7649 (mtp-110) cc_final: 0.7393 (mtm110) REVERT: B 141 TYR cc_start: 0.8552 (m-80) cc_final: 0.8180 (m-80) REVERT: B 178 MET cc_start: 0.8618 (mtt) cc_final: 0.8250 (mtt) REVERT: B 236 ARG cc_start: 0.8100 (mmt90) cc_final: 0.7890 (mmt90) REVERT: G 90 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.6949 (mmt) REVERT: G 116 ASP cc_start: 0.6945 (t0) cc_final: 0.6742 (m-30) REVERT: K 90 MET cc_start: 0.7929 (mmm) cc_final: 0.7716 (tpp) REVERT: K 240 PHE cc_start: 0.5882 (OUTLIER) cc_final: 0.4471 (t80) REVERT: J 236 ARG cc_start: 0.7814 (mmt90) cc_final: 0.7588 (mmt90) REVERT: E 375 ARG cc_start: 0.7668 (mtp-110) cc_final: 0.7367 (mtp85) REVERT: E 406 ASP cc_start: 0.7886 (p0) cc_final: 0.7608 (p0) REVERT: I 381 TYR cc_start: 0.6893 (t80) cc_final: 0.6252 (t80) outliers start: 58 outliers final: 34 residues processed: 274 average time/residue: 0.3138 time to fit residues: 139.3825 Evaluate side-chains 269 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 233 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 90 MET Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 234 TRP Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 7.9990 chunk 221 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 246 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 22899 Z= 0.383 Angle : 0.657 7.170 31017 Z= 0.337 Chirality : 0.049 0.216 3201 Planarity : 0.005 0.048 3717 Dihedral : 19.228 158.134 3971 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.59 % Favored : 94.06 % Rotamer: Outliers : 3.02 % Allowed : 13.35 % Favored : 83.63 % 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: -0.26 (0.16), residues: 2559 helix: 0.79 (0.15), residues: 1158 sheet: -0.79 (0.27), residues: 363 loop : -0.96 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 77 HIS 0.007 0.002 HIS I 192 PHE 0.024 0.002 PHE B 31 TYR 0.027 0.002 TYR K 184 ARG 0.004 0.001 ARG E 215 *********************** 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 324 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 258 time to evaluate : 2.260 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 231 THR cc_start: 0.8092 (p) cc_final: 0.7877 (p) REVERT: A 375 ARG cc_start: 0.7729 (mtp-110) cc_final: 0.7407 (mmp80) REVERT: B 141 TYR cc_start: 0.8696 (m-80) cc_final: 0.8391 (m-80) REVERT: B 178 MET cc_start: 0.8642 (mtt) cc_final: 0.8340 (mtt) REVERT: G 116 ASP cc_start: 0.7229 (t0) cc_final: 0.6959 (m-30) REVERT: K 90 MET cc_start: 0.7885 (mmm) cc_final: 0.7670 (tpp) REVERT: K 240 PHE cc_start: 0.5900 (OUTLIER) cc_final: 0.4466 (t80) REVERT: F 150 MET cc_start: 0.7222 (mmt) cc_final: 0.6860 (mtp) REVERT: J 150 MET cc_start: 0.7226 (mmt) cc_final: 0.7009 (mtp) REVERT: J 236 ARG cc_start: 0.7851 (mmt90) cc_final: 0.7650 (mmt90) REVERT: E 375 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.7338 (mmp80) REVERT: E 406 ASP cc_start: 0.7962 (p0) cc_final: 0.7717 (p0) REVERT: I 41 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.8042 (p90) REVERT: I 227 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8780 (mt) REVERT: I 381 TYR cc_start: 0.6914 (t80) cc_final: 0.6254 (t80) outliers start: 66 outliers final: 47 residues processed: 297 average time/residue: 0.3171 time to fit residues: 151.6048 Evaluate side-chains 297 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 247 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 219 MET Chi-restraints excluded: chain K residue 234 TRP Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 41 PHE 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 I residue 288 ASP Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 387 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 245 optimal weight: 6.9990 chunk 153 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22899 Z= 0.184 Angle : 0.559 6.761 31017 Z= 0.288 Chirality : 0.044 0.218 3201 Planarity : 0.004 0.046 3717 Dihedral : 18.409 157.289 3971 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.38 % Favored : 95.31 % Rotamer: Outliers : 2.79 % Allowed : 13.72 % Favored : 83.49 % 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: 0.07 (0.17), residues: 2559 helix: 1.10 (0.15), residues: 1161 sheet: -0.74 (0.27), residues: 381 loop : -0.78 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 77 HIS 0.004 0.001 HIS K 160 PHE 0.015 0.001 PHE B 31 TYR 0.024 0.001 TYR C 184 ARG 0.005 0.000 ARG B 236 *********************** 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 303 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 242 time to evaluate : 2.355 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 375 ARG cc_start: 0.7606 (mtp-110) cc_final: 0.7232 (mmp80) REVERT: B 141 TYR cc_start: 0.8563 (m-80) cc_final: 0.8196 (m-80) REVERT: B 178 MET cc_start: 0.8636 (mtt) cc_final: 0.8323 (mtt) REVERT: G 116 ASP cc_start: 0.6998 (t0) cc_final: 0.6783 (m-30) REVERT: K 90 MET cc_start: 0.7916 (mmm) cc_final: 0.7678 (tpp) REVERT: K 210 TYR cc_start: 0.8830 (t80) cc_final: 0.8297 (t80) REVERT: K 240 PHE cc_start: 0.5842 (OUTLIER) cc_final: 0.4544 (t80) REVERT: E 375 ARG cc_start: 0.7586 (mtp-110) cc_final: 0.7275 (mmp80) REVERT: E 406 ASP cc_start: 0.7889 (p0) cc_final: 0.7574 (p0) REVERT: I 321 SER cc_start: 0.8672 (OUTLIER) cc_final: 0.8413 (p) REVERT: I 381 TYR cc_start: 0.6818 (t80) cc_final: 0.6362 (t80) outliers start: 61 outliers final: 43 residues processed: 283 average time/residue: 0.3352 time to fit residues: 154.4546 Evaluate side-chains 277 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 232 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 219 MET Chi-restraints excluded: chain K residue 234 TRP Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 387 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 167 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN G 161 GLN J 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 22899 Z= 0.431 Angle : 0.683 7.478 31017 Z= 0.349 Chirality : 0.050 0.210 3201 Planarity : 0.005 0.045 3717 Dihedral : 18.668 158.485 3971 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.10 % Favored : 93.55 % Rotamer: Outliers : 3.11 % Allowed : 13.72 % Favored : 83.17 % 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: -0.34 (0.16), residues: 2559 helix: 0.73 (0.15), residues: 1164 sheet: -0.92 (0.27), residues: 381 loop : -0.97 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 234 HIS 0.007 0.002 HIS K 160 PHE 0.025 0.002 PHE B 31 TYR 0.028 0.002 TYR K 184 ARG 0.006 0.001 ARG A 360 *********************** 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 335 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 267 time to evaluate : 2.581 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 231 THR cc_start: 0.8132 (p) cc_final: 0.7896 (p) REVERT: A 375 ARG cc_start: 0.7707 (mtp-110) cc_final: 0.7383 (mmp80) REVERT: A 404 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: C 259 MET cc_start: 0.8635 (mtm) cc_final: 0.8369 (ptp) REVERT: B 141 TYR cc_start: 0.8751 (m-80) cc_final: 0.8455 (m-80) REVERT: B 150 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6966 (mtp) REVERT: B 178 MET cc_start: 0.8648 (mtt) cc_final: 0.8380 (mtt) REVERT: G 116 ASP cc_start: 0.7367 (t0) cc_final: 0.7047 (m-30) REVERT: K 90 MET cc_start: 0.7865 (mmm) cc_final: 0.7640 (tpp) REVERT: K 240 PHE cc_start: 0.5908 (OUTLIER) cc_final: 0.4423 (t80) REVERT: F 150 MET cc_start: 0.7204 (mmt) cc_final: 0.6941 (mtp) REVERT: E 375 ARG cc_start: 0.7655 (mtp-110) cc_final: 0.7342 (mmp80) REVERT: E 406 ASP cc_start: 0.7999 (p0) cc_final: 0.7766 (p0) REVERT: I 227 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8746 (mt) REVERT: I 381 TYR cc_start: 0.6879 (t80) cc_final: 0.6446 (t80) outliers start: 68 outliers final: 46 residues processed: 307 average time/residue: 0.3154 time to fit residues: 155.3377 Evaluate side-chains 309 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 259 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 219 MET Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 387 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 216 optimal weight: 0.8980 chunk 228 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22899 Z= 0.201 Angle : 0.571 6.728 31017 Z= 0.293 Chirality : 0.045 0.219 3201 Planarity : 0.004 0.045 3717 Dihedral : 18.011 157.938 3971 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.73 % Favored : 95.00 % Rotamer: Outliers : 2.93 % Allowed : 14.31 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.01 (0.17), residues: 2559 helix: 1.03 (0.15), residues: 1164 sheet: -0.82 (0.27), residues: 381 loop : -0.81 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 77 HIS 0.004 0.001 HIS I 139 PHE 0.016 0.001 PHE B 31 TYR 0.024 0.001 TYR C 184 ARG 0.005 0.000 ARG I 386 *********************** 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 319 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 255 time to evaluate : 2.231 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 231 THR cc_start: 0.8088 (p) cc_final: 0.7849 (p) REVERT: A 375 ARG cc_start: 0.7609 (mtp-110) cc_final: 0.7234 (mmp80) REVERT: C 116 ASP cc_start: 0.7258 (t0) cc_final: 0.6977 (m-30) REVERT: B 141 TYR cc_start: 0.8608 (m-80) cc_final: 0.8306 (m-80) REVERT: B 178 MET cc_start: 0.8613 (mtt) cc_final: 0.8317 (mtt) REVERT: G 116 ASP cc_start: 0.7160 (t0) cc_final: 0.6913 (m-30) REVERT: K 90 MET cc_start: 0.7876 (mmm) cc_final: 0.7642 (tpp) REVERT: K 240 PHE cc_start: 0.5847 (OUTLIER) cc_final: 0.4508 (t80) REVERT: F 141 TYR cc_start: 0.8661 (m-80) cc_final: 0.8273 (m-80) REVERT: E 381 TYR cc_start: 0.6931 (t80) cc_final: 0.6421 (t80) REVERT: E 406 ASP cc_start: 0.7993 (p0) cc_final: 0.7608 (p0) REVERT: I 321 SER cc_start: 0.8665 (OUTLIER) cc_final: 0.8425 (p) outliers start: 64 outliers final: 46 residues processed: 293 average time/residue: 0.3212 time to fit residues: 150.1574 Evaluate side-chains 292 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 244 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 219 MET Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 387 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 8.9990 chunk 242 optimal weight: 6.9990 chunk 147 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 168 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 202 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22899 Z= 0.226 Angle : 0.581 6.813 31017 Z= 0.297 Chirality : 0.046 0.218 3201 Planarity : 0.004 0.046 3717 Dihedral : 17.729 158.960 3971 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.04 % Favored : 94.69 % Rotamer: Outliers : 2.56 % Allowed : 14.68 % Favored : 82.76 % 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: 0.08 (0.17), residues: 2559 helix: 1.12 (0.15), residues: 1149 sheet: -0.78 (0.27), residues: 381 loop : -0.76 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 77 HIS 0.005 0.001 HIS G 245 PHE 0.018 0.001 PHE B 31 TYR 0.025 0.002 TYR K 184 ARG 0.005 0.000 ARG E 270 ********************** 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 297 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 241 time to evaluate : 2.407 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 231 THR cc_start: 0.8078 (p) cc_final: 0.7846 (p) REVERT: A 375 ARG cc_start: 0.7593 (mtp-110) cc_final: 0.7263 (mmp80) REVERT: C 116 ASP cc_start: 0.7288 (t0) cc_final: 0.7004 (m-30) REVERT: B 141 TYR cc_start: 0.8646 (m-80) cc_final: 0.8284 (m-80) REVERT: B 178 MET cc_start: 0.8625 (mtt) cc_final: 0.8327 (mtt) REVERT: G 116 ASP cc_start: 0.7173 (t0) cc_final: 0.6925 (m-30) REVERT: G 176 GLU cc_start: 0.8443 (tt0) cc_final: 0.8017 (tt0) REVERT: K 90 MET cc_start: 0.7899 (mmm) cc_final: 0.7657 (tpp) REVERT: K 240 PHE cc_start: 0.5844 (OUTLIER) cc_final: 0.4477 (t80) REVERT: F 141 TYR cc_start: 0.8598 (m-80) cc_final: 0.8157 (m-80) REVERT: F 178 MET cc_start: 0.8422 (mmm) cc_final: 0.8181 (mtt) REVERT: J 178 MET cc_start: 0.8480 (mmm) cc_final: 0.8228 (mtt) REVERT: E 406 ASP cc_start: 0.7954 (p0) cc_final: 0.7657 (p0) REVERT: I 321 SER cc_start: 0.8667 (OUTLIER) cc_final: 0.8438 (p) outliers start: 56 outliers final: 51 residues processed: 275 average time/residue: 0.3058 time to fit residues: 137.3168 Evaluate side-chains 288 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 235 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 219 MET Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 387 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 3.9990 chunk 215 optimal weight: 0.1980 chunk 61 optimal weight: 0.0050 chunk 186 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 202 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 25 optimal weight: 0.0060 chunk 37 optimal weight: 8.9990 overall best weight: 0.6012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.137239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.118074 restraints weight = 23523.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.118738 restraints weight = 22726.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.118759 restraints weight = 22087.163| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22899 Z= 0.171 Angle : 0.551 6.875 31017 Z= 0.282 Chirality : 0.044 0.223 3201 Planarity : 0.004 0.046 3717 Dihedral : 17.228 159.521 3971 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.77 % Favored : 95.00 % Rotamer: Outliers : 2.38 % Allowed : 14.95 % Favored : 82.67 % 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: 0.20 (0.17), residues: 2559 helix: 1.24 (0.15), residues: 1149 sheet: -0.73 (0.27), residues: 378 loop : -0.71 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 152 HIS 0.003 0.001 HIS K 160 PHE 0.015 0.001 PHE J 222 TYR 0.025 0.001 TYR K 184 ARG 0.006 0.000 ARG E 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4143.10 seconds wall clock time: 77 minutes 22.77 seconds (4642.77 seconds total)