Starting phenix.real_space_refine on Fri Feb 23 09:22:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4o_25683/02_2024/7t4o_25683_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4o_25683/02_2024/7t4o_25683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4o_25683/02_2024/7t4o_25683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4o_25683/02_2024/7t4o_25683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4o_25683/02_2024/7t4o_25683_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4o_25683/02_2024/7t4o_25683_trim_updated.pdb" } resolution = 3.65 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= 0.003 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 17751 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 5 5.60 5 P 12 5.49 5 S 87 5.16 5 C 12684 2.51 5 N 3054 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 382": "OD1" <-> "OD2" Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "G TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 242": "NH1" <-> "NH2" Residue "J PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 242": "NH1" <-> "NH2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 276": "OE1" <-> "OE2" Residue "E GLU 287": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "E TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 382": "OD1" <-> "OD2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 117": "OE1" <-> "OE2" Residue "I PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 276": "OE1" <-> "OE2" Residue "I GLU 287": "OE1" <-> "OE2" Residue "I GLU 338": "OE1" <-> "OE2" Residue "I ASP 368": "OD1" <-> "OD2" Residue "I GLU 372": "OE1" <-> "OE2" Residue "I TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 382": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19142 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: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 140} Chain breaks: 3 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: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 140} Chain breaks: 3 Chain: "K" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 140} Chain breaks: 3 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'P1O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'P1O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'P1O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.06, per 1000 atoms: 0.53 Number of scatterers: 19142 At special positions: 0 Unit cell: (106.288, 106.288, 121.107, 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 5 28.99 S 87 16.00 P 12 15.00 O 3300 8.00 N 3054 7.00 C 12684 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: 7.76 Conformation dependent library (CDL) restraints added in 3.0 seconds 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4254 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 24 sheets defined 44.0% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 185 through 207 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 232 through 256 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 377 through 380 removed outlier: 4.120A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 380' Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.549A pdb=" N LEU C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 149 removed outlier: 3.686A pdb=" N THR C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 158 removed outlier: 3.549A pdb=" N GLY C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 198 Processing helix chain 'C' and resid 208 through 219 Proline residue: C 217 - end of helix Processing helix chain 'C' and resid 248 through 269 removed outlier: 4.022A pdb=" N LEU C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU C 256 " --> pdb=" O GLY C 252 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N MET C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 44 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 59 through 83 Proline residue: B 65 - end of helix removed outlier: 4.615A pdb=" N THR B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N PHE B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Proline residue: B 72 - end of helix removed outlier: 3.681A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 106 Processing helix chain 'B' and resid 116 through 119 No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 141 through 168 removed outlier: 4.194A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Proline residue: B 158 - end of helix Proline residue: B 162 - end of helix Proline residue: B 166 - end of helix Processing helix chain 'B' and resid 180 through 187 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 212 through 237 removed outlier: 3.822A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 113 removed outlier: 3.549A pdb=" N LEU G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 149 removed outlier: 3.687A pdb=" N THR G 133 " --> pdb=" O ARG G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 158 removed outlier: 3.548A pdb=" N GLY G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 198 Processing helix chain 'G' and resid 208 through 219 Proline residue: G 217 - end of helix Processing helix chain 'G' and resid 248 through 269 removed outlier: 4.022A pdb=" N LEU G 254 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA G 255 " --> pdb=" O PHE G 251 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU G 256 " --> pdb=" O GLY G 252 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA G 257 " --> pdb=" O TRP G 253 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N MET G 259 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY G 260 " --> pdb=" O LEU G 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 113 removed outlier: 3.550A pdb=" N LEU K 111 " --> pdb=" O LEU K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 149 removed outlier: 3.687A pdb=" N THR K 133 " --> pdb=" O ARG K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 158 removed outlier: 3.549A pdb=" N GLY K 157 " --> pdb=" O THR K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 198 Processing helix chain 'K' and resid 208 through 219 Proline residue: K 217 - end of helix Processing helix chain 'K' and resid 248 through 269 removed outlier: 4.022A pdb=" N LEU K 254 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA K 255 " --> pdb=" O PHE K 251 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU K 256 " --> pdb=" O GLY K 252 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA K 257 " --> pdb=" O TRP K 253 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N MET K 259 " --> pdb=" O ALA K 255 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY K 260 " --> pdb=" O LEU K 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 44 Processing helix chain 'F' and resid 46 through 50 Processing helix chain 'F' and resid 59 through 83 Proline residue: F 65 - end of helix removed outlier: 4.616A pdb=" N THR F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix removed outlier: 3.680A pdb=" N GLU F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 106 Processing helix chain 'F' and resid 116 through 119 No H-bonds generated for 'chain 'F' and resid 116 through 119' Processing helix chain 'F' and resid 125 through 136 Processing helix chain 'F' and resid 141 through 168 removed outlier: 4.194A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET F 150 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Proline residue: F 162 - end of helix Proline residue: F 166 - end of helix Processing helix chain 'F' and resid 180 through 187 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 212 through 237 removed outlier: 3.821A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 44 Processing helix chain 'J' and resid 46 through 50 Processing helix chain 'J' and resid 59 through 83 Proline residue: J 65 - end of helix removed outlier: 4.615A pdb=" N THR J 70 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE J 71 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Proline residue: J 72 - end of helix removed outlier: 3.681A pdb=" N GLU J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 106 Processing helix chain 'J' and resid 116 through 119 No H-bonds generated for 'chain 'J' and resid 116 through 119' Processing helix chain 'J' and resid 125 through 136 Processing helix chain 'J' and resid 141 through 168 removed outlier: 4.195A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET J 150 " --> pdb=" O ILE J 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) Proline residue: J 158 - end of helix Proline residue: J 162 - end of helix Proline residue: J 166 - end of helix Processing helix chain 'J' and resid 180 through 187 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'J' and resid 212 through 237 removed outlier: 3.821A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 44 Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 185 through 207 Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'E' and resid 232 through 256 Processing helix chain 'E' and resid 369 through 373 Processing helix chain 'E' and resid 377 through 380 removed outlier: 4.121A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'I' and resid 40 through 44 Processing helix chain 'I' and resid 163 through 165 No H-bonds generated for 'chain 'I' and resid 163 through 165' Processing helix chain 'I' and resid 185 through 207 Processing helix chain 'I' and resid 213 through 220 Processing helix chain 'I' and resid 232 through 256 Processing helix chain 'I' and resid 369 through 373 Processing helix chain 'I' and resid 377 through 380 removed outlier: 4.120A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 377 through 380' Processing sheet with id= A, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.927A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 58 through 60 removed outlier: 8.450A pdb=" N VAL A 59 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR A 158 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 142 through 144 removed outlier: 3.600A 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: 3.760A pdb=" N LYS A 285 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 360 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 298 through 300 removed outlier: 3.670A pdb=" N TYR A 291 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.607A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU A 390 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 171 through 173 Processing sheet with id= I, first strand: chain 'F' and resid 171 through 173 Processing sheet with id= J, first strand: chain 'J' and resid 171 through 173 Processing sheet with id= K, first strand: chain 'E' and resid 47 through 50 removed outlier: 6.926A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 58 through 60 removed outlier: 8.450A pdb=" N VAL E 59 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR E 158 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 142 through 144 removed outlier: 3.599A 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: 3.760A pdb=" N LYS E 285 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG E 360 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 298 through 300 removed outlier: 3.670A pdb=" N TYR E 291 " --> pdb=" O ILE E 410 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 323 through 325 removed outlier: 6.606A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.260A 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: 6.927A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 58 through 60 removed outlier: 8.449A pdb=" N VAL I 59 " --> pdb=" O TRP I 156 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR I 158 " --> pdb=" O VAL I 59 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 142 through 144 removed outlier: 3.599A 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: 3.759A pdb=" N LYS I 285 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG I 360 " --> pdb=" O ILE I 304 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 298 through 300 removed outlier: 3.671A pdb=" N TYR I 291 " --> pdb=" O ILE I 410 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 323 through 325 removed outlier: 6.606A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU I 390 " --> pdb=" O PHE I 317 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2466 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: 5.54 Time building geometry restraints manager: 8.31 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: 3086 1.32 - 1.45: 5668 1.45 - 1.57: 10746 1.57 - 1.69: 39 1.69 - 1.81: 168 Bond restraints: 19707 Sorted by residual: bond pdb=" C19 P1O G 302 " pdb=" O7 P1O G 302 " ideal model delta sigma weight residual 1.331 1.456 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C19 P1O K 302 " pdb=" O7 P1O K 302 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C19 P1O C 302 " pdb=" O7 P1O C 302 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C9 P1O K 301 " pdb=" O5 P1O K 301 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C9 P1O C 301 " pdb=" O5 P1O C 301 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.77e+01 ... (remaining 19702 not shown) Histogram of bond angle deviations from ideal: 97.66 - 104.99: 435 104.99 - 112.32: 9852 112.32 - 119.65: 6654 119.65 - 126.98: 9434 126.98 - 134.30: 382 Bond angle restraints: 26757 Sorted by residual: angle pdb=" CA PRO K 200 " pdb=" C PRO K 200 " pdb=" O PRO K 200 " ideal model delta sigma weight residual 122.15 116.97 5.18 1.32e+00 5.74e-01 1.54e+01 angle pdb=" CA PRO C 200 " pdb=" C PRO C 200 " pdb=" O PRO C 200 " ideal model delta sigma weight residual 122.15 116.97 5.18 1.32e+00 5.74e-01 1.54e+01 angle pdb=" CA PRO G 200 " pdb=" C PRO G 200 " pdb=" O PRO G 200 " ideal model delta sigma weight residual 122.15 116.97 5.18 1.32e+00 5.74e-01 1.54e+01 angle pdb=" C GLU I 287 " pdb=" N ASP I 288 " pdb=" CA ASP I 288 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C GLU A 287 " pdb=" N ASP A 288 " pdb=" CA ASP A 288 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 ... (remaining 26752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.46: 10810 30.46 - 60.91: 536 60.91 - 91.37: 24 91.37 - 121.83: 6 121.83 - 152.28: 12 Dihedral angle restraints: 11388 sinusoidal: 4740 harmonic: 6648 Sorted by residual: dihedral pdb=" C1 P1O G 302 " pdb=" O3 P1O G 302 " pdb=" P1 P1O G 302 " pdb=" O4 P1O G 302 " ideal model delta sinusoidal sigma weight residual 168.75 16.47 152.28 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C1 P1O C 302 " pdb=" O3 P1O C 302 " pdb=" P1 P1O C 302 " pdb=" O4 P1O C 302 " ideal model delta sinusoidal sigma weight residual 168.75 16.51 152.24 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C1 P1O K 302 " pdb=" O3 P1O K 302 " pdb=" P1 P1O K 302 " pdb=" O4 P1O K 302 " ideal model delta sinusoidal sigma weight residual 168.75 16.53 152.22 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 11385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1976 0.042 - 0.084: 558 0.084 - 0.126: 280 0.126 - 0.167: 21 0.167 - 0.209: 18 Chirality restraints: 2853 Sorted by residual: chirality pdb=" CA ILE G 193 " pdb=" N ILE G 193 " pdb=" C ILE G 193 " pdb=" CB ILE G 193 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE K 193 " pdb=" N ILE K 193 " pdb=" C ILE K 193 " pdb=" CB ILE K 193 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE C 193 " pdb=" N ILE C 193 " pdb=" C ILE C 193 " pdb=" CB ILE C 193 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2850 not shown) Planarity restraints: 3261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY I 95 " -0.046 5.00e-02 4.00e+02 7.09e-02 8.03e+00 pdb=" N PRO I 96 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO I 96 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 96 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 95 " -0.046 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO E 96 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 95 " 0.046 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO A 96 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " 0.038 5.00e-02 4.00e+02 ... (remaining 3258 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 62 2.40 - 3.03: 11426 3.03 - 3.65: 29848 3.65 - 4.28: 45402 4.28 - 4.90: 75689 Nonbonded interactions: 162427 Sorted by model distance: nonbonded pdb=" ND1 HIS E 33 " pdb="CU CU E 501 " model vdw 1.776 2.320 nonbonded pdb=" ND1 HIS I 33 " pdb="CU CU I 501 " model vdw 1.776 2.320 nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU A 501 " model vdw 1.777 2.320 nonbonded pdb=" NE2 HIS I 139 " pdb="CU CU I 501 " model vdw 1.783 2.320 nonbonded pdb=" NE2 HIS E 139 " pdb="CU CU E 501 " model vdw 1.783 2.320 ... (remaining 162422 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 501)) selection = (chain 'E' and (resid 33 through 414 or resid 501)) selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 303 through 304)) selection = (chain 'F' and (resid 7 through 247 or resid 303 through 304)) selection = (chain 'J' and (resid 7 through 247 or resid 303 through 304)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.020 Extract box with map and model: 6.980 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 49.770 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 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 : 0.007 0.125 19707 Z= 0.431 Angle : 0.877 10.792 26757 Z= 0.474 Chirality : 0.049 0.209 2853 Planarity : 0.005 0.071 3261 Dihedral : 16.839 152.282 7134 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.36 % Favored : 94.37 % Rotamer: Outliers : 1.85 % Allowed : 0.97 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: 0.05 (0.18), residues: 2274 helix: 0.63 (0.16), residues: 951 sheet: 0.51 (0.29), residues: 348 loop : -0.65 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP J 54 HIS 0.023 0.002 HIS E 33 PHE 0.026 0.001 PHE G 251 TYR 0.029 0.002 TYR F 37 ARG 0.007 0.001 ARG I 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 427 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6685 (pm20) REVERT: A 68 LYS cc_start: 0.7309 (mtmm) cc_final: 0.6315 (mtmt) REVERT: A 75 GLU cc_start: 0.7129 (mp0) cc_final: 0.6922 (pm20) REVERT: A 86 VAL cc_start: 0.8136 (t) cc_final: 0.7669 (t) REVERT: A 112 ARG cc_start: 0.7864 (ptp-170) cc_final: 0.7662 (ptp-170) REVERT: A 118 ILE cc_start: 0.8235 (mm) cc_final: 0.7830 (mm) REVERT: A 120 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7598 (mmtm) REVERT: A 158 THR cc_start: 0.7071 (m) cc_final: 0.6808 (m) REVERT: A 181 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 218 MET cc_start: 0.4968 (mmp) cc_final: 0.4494 (mmp) REVERT: A 237 MET cc_start: 0.6290 (mtt) cc_final: 0.5520 (mtt) REVERT: C 49 LYS cc_start: 0.5108 (OUTLIER) cc_final: 0.3943 (ptmm) REVERT: C 219 MET cc_start: 0.4543 (tmm) cc_final: 0.4311 (ppp) REVERT: C 266 PHE cc_start: 0.7410 (m-10) cc_final: 0.7069 (m-10) REVERT: B 202 LYS cc_start: 0.6585 (mttm) cc_final: 0.6208 (mtmt) REVERT: B 236 ARG cc_start: 0.5682 (tpp80) cc_final: 0.5134 (mmm160) REVERT: G 49 LYS cc_start: 0.4971 (OUTLIER) cc_final: 0.3869 (ptmt) REVERT: K 49 LYS cc_start: 0.4883 (OUTLIER) cc_final: 0.3854 (ptmt) REVERT: F 202 LYS cc_start: 0.6465 (mttm) cc_final: 0.6149 (mtmt) REVERT: F 236 ARG cc_start: 0.5715 (tpp80) cc_final: 0.5138 (mmm160) REVERT: J 202 LYS cc_start: 0.6592 (mttm) cc_final: 0.6241 (mtmt) REVERT: J 236 ARG cc_start: 0.5662 (tpp80) cc_final: 0.5111 (mmm160) REVERT: E 36 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6562 (ptpp) REVERT: E 68 LYS cc_start: 0.7199 (mtmm) cc_final: 0.6414 (mttp) REVERT: E 86 VAL cc_start: 0.8217 (t) cc_final: 0.7953 (t) REVERT: E 120 LYS cc_start: 0.8046 (mmtm) cc_final: 0.7537 (mmtm) REVERT: E 151 ILE cc_start: 0.8280 (mm) cc_final: 0.8041 (mm) REVERT: E 181 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7234 (mm-30) REVERT: E 237 MET cc_start: 0.6237 (mtt) cc_final: 0.5781 (mtt) REVERT: E 310 SER cc_start: 0.7863 (t) cc_final: 0.7535 (t) REVERT: I 57 GLU cc_start: 0.7516 (tm-30) cc_final: 0.6577 (pm20) REVERT: I 58 LYS cc_start: 0.7486 (ttmt) cc_final: 0.7202 (mtpp) REVERT: I 68 LYS cc_start: 0.7293 (mtmm) cc_final: 0.6366 (mtmt) REVERT: I 82 ASP cc_start: 0.6187 (m-30) cc_final: 0.5659 (m-30) REVERT: I 86 VAL cc_start: 0.8200 (t) cc_final: 0.7899 (t) REVERT: I 102 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6899 (mt-10) REVERT: I 120 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7605 (mmtm) REVERT: I 151 ILE cc_start: 0.8244 (mm) cc_final: 0.7973 (mm) REVERT: I 158 THR cc_start: 0.7167 (m) cc_final: 0.6892 (m) REVERT: I 181 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7189 (mm-30) REVERT: I 218 MET cc_start: 0.4867 (mmp) cc_final: 0.4635 (mmp) REVERT: I 237 MET cc_start: 0.6273 (mtt) cc_final: 0.5728 (mtt) REVERT: I 285 LYS cc_start: 0.6941 (tmmt) cc_final: 0.6664 (ttpt) REVERT: I 372 GLU cc_start: 0.6656 (pt0) cc_final: 0.5863 (tm-30) outliers start: 36 outliers final: 6 residues processed: 451 average time/residue: 0.3667 time to fit residues: 236.2119 Evaluate side-chains 282 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 272 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 251 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.0570 chunk 172 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 overall best weight: 2.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19707 Z= 0.257 Angle : 0.631 6.542 26757 Z= 0.321 Chirality : 0.046 0.204 2853 Planarity : 0.005 0.052 3261 Dihedral : 15.232 149.019 3013 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.23 % Favored : 94.50 % Rotamer: Outliers : 1.85 % Allowed : 8.92 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: 0.13 (0.17), residues: 2274 helix: 0.69 (0.16), residues: 1020 sheet: 0.65 (0.30), residues: 327 loop : -0.72 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 54 HIS 0.006 0.001 HIS B 11 PHE 0.032 0.002 PHE K 251 TYR 0.030 0.002 TYR C 184 ARG 0.006 0.001 ARG E 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 290 time to evaluate : 1.785 Fit side-chains REVERT: A 75 GLU cc_start: 0.7265 (mp0) cc_final: 0.6870 (pm20) REVERT: A 218 MET cc_start: 0.5037 (mmp) cc_final: 0.4774 (mmp) REVERT: A 237 MET cc_start: 0.6342 (mtt) cc_final: 0.5561 (mtt) REVERT: A 269 MET cc_start: 0.7781 (mtp) cc_final: 0.7431 (mtp) REVERT: C 49 LYS cc_start: 0.5617 (OUTLIER) cc_final: 0.4204 (ptmm) REVERT: C 210 TYR cc_start: 0.7280 (t80) cc_final: 0.7069 (t80) REVERT: C 219 MET cc_start: 0.4685 (tmm) cc_final: 0.4466 (ppp) REVERT: B 236 ARG cc_start: 0.5821 (tpp80) cc_final: 0.5030 (mtp85) REVERT: G 49 LYS cc_start: 0.5362 (OUTLIER) cc_final: 0.3984 (ptmt) REVERT: F 230 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6957 (ttt) REVERT: F 236 ARG cc_start: 0.5790 (tpp80) cc_final: 0.5025 (mtp85) REVERT: J 202 LYS cc_start: 0.6733 (mttm) cc_final: 0.6412 (mtmt) REVERT: J 236 ARG cc_start: 0.5765 (tpp80) cc_final: 0.4956 (mtp85) REVERT: E 237 MET cc_start: 0.6182 (mtt) cc_final: 0.5694 (mtt) REVERT: E 380 ILE cc_start: 0.6655 (tt) cc_final: 0.6367 (pt) REVERT: I 68 LYS cc_start: 0.7271 (mtmm) cc_final: 0.6550 (mttp) REVERT: I 82 ASP cc_start: 0.6026 (m-30) cc_final: 0.5590 (m-30) REVERT: I 237 MET cc_start: 0.6386 (mtt) cc_final: 0.5783 (mtt) REVERT: I 372 GLU cc_start: 0.6810 (pt0) cc_final: 0.6353 (pm20) REVERT: I 375 ARG cc_start: 0.7017 (mtt-85) cc_final: 0.6562 (ptp90) outliers start: 36 outliers final: 19 residues processed: 307 average time/residue: 0.3594 time to fit residues: 162.8151 Evaluate side-chains 288 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 266 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 251 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 184 optimal weight: 0.0050 chunk 205 optimal weight: 3.9990 chunk 70 optimal weight: 0.0010 chunk 166 optimal weight: 6.9990 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19707 Z= 0.254 Angle : 0.598 6.402 26757 Z= 0.306 Chirality : 0.046 0.216 2853 Planarity : 0.005 0.044 3261 Dihedral : 14.352 142.346 2999 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.34 % Rotamer: Outliers : 2.77 % Allowed : 10.92 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: 2274 helix: 0.78 (0.16), residues: 1002 sheet: 0.26 (0.30), residues: 339 loop : -0.75 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 253 HIS 0.007 0.001 HIS B 11 PHE 0.018 0.002 PHE G 251 TYR 0.029 0.002 TYR C 184 ARG 0.007 0.001 ARG E 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 287 time to evaluate : 2.223 Fit side-chains REVERT: A 75 GLU cc_start: 0.7456 (mp0) cc_final: 0.7223 (mp0) REVERT: A 82 ASP cc_start: 0.6124 (m-30) cc_final: 0.5728 (m-30) REVERT: A 90 ASN cc_start: 0.8182 (t0) cc_final: 0.7859 (t0) REVERT: A 218 MET cc_start: 0.5152 (mmp) cc_final: 0.4921 (mmp) REVERT: A 237 MET cc_start: 0.6358 (mtt) cc_final: 0.5857 (mtt) REVERT: A 269 MET cc_start: 0.7750 (mtp) cc_final: 0.7487 (mtp) REVERT: A 375 ARG cc_start: 0.7146 (mtt-85) cc_final: 0.6783 (ptp-170) REVERT: C 49 LYS cc_start: 0.5325 (OUTLIER) cc_final: 0.3884 (ptmm) REVERT: C 210 TYR cc_start: 0.7364 (t80) cc_final: 0.7157 (t80) REVERT: C 219 MET cc_start: 0.4897 (tmm) cc_final: 0.4674 (ppp) REVERT: B 236 ARG cc_start: 0.6119 (tpp80) cc_final: 0.5235 (mtp85) REVERT: G 49 LYS cc_start: 0.5228 (OUTLIER) cc_final: 0.3826 (ptmt) REVERT: F 236 ARG cc_start: 0.6175 (tpp80) cc_final: 0.5244 (mtp85) REVERT: J 236 ARG cc_start: 0.6068 (tpp80) cc_final: 0.5166 (mtp85) REVERT: E 75 GLU cc_start: 0.7869 (mp0) cc_final: 0.7641 (mp0) REVERT: E 82 ASP cc_start: 0.6197 (m-30) cc_final: 0.5795 (m-30) REVERT: E 237 MET cc_start: 0.6319 (mtt) cc_final: 0.5855 (mtt) REVERT: E 372 GLU cc_start: 0.7630 (mt-10) cc_final: 0.6734 (tm-30) REVERT: I 68 LYS cc_start: 0.7159 (mtmm) cc_final: 0.6469 (mttp) REVERT: I 82 ASP cc_start: 0.6069 (m-30) cc_final: 0.5580 (m-30) REVERT: I 218 MET cc_start: 0.4561 (mmp) cc_final: 0.4343 (mmp) REVERT: I 237 MET cc_start: 0.6375 (mtt) cc_final: 0.5854 (mtt) REVERT: I 372 GLU cc_start: 0.6945 (pt0) cc_final: 0.6084 (tm-30) outliers start: 54 outliers final: 35 residues processed: 315 average time/residue: 0.3258 time to fit residues: 154.1119 Evaluate side-chains 304 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 267 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 139 optimal weight: 0.9990 chunk 208 optimal weight: 8.9990 chunk 220 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN B 245 GLN F 245 GLN J 174 ASN J 245 GLN E 33 HIS I 38 GLN ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 19707 Z= 0.291 Angle : 0.617 7.550 26757 Z= 0.317 Chirality : 0.047 0.241 2853 Planarity : 0.005 0.047 3261 Dihedral : 14.022 145.297 2999 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.66 % Favored : 95.07 % Rotamer: Outliers : 3.18 % Allowed : 12.97 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: -0.15 (0.17), residues: 2274 helix: 0.58 (0.16), residues: 1005 sheet: 0.07 (0.28), residues: 342 loop : -0.82 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP G 253 HIS 0.008 0.001 HIS J 11 PHE 0.022 0.002 PHE K 251 TYR 0.029 0.002 TYR K 184 ARG 0.007 0.001 ARG I 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 283 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7572 (mp0) cc_final: 0.7221 (mp0) REVERT: A 82 ASP cc_start: 0.6135 (m-30) cc_final: 0.5773 (m-30) REVERT: A 219 VAL cc_start: 0.7074 (OUTLIER) cc_final: 0.6835 (m) REVERT: A 237 MET cc_start: 0.6385 (mtt) cc_final: 0.5872 (mtt) REVERT: A 269 MET cc_start: 0.7702 (mtp) cc_final: 0.7382 (mtp) REVERT: A 375 ARG cc_start: 0.7229 (mtt-85) cc_final: 0.6160 (mtp85) REVERT: A 401 GLN cc_start: 0.6766 (mt0) cc_final: 0.6506 (mt0) REVERT: A 406 ASP cc_start: 0.7944 (p0) cc_final: 0.7582 (p0) REVERT: C 49 LYS cc_start: 0.4937 (OUTLIER) cc_final: 0.3526 (ptmm) REVERT: C 219 MET cc_start: 0.5127 (tmm) cc_final: 0.4920 (ppp) REVERT: B 223 MET cc_start: 0.7317 (tpp) cc_final: 0.6860 (tpp) REVERT: B 236 ARG cc_start: 0.6336 (tpp80) cc_final: 0.5838 (mtt180) REVERT: G 49 LYS cc_start: 0.4866 (OUTLIER) cc_final: 0.3414 (ptmt) REVERT: F 236 ARG cc_start: 0.6350 (tpp80) cc_final: 0.6060 (mtt180) REVERT: J 22 ASP cc_start: 0.7635 (m-30) cc_final: 0.7296 (m-30) REVERT: J 236 ARG cc_start: 0.6327 (tpp80) cc_final: 0.5229 (mtp85) REVERT: J 242 ARG cc_start: 0.7163 (mmm-85) cc_final: 0.6596 (mtp180) REVERT: E 75 GLU cc_start: 0.7926 (mp0) cc_final: 0.7662 (pm20) REVERT: E 82 ASP cc_start: 0.6234 (m-30) cc_final: 0.5850 (m-30) REVERT: E 218 MET cc_start: 0.4870 (mmp) cc_final: 0.4565 (tpt) REVERT: E 219 VAL cc_start: 0.7017 (OUTLIER) cc_final: 0.6775 (m) REVERT: E 237 MET cc_start: 0.6311 (mtt) cc_final: 0.5838 (mtt) REVERT: E 298 MET cc_start: 0.7947 (ttt) cc_final: 0.7629 (ttp) REVERT: E 310 SER cc_start: 0.8013 (t) cc_final: 0.7694 (t) REVERT: E 375 ARG cc_start: 0.7372 (ptp-110) cc_final: 0.6942 (ptp-170) REVERT: E 406 ASP cc_start: 0.8098 (p0) cc_final: 0.7715 (p0) REVERT: I 60 LYS cc_start: 0.7202 (pttm) cc_final: 0.6611 (ptmt) REVERT: I 68 LYS cc_start: 0.7127 (mtmm) cc_final: 0.6476 (mttp) REVERT: I 82 ASP cc_start: 0.6064 (m-30) cc_final: 0.5620 (m-30) REVERT: I 181 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7574 (mm-30) REVERT: I 237 MET cc_start: 0.6391 (mtt) cc_final: 0.5905 (mtt) REVERT: I 372 GLU cc_start: 0.7038 (pt0) cc_final: 0.6183 (tm-30) REVERT: I 375 ARG cc_start: 0.7151 (mtt-85) cc_final: 0.6289 (mtp85) REVERT: I 401 GLN cc_start: 0.6715 (mt0) cc_final: 0.6434 (mt0) outliers start: 62 outliers final: 41 residues processed: 323 average time/residue: 0.3394 time to fit residues: 161.8855 Evaluate side-chains 314 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 269 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 381 TYR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 381 TYR Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 90 optimal weight: 0.0270 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 112 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS B 245 GLN ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 19707 Z= 0.313 Angle : 0.627 7.482 26757 Z= 0.323 Chirality : 0.047 0.150 2853 Planarity : 0.005 0.046 3261 Dihedral : 14.249 155.718 2996 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.35 % Favored : 95.51 % Rotamer: Outliers : 3.59 % Allowed : 13.69 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: -0.31 (0.17), residues: 2274 helix: 0.49 (0.16), residues: 1005 sheet: 0.09 (0.27), residues: 333 loop : -1.01 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 253 HIS 0.008 0.001 HIS B 11 PHE 0.021 0.002 PHE G 251 TYR 0.031 0.002 TYR K 184 ARG 0.005 0.001 ARG I 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 286 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7609 (mp0) cc_final: 0.7192 (mp0) REVERT: A 82 ASP cc_start: 0.6107 (m-30) cc_final: 0.5772 (m-30) REVERT: A 187 ASN cc_start: 0.8158 (t0) cc_final: 0.7760 (t0) REVERT: A 237 MET cc_start: 0.6409 (mtt) cc_final: 0.5792 (mtt) REVERT: A 310 SER cc_start: 0.7964 (t) cc_final: 0.7748 (m) REVERT: A 375 ARG cc_start: 0.7240 (mtt-85) cc_final: 0.6373 (mtp85) REVERT: A 406 ASP cc_start: 0.7909 (p0) cc_final: 0.7680 (p0) REVERT: C 49 LYS cc_start: 0.4546 (OUTLIER) cc_final: 0.2974 (mttt) REVERT: C 127 GLU cc_start: 0.6149 (tt0) cc_final: 0.5602 (tp30) REVERT: B 223 MET cc_start: 0.7382 (tpp) cc_final: 0.6868 (tpp) REVERT: B 236 ARG cc_start: 0.6546 (tpp80) cc_final: 0.5355 (mtp85) REVERT: G 49 LYS cc_start: 0.4409 (OUTLIER) cc_final: 0.3014 (ptmt) REVERT: F 229 PHE cc_start: 0.6834 (t80) cc_final: 0.6308 (t80) REVERT: F 236 ARG cc_start: 0.6475 (tpp80) cc_final: 0.5264 (mtp85) REVERT: J 22 ASP cc_start: 0.7608 (m-30) cc_final: 0.7309 (m-30) REVERT: J 236 ARG cc_start: 0.6478 (tpp80) cc_final: 0.5322 (mtp85) REVERT: J 242 ARG cc_start: 0.7175 (mmm-85) cc_final: 0.6654 (mtp180) REVERT: E 75 GLU cc_start: 0.7903 (mp0) cc_final: 0.7647 (pm20) REVERT: E 82 ASP cc_start: 0.6273 (m-30) cc_final: 0.5875 (m-30) REVERT: E 142 MET cc_start: 0.8299 (tpt) cc_final: 0.7964 (tpt) REVERT: E 219 VAL cc_start: 0.7156 (OUTLIER) cc_final: 0.6853 (m) REVERT: E 237 MET cc_start: 0.6370 (mtt) cc_final: 0.5946 (mtt) REVERT: E 310 SER cc_start: 0.8047 (t) cc_final: 0.7740 (t) REVERT: E 375 ARG cc_start: 0.7451 (ptp-110) cc_final: 0.7039 (ptp-170) REVERT: E 406 ASP cc_start: 0.8044 (p0) cc_final: 0.7785 (p0) REVERT: I 68 LYS cc_start: 0.7063 (mtmm) cc_final: 0.6484 (mttp) REVERT: I 82 ASP cc_start: 0.5992 (m-30) cc_final: 0.5564 (m-30) REVERT: I 181 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7664 (mm-30) REVERT: I 187 ASN cc_start: 0.8014 (t0) cc_final: 0.7643 (t0) REVERT: I 237 MET cc_start: 0.6417 (mtt) cc_final: 0.6060 (mtt) REVERT: I 310 SER cc_start: 0.7954 (t) cc_final: 0.7720 (m) REVERT: I 372 GLU cc_start: 0.7048 (pt0) cc_final: 0.6136 (tm-30) REVERT: I 375 ARG cc_start: 0.7224 (mtt-85) cc_final: 0.6168 (mtp85) REVERT: I 401 GLN cc_start: 0.6760 (mt0) cc_final: 0.6463 (mt0) outliers start: 70 outliers final: 50 residues processed: 327 average time/residue: 0.3464 time to fit residues: 167.8357 Evaluate side-chains 323 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 270 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 381 TYR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 381 TYR Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 72 optimal weight: 0.4980 chunk 115 optimal weight: 5.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN F 245 GLN J 245 GLN I 33 HIS ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 19707 Z= 0.293 Angle : 0.599 6.087 26757 Z= 0.310 Chirality : 0.046 0.154 2853 Planarity : 0.005 0.048 3261 Dihedral : 14.371 164.863 2990 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.40 % Favored : 95.43 % Rotamer: Outliers : 3.79 % Allowed : 13.69 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: -0.37 (0.17), residues: 2274 helix: 0.45 (0.16), residues: 1008 sheet: 0.02 (0.28), residues: 333 loop : -1.04 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 253 HIS 0.006 0.001 HIS F 11 PHE 0.017 0.002 PHE G 202 TYR 0.028 0.002 TYR G 184 ARG 0.004 0.001 ARG I 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 283 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.7648 (p90) cc_final: 0.7331 (p90) REVERT: A 75 GLU cc_start: 0.7635 (mp0) cc_final: 0.7208 (mp0) REVERT: A 82 ASP cc_start: 0.6083 (m-30) cc_final: 0.5755 (m-30) REVERT: A 142 MET cc_start: 0.8292 (tpt) cc_final: 0.7959 (tpt) REVERT: A 187 ASN cc_start: 0.8144 (t0) cc_final: 0.7751 (t0) REVERT: A 212 PHE cc_start: 0.7606 (m-80) cc_final: 0.7280 (m-80) REVERT: A 237 MET cc_start: 0.6386 (mtt) cc_final: 0.6085 (mtt) REVERT: A 269 MET cc_start: 0.7796 (mtp) cc_final: 0.7571 (mtp) REVERT: A 310 SER cc_start: 0.7987 (t) cc_final: 0.7742 (m) REVERT: A 375 ARG cc_start: 0.7195 (mtt-85) cc_final: 0.6361 (mtp85) REVERT: A 387 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7761 (p90) REVERT: C 49 LYS cc_start: 0.4200 (OUTLIER) cc_final: 0.2688 (mttt) REVERT: B 236 ARG cc_start: 0.6661 (tpp80) cc_final: 0.5455 (mtp85) REVERT: B 242 ARG cc_start: 0.7050 (mmm-85) cc_final: 0.6583 (mtp180) REVERT: G 49 LYS cc_start: 0.3948 (OUTLIER) cc_final: 0.2631 (ptmt) REVERT: K 114 THR cc_start: 0.6601 (OUTLIER) cc_final: 0.6096 (p) REVERT: F 223 MET cc_start: 0.7361 (tpp) cc_final: 0.6870 (tpp) REVERT: F 229 PHE cc_start: 0.6931 (t80) cc_final: 0.6366 (t80) REVERT: F 236 ARG cc_start: 0.6561 (tpp80) cc_final: 0.5304 (mtp85) REVERT: J 223 MET cc_start: 0.7322 (tpp) cc_final: 0.6782 (tpp) REVERT: J 236 ARG cc_start: 0.6633 (tpp80) cc_final: 0.5373 (mtp85) REVERT: J 242 ARG cc_start: 0.7203 (mmm-85) cc_final: 0.6697 (mtp180) REVERT: E 75 GLU cc_start: 0.7910 (mp0) cc_final: 0.7645 (pm20) REVERT: E 82 ASP cc_start: 0.6285 (m-30) cc_final: 0.5887 (m-30) REVERT: E 142 MET cc_start: 0.8337 (tpt) cc_final: 0.8045 (tpt) REVERT: E 237 MET cc_start: 0.6374 (mtt) cc_final: 0.6009 (mtt) REVERT: E 310 SER cc_start: 0.7995 (t) cc_final: 0.7677 (t) REVERT: I 68 LYS cc_start: 0.7041 (mtmm) cc_final: 0.6468 (mttp) REVERT: I 82 ASP cc_start: 0.5977 (m-30) cc_final: 0.5578 (m-30) REVERT: I 187 ASN cc_start: 0.8005 (t0) cc_final: 0.7655 (t0) REVERT: I 237 MET cc_start: 0.6342 (mtt) cc_final: 0.5839 (mtt) REVERT: I 372 GLU cc_start: 0.7017 (pt0) cc_final: 0.6032 (tm-30) REVERT: I 375 ARG cc_start: 0.7339 (mtt-85) cc_final: 0.6416 (mtp85) REVERT: I 404 GLN cc_start: 0.7417 (tt0) cc_final: 0.6715 (mp10) outliers start: 74 outliers final: 56 residues processed: 327 average time/residue: 0.3398 time to fit residues: 164.4314 Evaluate side-chains 325 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 265 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 381 TYR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 381 TYR Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 185 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 219 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN B 245 GLN F 174 ASN F 245 GLN J 245 GLN ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19707 Z= 0.319 Angle : 0.621 6.694 26757 Z= 0.320 Chirality : 0.046 0.175 2853 Planarity : 0.005 0.050 3261 Dihedral : 14.631 177.411 2990 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.53 % Favored : 95.29 % Rotamer: Outliers : 4.00 % Allowed : 14.36 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2274 helix: 0.40 (0.16), residues: 1005 sheet: -0.28 (0.26), residues: 363 loop : -1.00 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 253 HIS 0.007 0.002 HIS F 11 PHE 0.018 0.002 PHE K 202 TYR 0.027 0.002 TYR K 184 ARG 0.005 0.001 ARG E 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 276 time to evaluate : 2.164 Fit side-chains revert: symmetry clash REVERT: A 41 PHE cc_start: 0.7672 (p90) cc_final: 0.7332 (p90) REVERT: A 75 GLU cc_start: 0.7614 (mp0) cc_final: 0.7191 (mp0) REVERT: A 82 ASP cc_start: 0.6081 (m-30) cc_final: 0.5746 (m-30) REVERT: A 142 MET cc_start: 0.8363 (tpt) cc_final: 0.8030 (tpt) REVERT: A 212 PHE cc_start: 0.7526 (m-80) cc_final: 0.7314 (m-80) REVERT: A 237 MET cc_start: 0.6410 (mtt) cc_final: 0.6115 (mtt) REVERT: A 310 SER cc_start: 0.7922 (t) cc_final: 0.7707 (m) REVERT: A 375 ARG cc_start: 0.7175 (mtt-85) cc_final: 0.6328 (mtp85) REVERT: A 387 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7817 (p90) REVERT: C 49 LYS cc_start: 0.4084 (OUTLIER) cc_final: 0.2575 (mttt) REVERT: C 127 GLU cc_start: 0.6099 (tt0) cc_final: 0.5576 (tp30) REVERT: C 218 PHE cc_start: 0.5083 (OUTLIER) cc_final: 0.4749 (t80) REVERT: B 229 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.5811 (t80) REVERT: B 236 ARG cc_start: 0.6757 (tpp80) cc_final: 0.5536 (mtp85) REVERT: G 49 LYS cc_start: 0.3794 (OUTLIER) cc_final: 0.2525 (ptmt) REVERT: K 114 THR cc_start: 0.6763 (OUTLIER) cc_final: 0.6270 (p) REVERT: F 223 MET cc_start: 0.7367 (tpp) cc_final: 0.6882 (tpp) REVERT: F 236 ARG cc_start: 0.6646 (tpp80) cc_final: 0.5361 (mtp85) REVERT: J 223 MET cc_start: 0.7342 (tpp) cc_final: 0.6808 (tpp) REVERT: J 236 ARG cc_start: 0.6751 (tpp80) cc_final: 0.5486 (mtp85) REVERT: J 242 ARG cc_start: 0.7208 (mmm-85) cc_final: 0.6731 (mtp180) REVERT: E 75 GLU cc_start: 0.7853 (mp0) cc_final: 0.7587 (pm20) REVERT: E 82 ASP cc_start: 0.6258 (m-30) cc_final: 0.5875 (m-30) REVERT: E 142 MET cc_start: 0.8363 (tpt) cc_final: 0.8106 (tpt) REVERT: E 237 MET cc_start: 0.6422 (mtt) cc_final: 0.5657 (tpt) REVERT: E 310 SER cc_start: 0.7975 (t) cc_final: 0.7663 (t) REVERT: E 375 ARG cc_start: 0.7500 (ptp-110) cc_final: 0.7075 (ptp90) REVERT: I 68 LYS cc_start: 0.7010 (mtmm) cc_final: 0.6493 (mttp) REVERT: I 82 ASP cc_start: 0.6009 (m-30) cc_final: 0.5610 (m-30) REVERT: I 187 ASN cc_start: 0.8028 (t0) cc_final: 0.7680 (t0) REVERT: I 237 MET cc_start: 0.6339 (mtt) cc_final: 0.5824 (mtt) REVERT: I 372 GLU cc_start: 0.7026 (pt0) cc_final: 0.6042 (tm-30) REVERT: I 375 ARG cc_start: 0.7254 (mtt-85) cc_final: 0.6217 (mtp85) REVERT: I 401 GLN cc_start: 0.6722 (mt0) cc_final: 0.6423 (mt0) REVERT: I 404 GLN cc_start: 0.7398 (tt0) cc_final: 0.6748 (mp10) outliers start: 78 outliers final: 59 residues processed: 326 average time/residue: 0.3378 time to fit residues: 162.1409 Evaluate side-chains 325 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 260 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 381 TYR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 381 TYR Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 172 optimal weight: 0.0980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN F 245 GLN J 245 GLN ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19707 Z= 0.217 Angle : 0.554 6.406 26757 Z= 0.286 Chirality : 0.044 0.139 2853 Planarity : 0.004 0.051 3261 Dihedral : 14.342 177.091 2990 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.66 % Favored : 95.16 % Rotamer: Outliers : 3.13 % Allowed : 16.15 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: -0.18 (0.17), residues: 2274 helix: 0.67 (0.16), residues: 1002 sheet: 0.19 (0.28), residues: 339 loop : -1.05 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 253 HIS 0.005 0.001 HIS B 11 PHE 0.013 0.001 PHE G 251 TYR 0.024 0.002 TYR K 184 ARG 0.005 0.000 ARG E 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 265 time to evaluate : 2.258 Fit side-chains revert: symmetry clash REVERT: A 41 PHE cc_start: 0.7668 (p90) cc_final: 0.7331 (p90) REVERT: A 82 ASP cc_start: 0.6067 (m-30) cc_final: 0.5746 (m-30) REVERT: A 142 MET cc_start: 0.8330 (tpt) cc_final: 0.8008 (tpt) REVERT: A 212 PHE cc_start: 0.7585 (m-80) cc_final: 0.7098 (m-80) REVERT: A 237 MET cc_start: 0.6409 (mtt) cc_final: 0.6108 (mtt) REVERT: A 375 ARG cc_start: 0.7186 (mtt-85) cc_final: 0.6372 (mtp85) REVERT: A 387 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7780 (p90) REVERT: C 49 LYS cc_start: 0.3986 (OUTLIER) cc_final: 0.2532 (mttt) REVERT: C 114 THR cc_start: 0.6668 (OUTLIER) cc_final: 0.6219 (p) REVERT: C 127 GLU cc_start: 0.6084 (tt0) cc_final: 0.5575 (tp30) REVERT: C 218 PHE cc_start: 0.5090 (OUTLIER) cc_final: 0.4811 (t80) REVERT: B 236 ARG cc_start: 0.6734 (tpp80) cc_final: 0.5542 (mtp85) REVERT: G 49 LYS cc_start: 0.3633 (OUTLIER) cc_final: 0.2419 (ptmt) REVERT: K 114 THR cc_start: 0.6760 (OUTLIER) cc_final: 0.6299 (p) REVERT: F 223 MET cc_start: 0.7305 (tpp) cc_final: 0.6862 (tpp) REVERT: F 236 ARG cc_start: 0.6678 (tpp80) cc_final: 0.6330 (mtt180) REVERT: J 223 MET cc_start: 0.7290 (tpp) cc_final: 0.6737 (tpp) REVERT: J 236 ARG cc_start: 0.6693 (tpp80) cc_final: 0.5521 (mtp85) REVERT: J 242 ARG cc_start: 0.7182 (mmm-85) cc_final: 0.6699 (mtp180) REVERT: E 75 GLU cc_start: 0.7865 (mp0) cc_final: 0.7614 (pm20) REVERT: E 82 ASP cc_start: 0.6233 (m-30) cc_final: 0.5852 (m-30) REVERT: E 142 MET cc_start: 0.8330 (tpt) cc_final: 0.8087 (tpt) REVERT: E 237 MET cc_start: 0.6368 (mtt) cc_final: 0.5611 (tpt) REVERT: E 310 SER cc_start: 0.7978 (t) cc_final: 0.7657 (t) REVERT: I 68 LYS cc_start: 0.6987 (mtmm) cc_final: 0.6485 (mttp) REVERT: I 82 ASP cc_start: 0.5967 (m-30) cc_final: 0.5566 (m-30) REVERT: I 237 MET cc_start: 0.6331 (mtt) cc_final: 0.5820 (mtt) REVERT: I 372 GLU cc_start: 0.6950 (pt0) cc_final: 0.5977 (tm-30) REVERT: I 375 ARG cc_start: 0.7198 (mtt-85) cc_final: 0.6259 (mtp85) REVERT: I 401 GLN cc_start: 0.6653 (mt0) cc_final: 0.6364 (mt0) REVERT: I 404 GLN cc_start: 0.7441 (tt0) cc_final: 0.6720 (mp10) outliers start: 61 outliers final: 50 residues processed: 297 average time/residue: 0.3608 time to fit residues: 158.3534 Evaluate side-chains 314 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 258 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 381 TYR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 381 TYR Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN F 245 GLN J 245 GLN ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19707 Z= 0.291 Angle : 0.597 6.668 26757 Z= 0.307 Chirality : 0.046 0.142 2853 Planarity : 0.005 0.052 3261 Dihedral : 14.397 179.137 2990 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.57 % Favored : 95.25 % Rotamer: Outliers : 3.69 % Allowed : 15.85 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: -0.29 (0.17), residues: 2274 helix: 0.61 (0.16), residues: 993 sheet: -0.15 (0.26), residues: 369 loop : -1.02 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 253 HIS 0.006 0.001 HIS F 11 PHE 0.017 0.002 PHE K 202 TYR 0.026 0.002 TYR C 184 ARG 0.005 0.001 ARG E 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 265 time to evaluate : 1.960 Fit side-chains revert: symmetry clash REVERT: A 41 PHE cc_start: 0.7673 (p90) cc_final: 0.7320 (p90) REVERT: A 75 GLU cc_start: 0.7810 (mp0) cc_final: 0.7327 (mp0) REVERT: A 82 ASP cc_start: 0.6048 (m-30) cc_final: 0.5732 (m-30) REVERT: A 142 MET cc_start: 0.8365 (tpt) cc_final: 0.8056 (tpt) REVERT: A 187 ASN cc_start: 0.8158 (t0) cc_final: 0.7748 (t0) REVERT: A 212 PHE cc_start: 0.7533 (m-80) cc_final: 0.7245 (m-80) REVERT: A 237 MET cc_start: 0.6436 (mtt) cc_final: 0.6150 (mtt) REVERT: A 375 ARG cc_start: 0.7198 (mtt-85) cc_final: 0.6386 (mtp85) REVERT: A 387 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7785 (p90) REVERT: C 49 LYS cc_start: 0.3854 (OUTLIER) cc_final: 0.2413 (mttt) REVERT: C 127 GLU cc_start: 0.6072 (tt0) cc_final: 0.5515 (tp30) REVERT: C 218 PHE cc_start: 0.5029 (OUTLIER) cc_final: 0.4749 (t80) REVERT: B 49 ASP cc_start: 0.7367 (t0) cc_final: 0.7118 (t70) REVERT: B 229 PHE cc_start: 0.7442 (t80) cc_final: 0.7038 (m-80) REVERT: B 230 MET cc_start: 0.7016 (ttt) cc_final: 0.6814 (ttt) REVERT: B 236 ARG cc_start: 0.6812 (tpp80) cc_final: 0.5622 (mtp85) REVERT: G 49 LYS cc_start: 0.3559 (OUTLIER) cc_final: 0.2380 (ptmt) REVERT: G 218 PHE cc_start: 0.4906 (OUTLIER) cc_final: 0.4306 (t80) REVERT: K 114 THR cc_start: 0.6868 (OUTLIER) cc_final: 0.6395 (p) REVERT: F 223 MET cc_start: 0.7343 (tpp) cc_final: 0.6880 (tpp) REVERT: F 236 ARG cc_start: 0.6770 (tpp80) cc_final: 0.5455 (mtp85) REVERT: J 223 MET cc_start: 0.7304 (tpp) cc_final: 0.6759 (tpp) REVERT: J 236 ARG cc_start: 0.6797 (tpp80) cc_final: 0.5623 (mtp85) REVERT: J 242 ARG cc_start: 0.7189 (mmm-85) cc_final: 0.6730 (mtp180) REVERT: E 41 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7322 (p90) REVERT: E 75 GLU cc_start: 0.7874 (mp0) cc_final: 0.7610 (pm20) REVERT: E 82 ASP cc_start: 0.6240 (m-30) cc_final: 0.5869 (m-30) REVERT: E 142 MET cc_start: 0.8378 (tpt) cc_final: 0.8142 (tpt) REVERT: E 237 MET cc_start: 0.6394 (mtt) cc_final: 0.5655 (tpt) REVERT: E 310 SER cc_start: 0.7955 (t) cc_final: 0.7640 (t) REVERT: I 68 LYS cc_start: 0.7007 (mtmm) cc_final: 0.6507 (mttp) REVERT: I 82 ASP cc_start: 0.5981 (m-30) cc_final: 0.5598 (m-30) REVERT: I 187 ASN cc_start: 0.7988 (t0) cc_final: 0.7626 (t0) REVERT: I 237 MET cc_start: 0.6347 (mtt) cc_final: 0.5841 (mtt) REVERT: I 372 GLU cc_start: 0.6995 (pt0) cc_final: 0.5991 (tm-30) REVERT: I 375 ARG cc_start: 0.7163 (mtt-85) cc_final: 0.6232 (mtp85) REVERT: I 401 GLN cc_start: 0.6715 (mt0) cc_final: 0.6386 (mt0) REVERT: I 404 GLN cc_start: 0.7390 (tt0) cc_final: 0.6731 (mp10) outliers start: 72 outliers final: 61 residues processed: 310 average time/residue: 0.3523 time to fit residues: 161.1856 Evaluate side-chains 330 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 262 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 218 PHE Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 381 TYR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 381 TYR Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 209 optimal weight: 0.4980 chunk 180 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN F 245 GLN J 245 GLN ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19707 Z= 0.214 Angle : 0.555 9.512 26757 Z= 0.286 Chirality : 0.044 0.140 2853 Planarity : 0.005 0.053 3261 Dihedral : 14.135 177.485 2990 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.53 % Favored : 95.29 % Rotamer: Outliers : 3.44 % Allowed : 16.31 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: -0.16 (0.17), residues: 2274 helix: 0.70 (0.16), residues: 1002 sheet: -0.10 (0.26), residues: 369 loop : -0.95 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 253 HIS 0.005 0.001 HIS J 11 PHE 0.018 0.001 PHE C 251 TYR 0.023 0.001 TYR K 184 ARG 0.005 0.000 ARG E 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 266 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.7646 (p90) cc_final: 0.7321 (p90) REVERT: A 75 GLU cc_start: 0.7782 (mp0) cc_final: 0.7154 (pm20) REVERT: A 82 ASP cc_start: 0.6068 (m-30) cc_final: 0.5747 (m-30) REVERT: A 142 MET cc_start: 0.8368 (tpt) cc_final: 0.8059 (tpt) REVERT: A 212 PHE cc_start: 0.7612 (m-80) cc_final: 0.7138 (m-80) REVERT: A 237 MET cc_start: 0.6463 (mtt) cc_final: 0.6172 (mtt) REVERT: A 374 TYR cc_start: 0.7022 (m-80) cc_final: 0.6629 (m-10) REVERT: A 375 ARG cc_start: 0.7224 (mtt-85) cc_final: 0.6400 (mtp85) REVERT: A 387 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7803 (p90) REVERT: C 49 LYS cc_start: 0.3876 (OUTLIER) cc_final: 0.2471 (mttt) REVERT: C 114 THR cc_start: 0.6716 (OUTLIER) cc_final: 0.6266 (p) REVERT: C 218 PHE cc_start: 0.5017 (OUTLIER) cc_final: 0.4706 (t80) REVERT: B 49 ASP cc_start: 0.7362 (t0) cc_final: 0.7117 (t70) REVERT: B 229 PHE cc_start: 0.7441 (t80) cc_final: 0.7033 (m-80) REVERT: B 230 MET cc_start: 0.6993 (ttt) cc_final: 0.6789 (ttt) REVERT: B 236 ARG cc_start: 0.6789 (tpp80) cc_final: 0.5587 (mtp85) REVERT: G 49 LYS cc_start: 0.3531 (OUTLIER) cc_final: 0.2371 (ptmt) REVERT: G 114 THR cc_start: 0.6602 (OUTLIER) cc_final: 0.6161 (p) REVERT: G 218 PHE cc_start: 0.4960 (OUTLIER) cc_final: 0.4424 (t80) REVERT: K 114 THR cc_start: 0.6866 (OUTLIER) cc_final: 0.6390 (p) REVERT: F 223 MET cc_start: 0.7317 (tpp) cc_final: 0.6880 (tpp) REVERT: F 236 ARG cc_start: 0.6792 (tpp80) cc_final: 0.5459 (mtp85) REVERT: J 223 MET cc_start: 0.7253 (tpp) cc_final: 0.6734 (tpp) REVERT: J 236 ARG cc_start: 0.6780 (tpp80) cc_final: 0.5608 (mtp85) REVERT: J 242 ARG cc_start: 0.7178 (mmm-85) cc_final: 0.6716 (mtp180) REVERT: E 75 GLU cc_start: 0.7872 (mp0) cc_final: 0.7614 (pm20) REVERT: E 82 ASP cc_start: 0.6200 (m-30) cc_final: 0.5841 (m-30) REVERT: E 142 MET cc_start: 0.8369 (tpt) cc_final: 0.8147 (tpt) REVERT: E 237 MET cc_start: 0.6412 (mtt) cc_final: 0.5643 (tpt) REVERT: E 310 SER cc_start: 0.7935 (t) cc_final: 0.7620 (t) REVERT: I 68 LYS cc_start: 0.7012 (mtmm) cc_final: 0.6510 (mttp) REVERT: I 82 ASP cc_start: 0.5987 (m-30) cc_final: 0.5608 (m-30) REVERT: I 237 MET cc_start: 0.6335 (mtt) cc_final: 0.5811 (mtt) REVERT: I 372 GLU cc_start: 0.6957 (pt0) cc_final: 0.5941 (tm-30) REVERT: I 375 ARG cc_start: 0.7114 (mtt-85) cc_final: 0.6219 (mtp85) REVERT: I 401 GLN cc_start: 0.6571 (mt0) cc_final: 0.6284 (mt0) REVERT: I 404 GLN cc_start: 0.7423 (tt0) cc_final: 0.6712 (mp10) outliers start: 67 outliers final: 55 residues processed: 305 average time/residue: 0.3478 time to fit residues: 157.6988 Evaluate side-chains 324 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 261 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 218 PHE Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 381 TYR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 381 TYR Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 33 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN F 245 GLN J 245 GLN ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.149814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.126972 restraints weight = 21623.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.126743 restraints weight = 23611.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.127745 restraints weight = 20419.097| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19707 Z= 0.268 Angle : 0.582 8.975 26757 Z= 0.300 Chirality : 0.045 0.144 2853 Planarity : 0.005 0.053 3261 Dihedral : 13.981 178.699 2990 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.84 % Favored : 94.99 % Rotamer: Outliers : 3.64 % Allowed : 16.00 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: -0.22 (0.17), residues: 2274 helix: 0.69 (0.16), residues: 990 sheet: -0.12 (0.26), residues: 369 loop : -1.01 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP K 253 HIS 0.006 0.001 HIS F 11 PHE 0.016 0.002 PHE K 202 TYR 0.024 0.002 TYR G 184 ARG 0.004 0.000 ARG A 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3868.11 seconds wall clock time: 71 minutes 15.45 seconds (4275.45 seconds total)