Starting phenix.real_space_refine on Sun Feb 18 02:05:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/02_2024/6vqw_21359.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/02_2024/6vqw_21359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/02_2024/6vqw_21359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/02_2024/6vqw_21359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/02_2024/6vqw_21359.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/02_2024/6vqw_21359.pdb" } resolution = 3.42 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= 0.016 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians P 39 5.49 5 S 17 5.16 5 C 12609 2.51 5 N 3779 2.21 5 O 4035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 5": "OD1" <-> "OD2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 327": "OD1" <-> "OD2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 33": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F ASP 52": "OD1" <-> "OD2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 301": "OE1" <-> "OE2" Residue "G ASP 134": "OD1" <-> "OD2" Residue "G ARG 190": "NH1" <-> "NH2" Residue "G ASP 269": "OD1" <-> "OD2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H ASP 98": "OD1" <-> "OD2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "H ASP 293": "OD1" <-> "OD2" Residue "H GLU 301": "OE1" <-> "OE2" Residue "I ASP 40": "OD1" <-> "OD2" Residue "I GLU 56": "OE1" <-> "OE2" Residue "I ARG 80": "NH1" <-> "NH2" Residue "I GLU 242": "OE1" <-> "OE2" Residue "I ASP 255": "OD1" <-> "OD2" Residue "B TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 257": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20479 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2309 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 274} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Chain: "E" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2575 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2587 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 12, 'TRANS': 321} Chain: "G" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2559 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2516 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2523 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 350 Classifications: {'peptide': 87} Incomplete info: {'backbone_only': 80} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 506 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 101 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 176 Chain: "A" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 552 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1391 Classifications: {'peptide': 242} Incomplete info: {'backbone_only': 133} Link IDs: {'PTRANS': 16, 'TRANS': 225} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 616 Unresolved non-hydrogen angles: 885 Unresolved non-hydrogen dihedrals: 410 Unresolved non-hydrogen chiralities: 163 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 347 Chain: "K" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 845 Classifications: {'RNA': 40} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 11, 'rna3p_pyr': 10} Link IDs: {'rna2p': 18, 'rna3p': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 11.77, per 1000 atoms: 0.57 Number of scatterers: 20479 At special positions: 0 Unit cell: (106, 138.86, 151.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 39 15.00 O 4035 8.00 N 3779 7.00 C 12609 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.18 Conformation dependent library (CDL) restraints added in 4.0 seconds 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 38 sheets defined 26.2% alpha, 14.2% beta 0 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 7.09 Creating SS restraints... Processing helix chain 'C' and resid 33 through 48 removed outlier: 3.949A pdb=" N PHE C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 41 " --> pdb=" O PHE C 37 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 42 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.690A pdb=" N VAL C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 178 removed outlier: 3.752A pdb=" N ARG C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 removed outlier: 4.400A pdb=" N LEU C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLU C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'D' and resid 50 through 54 removed outlier: 3.770A pdb=" N SER D 54 " --> pdb=" O ARG D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 147 removed outlier: 4.083A pdb=" N LYS D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP D 146 " --> pdb=" O THR D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 162 removed outlier: 3.640A pdb=" N ASN D 159 " --> pdb=" O ARG D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 223 removed outlier: 3.597A pdb=" N LEU D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 282 removed outlier: 3.608A pdb=" N ILE D 278 " --> pdb=" O HIS D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 331 Processing helix chain 'D' and resid 337 through 351 removed outlier: 4.057A pdb=" N TYR D 343 " --> pdb=" O GLU D 339 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 350 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 145 removed outlier: 4.161A pdb=" N LYS E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 162 Processing helix chain 'E' and resid 208 through 222 removed outlier: 3.854A pdb=" N ALA E 212 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU E 216 " --> pdb=" O ALA E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 283 removed outlier: 3.684A pdb=" N ARG E 283 " --> pdb=" O GLY E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 331 Processing helix chain 'E' and resid 337 through 351 removed outlier: 3.664A pdb=" N HIS E 342 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR E 343 " --> pdb=" O GLU E 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 91 Processing helix chain 'F' and resid 129 through 147 removed outlier: 3.791A pdb=" N ALA F 141 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 162 removed outlier: 3.683A pdb=" N ASN F 159 " --> pdb=" O ARG F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 222 removed outlier: 3.841A pdb=" N GLU F 215 " --> pdb=" O ASP F 211 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 283 removed outlier: 3.760A pdb=" N ALA F 281 " --> pdb=" O LYS F 277 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 331 removed outlier: 3.734A pdb=" N ASP F 327 " --> pdb=" O TYR F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 351 removed outlier: 4.546A pdb=" N TYR F 343 " --> pdb=" O GLU F 339 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 344 " --> pdb=" O GLN F 340 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE F 345 " --> pdb=" O GLN F 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 51 Processing helix chain 'G' and resid 81 through 91 removed outlier: 3.615A pdb=" N LEU G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP G 86 " --> pdb=" O PRO G 82 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA G 87 " --> pdb=" O ALA G 83 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 147 removed outlier: 3.686A pdb=" N GLN G 147 " --> pdb=" O TYR G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 162 Processing helix chain 'G' and resid 211 through 223 removed outlier: 3.637A pdb=" N LEU G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 327 Processing helix chain 'G' and resid 337 through 350 removed outlier: 4.937A pdb=" N TYR G 343 " --> pdb=" O GLU G 339 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE G 345 " --> pdb=" O GLN G 341 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA G 346 " --> pdb=" O HIS G 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 90 removed outlier: 4.062A pdb=" N ASP H 86 " --> pdb=" O PRO H 82 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA H 87 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN H 90 " --> pdb=" O ASP H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 147 removed outlier: 3.773A pdb=" N LYS H 135 " --> pdb=" O ALA H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 162 removed outlier: 3.610A pdb=" N ARG H 155 " --> pdb=" O GLU H 151 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS H 158 " --> pdb=" O ARG H 154 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU H 160 " --> pdb=" O TYR H 156 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN H 162 " --> pdb=" O HIS H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 222 removed outlier: 3.628A pdb=" N LEU H 213 " --> pdb=" O GLU H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 283 removed outlier: 3.646A pdb=" N ILE H 278 " --> pdb=" O HIS H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 296 removed outlier: 4.047A pdb=" N LEU H 295 " --> pdb=" O GLU H 292 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY H 296 " --> pdb=" O ASP H 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 292 through 296' Processing helix chain 'H' and resid 322 through 327 removed outlier: 4.077A pdb=" N ASP H 327 " --> pdb=" O TYR H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 350 removed outlier: 3.922A pdb=" N HIS H 342 " --> pdb=" O VAL H 338 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR H 343 " --> pdb=" O GLU H 339 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU H 348 " --> pdb=" O VAL H 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 54 removed outlier: 3.569A pdb=" N SER I 54 " --> pdb=" O ARG I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 90 removed outlier: 4.007A pdb=" N ASP I 86 " --> pdb=" O PRO I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 145 removed outlier: 3.790A pdb=" N LYS I 135 " --> pdb=" O ALA I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 157 Processing helix chain 'I' and resid 157 through 162 Processing helix chain 'I' and resid 209 through 223 Processing helix chain 'I' and resid 274 through 283 removed outlier: 3.925A pdb=" N ALA I 281 " --> pdb=" O LYS I 277 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG I 283 " --> pdb=" O GLY I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 331 removed outlier: 3.713A pdb=" N ASP I 327 " --> pdb=" O TYR I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 351 Processing helix chain 'J' and resid 16 through 24 removed outlier: 4.468A pdb=" N MET J 21 " --> pdb=" O PRO J 17 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER J 22 " --> pdb=" O ALA J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 69 Processing helix chain 'J' and resid 73 through 77 removed outlier: 3.912A pdb=" N LEU J 76 " --> pdb=" O ARG J 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'B' and resid 199 through 211 removed outlier: 4.644A pdb=" N ALA B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 319 through 339 removed outlier: 3.841A pdb=" N ALA B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 334 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 335 " --> pdb=" O ASP B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 395 removed outlier: 4.185A pdb=" N ALA B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN B 393 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 433 removed outlier: 3.644A pdb=" N GLU B 432 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 8 through 11 removed outlier: 3.596A pdb=" N LEU C 159 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 11 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 157 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 65 through 68 removed outlier: 3.975A pdb=" N LEU C 105 " --> pdb=" O ILE C 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'C' and resid 186 through 188 removed outlier: 7.495A pdb=" N PHE C 279 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA C 257 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU C 281 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR C 255 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU C 283 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL C 249 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 186 through 188 Processing sheet with id=AA6, first strand: chain 'D' and resid 30 through 32 Processing sheet with id=AA7, first strand: chain 'D' and resid 42 through 44 removed outlier: 3.735A pdb=" N LYS D 110 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 117 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL D 227 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU D 228 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN D 181 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 62 through 64 Processing sheet with id=AA9, first strand: chain 'D' and resid 247 through 248 Processing sheet with id=AB1, first strand: chain 'E' and resid 30 through 31 removed outlier: 4.070A pdb=" N ALA E 126 " --> pdb=" O ALA E 31 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 42 through 46 removed outlier: 3.752A pdb=" N VAL E 117 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL E 227 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA E 175 " --> pdb=" O ARG E 236 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 62 through 68 Processing sheet with id=AB4, first strand: chain 'F' and resid 126 through 127 removed outlier: 3.736A pdb=" N ALA F 126 " --> pdb=" O ALA F 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.594A pdb=" N VAL F 117 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL F 227 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU F 228 " --> pdb=" O ILE F 183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AB7, first strand: chain 'F' and resid 63 through 64 Processing sheet with id=AB8, first strand: chain 'F' and resid 67 through 68 Processing sheet with id=AB9, first strand: chain 'F' and resid 284 through 286 Processing sheet with id=AC1, first strand: chain 'G' and resid 31 through 32 Processing sheet with id=AC2, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AC3, first strand: chain 'G' and resid 37 through 38 removed outlier: 4.289A pdb=" N VAL G 227 " --> pdb=" O VAL G 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 63 through 64 Processing sheet with id=AC5, first strand: chain 'G' and resid 284 through 286 Processing sheet with id=AC6, first strand: chain 'H' and resid 30 through 32 removed outlier: 3.638A pdb=" N LEU H 30 " --> pdb=" O PHE H 354 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 37 through 38 removed outlier: 3.975A pdb=" N VAL H 227 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU H 228 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG H 190 " --> pdb=" O HIS H 182 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 37 through 38 removed outlier: 3.671A pdb=" N ALA H 41 " --> pdb=" O ILE H 273 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 63 through 64 removed outlier: 4.356A pdb=" N ALA H 100 " --> pdb=" O VAL H 243 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 284 through 286 Processing sheet with id=AD2, first strand: chain 'H' and resid 304 through 305 Processing sheet with id=AD3, first strand: chain 'I' and resid 30 through 32 Processing sheet with id=AD4, first strand: chain 'I' and resid 41 through 46 removed outlier: 3.970A pdb=" N LEU I 228 " --> pdb=" O ILE I 183 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE I 183 " --> pdb=" O LEU I 228 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL I 178 " --> pdb=" O ARG I 193 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG I 193 " --> pdb=" O VAL I 178 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE I 180 " --> pdb=" O ALA I 191 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA I 191 " --> pdb=" O ILE I 180 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N HIS I 182 " --> pdb=" O ALA I 189 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 63 through 64 Processing sheet with id=AD6, first strand: chain 'I' and resid 67 through 69 Processing sheet with id=AD7, first strand: chain 'I' and resid 247 through 248 removed outlier: 4.534A pdb=" N THR I 263 " --> pdb=" O GLU I 248 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 284 through 286 Processing sheet with id=AD9, first strand: chain 'J' and resid 42 through 43 Processing sheet with id=AE1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AE2, first strand: chain 'B' and resid 239 through 241 removed outlier: 3.877A pdb=" N GLN B 241 " --> pdb=" O ASN B 262 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN B 262 " --> pdb=" O GLN B 241 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 6.04 Time building geometry restraints manager: 9.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4849 1.33 - 1.45: 4762 1.45 - 1.57: 11221 1.57 - 1.70: 78 1.70 - 1.82: 25 Bond restraints: 20935 Sorted by residual: bond pdb=" C SER C 33 " pdb=" N PRO C 34 " ideal model delta sigma weight residual 1.334 1.307 0.026 8.40e-03 1.42e+04 9.75e+00 bond pdb=" C THR G 96 " pdb=" N VAL G 97 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.97e-02 2.58e+03 5.73e+00 bond pdb=" CG GLN H 241 " pdb=" CD GLN H 241 " ideal model delta sigma weight residual 1.516 1.463 0.053 2.50e-02 1.60e+03 4.56e+00 bond pdb=" N LYS E 256 " pdb=" CA LYS E 256 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.51e+00 bond pdb=" CB GLN G 276 " pdb=" CG GLN G 276 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.07e+00 ... (remaining 20930 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.24: 658 106.24 - 113.23: 11202 113.23 - 120.23: 7912 120.23 - 127.23: 8436 127.23 - 134.23: 301 Bond angle restraints: 28509 Sorted by residual: angle pdb=" C LYS H 76 " pdb=" N THR H 77 " pdb=" CA THR H 77 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C ILE G 278 " pdb=" N GLY G 279 " pdb=" CA GLY G 279 " ideal model delta sigma weight residual 122.97 115.15 7.82 1.84e+00 2.95e-01 1.81e+01 angle pdb=" C ARG B 224 " pdb=" N GLN B 225 " pdb=" CA GLN B 225 " ideal model delta sigma weight residual 122.46 128.16 -5.70 1.41e+00 5.03e-01 1.64e+01 angle pdb=" C SER B 227 " pdb=" N TRP B 228 " pdb=" CA TRP B 228 " ideal model delta sigma weight residual 120.09 125.14 -5.05 1.25e+00 6.40e-01 1.63e+01 angle pdb=" N GLN H 185 " pdb=" CA GLN H 185 " pdb=" C GLN H 185 " ideal model delta sigma weight residual 110.80 102.38 8.42 2.13e+00 2.20e-01 1.56e+01 ... (remaining 28504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.14: 11741 30.14 - 60.28: 481 60.28 - 90.42: 83 90.42 - 120.55: 1 120.55 - 150.69: 1 Dihedral angle restraints: 12307 sinusoidal: 5111 harmonic: 7196 Sorted by residual: dihedral pdb=" O4' U K 21 " pdb=" C1' U K 21 " pdb=" N1 U K 21 " pdb=" C2 U K 21 " ideal model delta sinusoidal sigma weight residual 200.00 49.31 150.69 1 1.50e+01 4.44e-03 7.99e+01 dihedral pdb=" O4' U K 35 " pdb=" C1' U K 35 " pdb=" N1 U K 35 " pdb=" C2 U K 35 " ideal model delta sinusoidal sigma weight residual -160.00 -87.71 -72.29 1 1.50e+01 4.44e-03 2.97e+01 dihedral pdb=" CA ASN G 159 " pdb=" C ASN G 159 " pdb=" N LEU G 160 " pdb=" CA LEU G 160 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 12304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2145 0.056 - 0.112: 798 0.112 - 0.168: 122 0.168 - 0.225: 27 0.225 - 0.281: 2 Chirality restraints: 3094 Sorted by residual: chirality pdb=" CB VAL A 44 " pdb=" CA VAL A 44 " pdb=" CG1 VAL A 44 " pdb=" CG2 VAL A 44 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL C 59 " pdb=" CA VAL C 59 " pdb=" CG1 VAL C 59 " pdb=" CG2 VAL C 59 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB THR H 96 " pdb=" CA THR H 96 " pdb=" OG1 THR H 96 " pdb=" CG2 THR H 96 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3091 not shown) Planarity restraints: 3683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 154 " -0.054 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO C 155 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 155 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 155 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 33 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.43e+00 pdb=" N PRO C 34 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 34 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 34 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 289 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO E 290 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 290 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 290 " 0.037 5.00e-02 4.00e+02 ... (remaining 3680 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5133 2.78 - 3.31: 18181 3.31 - 3.84: 33556 3.84 - 4.37: 37718 4.37 - 4.90: 63621 Nonbonded interactions: 158209 Sorted by model distance: nonbonded pdb=" OG SER F 54 " pdb=" OE1 GLN F 55 " model vdw 2.245 2.440 nonbonded pdb=" O GLY E 46 " pdb=" OG1 THR E 108 " model vdw 2.273 2.440 nonbonded pdb=" OD2 ASP G 40 " pdb=" OH TYR G 265 " model vdw 2.275 2.440 nonbonded pdb=" OH TYR H 289 " pdb=" O GLY H 296 " model vdw 2.283 2.440 nonbonded pdb=" O GLY I 46 " pdb=" OG1 THR I 108 " model vdw 2.296 2.440 ... (remaining 158204 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 'D' and resid 26 through 355) selection = (chain 'E' and (resid 26 through 66 or resid 95 through 249 or resid 262 through \ 355)) selection = (chain 'F' and (resid 26 through 66 or resid 95 through 249 or resid 262 through \ 355)) selection = (chain 'G' and (resid 26 through 66 or resid 95 through 249 or resid 262 through \ 355)) selection = (chain 'H' and (resid 26 through 66 or resid 95 through 249 or resid 262 through \ 355)) selection = (chain 'I' and (resid 26 through 66 or resid 95 through 249 or resid 262 through \ 355)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.700 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 61.060 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 : 0.010 0.080 20935 Z= 0.640 Angle : 0.940 11.865 28509 Z= 0.512 Chirality : 0.057 0.281 3094 Planarity : 0.006 0.081 3683 Dihedral : 16.438 150.693 7803 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 0.57 % Allowed : 14.92 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -5.04 (0.12), residues: 2610 helix: -3.67 (0.11), residues: 727 sheet: -2.07 (0.24), residues: 419 loop : -3.70 (0.12), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 329 HIS 0.011 0.002 HIS C 64 PHE 0.027 0.003 PHE G 165 TYR 0.029 0.003 TYR D 303 ARG 0.022 0.001 ARG F 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 217 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8804 (pmt170) cc_final: 0.8354 (pmt170) REVERT: C 171 LYS cc_start: 0.9377 (tptt) cc_final: 0.8953 (tppt) REVERT: C 262 TYR cc_start: 0.9056 (m-10) cc_final: 0.8705 (m-10) REVERT: E 68 ARG cc_start: 0.8138 (ttt-90) cc_final: 0.7680 (ttp-170) REVERT: E 132 TYR cc_start: 0.8841 (t80) cc_final: 0.8557 (t80) REVERT: F 37 ASP cc_start: 0.8414 (t70) cc_final: 0.8099 (t70) REVERT: F 301 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7986 (mm-30) REVERT: G 93 ASN cc_start: 0.8590 (p0) cc_final: 0.8315 (p0) REVERT: G 134 ASP cc_start: 0.9154 (t0) cc_final: 0.8926 (t0) REVERT: G 252 ASP cc_start: 0.7084 (t0) cc_final: 0.6487 (p0) REVERT: H 78 LYS cc_start: 0.8761 (tptp) cc_final: 0.8301 (tptp) REVERT: H 264 LEU cc_start: 0.8514 (mt) cc_final: 0.8116 (mt) REVERT: H 301 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8472 (mm-30) REVERT: I 50 GLN cc_start: 0.8996 (tt0) cc_final: 0.8529 (tm-30) REVERT: I 298 ILE cc_start: 0.8882 (mp) cc_final: 0.8560 (mp) REVERT: I 301 GLU cc_start: 0.8632 (tp30) cc_final: 0.8407 (tp30) REVERT: A 46 GLU cc_start: 0.8661 (mm-30) cc_final: 0.7743 (tp30) REVERT: A 51 ASN cc_start: 0.8839 (m110) cc_final: 0.8504 (m110) REVERT: A 85 ASN cc_start: 0.7693 (t0) cc_final: 0.7160 (t0) REVERT: B 219 ARG cc_start: 0.8356 (tpm170) cc_final: 0.7409 (ptm-80) REVERT: B 235 TYR cc_start: 0.5804 (p90) cc_final: 0.5525 (p90) outliers start: 11 outliers final: 5 residues processed: 226 average time/residue: 0.3900 time to fit residues: 131.0802 Evaluate side-chains 167 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 162 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain G residue 333 ASP Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 353 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 223 optimal weight: 50.0000 chunk 200 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 240 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN C 69 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN D 226 HIS D 241 GLN D 309 GLN D 315 GLN D 318 GLN D 340 GLN D 341 GLN E 55 GLN E 101 ASN E 169 ASN E 342 HIS F 93 ASN F 147 GLN F 181 ASN F 182 HIS F 309 GLN ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 ASN G 73 ASN G 226 HIS G 318 GLN H 73 ASN H 147 GLN H 181 ASN H 341 GLN H 347 ASN I 90 GLN I 182 HIS I 241 GLN I 274 HIS I 309 GLN I 347 ASN B 188 HIS B 230 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20935 Z= 0.147 Angle : 0.507 7.389 28509 Z= 0.268 Chirality : 0.039 0.170 3094 Planarity : 0.004 0.062 3683 Dihedral : 13.144 147.995 3501 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.03 % Allowed : 17.63 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.85 (0.14), residues: 2610 helix: -2.00 (0.16), residues: 731 sheet: -1.61 (0.25), residues: 417 loop : -3.28 (0.13), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 329 HIS 0.005 0.001 HIS H 158 PHE 0.014 0.001 PHE D 165 TYR 0.019 0.001 TYR D 132 ARG 0.006 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 204 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 147 TRP cc_start: 0.6769 (OUTLIER) cc_final: 0.6302 (t60) REVERT: C 151 ARG cc_start: 0.8593 (pmt170) cc_final: 0.8219 (pmt170) REVERT: C 171 LYS cc_start: 0.9357 (tptt) cc_final: 0.8975 (tppt) REVERT: C 262 TYR cc_start: 0.9025 (m-10) cc_final: 0.8705 (m-10) REVERT: D 317 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8246 (mmtm) REVERT: D 328 ASN cc_start: 0.8580 (p0) cc_final: 0.8288 (p0) REVERT: D 347 ASN cc_start: 0.9264 (t0) cc_final: 0.8864 (t0) REVERT: E 68 ARG cc_start: 0.8202 (ttt-90) cc_final: 0.7609 (tmm-80) REVERT: F 37 ASP cc_start: 0.8274 (t70) cc_final: 0.7792 (p0) REVERT: F 264 LEU cc_start: 0.9224 (mt) cc_final: 0.8984 (mt) REVERT: F 301 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7794 (mm-30) REVERT: G 93 ASN cc_start: 0.8640 (p0) cc_final: 0.8431 (p0) REVERT: G 286 ASP cc_start: 0.9058 (t0) cc_final: 0.8713 (t0) REVERT: I 274 HIS cc_start: 0.7625 (OUTLIER) cc_final: 0.6870 (m90) REVERT: I 298 ILE cc_start: 0.8320 (mp) cc_final: 0.8058 (mp) REVERT: I 301 GLU cc_start: 0.8696 (tp30) cc_final: 0.8369 (tp30) REVERT: A 42 VAL cc_start: 0.8850 (t) cc_final: 0.8636 (p) REVERT: A 46 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7812 (tp30) REVERT: A 51 ASN cc_start: 0.8835 (m110) cc_final: 0.8540 (m110) REVERT: A 85 ASN cc_start: 0.7720 (t0) cc_final: 0.7198 (t0) REVERT: B 219 ARG cc_start: 0.8197 (tpm170) cc_final: 0.7242 (ptm-80) REVERT: B 235 TYR cc_start: 0.5584 (p90) cc_final: 0.4993 (p90) REVERT: B 268 LEU cc_start: 0.8992 (mp) cc_final: 0.8695 (mp) outliers start: 39 outliers final: 18 residues processed: 231 average time/residue: 0.3255 time to fit residues: 115.5887 Evaluate side-chains 193 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 349 ILE Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 230 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 133 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 241 optimal weight: 6.9990 chunk 260 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 chunk 239 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN E 147 GLN E 347 ASN F 162 ASN ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 ASN H 347 ASN I 274 HIS B 188 HIS B 230 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 20935 Z= 0.425 Angle : 0.642 6.659 28509 Z= 0.333 Chirality : 0.043 0.191 3094 Planarity : 0.004 0.058 3683 Dihedral : 13.184 150.058 3497 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 4.17 % Allowed : 19.04 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.47 (0.15), residues: 2610 helix: -1.27 (0.18), residues: 729 sheet: -1.59 (0.25), residues: 425 loop : -3.22 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 329 HIS 0.013 0.002 HIS I 274 PHE 0.020 0.002 PHE G 165 TYR 0.027 0.002 TYR B 179 ARG 0.005 0.000 ARG D 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 163 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6378 (pm20) cc_final: 0.5827 (pm20) REVERT: C 106 GLU cc_start: 0.6318 (tt0) cc_final: 0.5772 (mt-10) REVERT: C 147 TRP cc_start: 0.7069 (OUTLIER) cc_final: 0.6329 (t60) REVERT: C 151 ARG cc_start: 0.8599 (pmt170) cc_final: 0.8305 (pmt170) REVERT: C 171 LYS cc_start: 0.9366 (tptt) cc_final: 0.8969 (tppt) REVERT: C 262 TYR cc_start: 0.9041 (m-10) cc_final: 0.8773 (m-10) REVERT: D 317 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8113 (mmtm) REVERT: D 328 ASN cc_start: 0.8596 (p0) cc_final: 0.8330 (p0) REVERT: D 347 ASN cc_start: 0.9292 (t0) cc_final: 0.8787 (t0) REVERT: E 80 ARG cc_start: 0.8802 (mmm160) cc_final: 0.8591 (mmp-170) REVERT: F 37 ASP cc_start: 0.8340 (t70) cc_final: 0.7881 (p0) REVERT: F 43 MET cc_start: 0.8370 (mtt) cc_final: 0.8117 (mtt) REVERT: G 93 ASN cc_start: 0.8615 (p0) cc_final: 0.8320 (p0) REVERT: H 248 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: I 298 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8227 (mp) REVERT: I 301 GLU cc_start: 0.8689 (tp30) cc_final: 0.8437 (tp30) REVERT: A 45 LYS cc_start: 0.7498 (mtmm) cc_final: 0.6573 (pptt) REVERT: A 46 GLU cc_start: 0.8589 (mm-30) cc_final: 0.7733 (tp30) REVERT: A 51 ASN cc_start: 0.8714 (m110) cc_final: 0.8384 (m-40) REVERT: A 85 ASN cc_start: 0.7761 (t0) cc_final: 0.7561 (t0) REVERT: B 210 ARG cc_start: 0.8037 (mtp180) cc_final: 0.7705 (mtp180) REVERT: B 219 ARG cc_start: 0.8383 (tpm170) cc_final: 0.7374 (ptm-80) outliers start: 80 outliers final: 52 residues processed: 229 average time/residue: 0.3317 time to fit residues: 116.9141 Evaluate side-chains 210 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 154 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 333 ASP Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 321 ASP Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 269 ASP Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 349 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 240 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 238 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 125 optimal weight: 0.0170 chunk 26 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 241 optimal weight: 30.0000 chunk 256 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 229 optimal weight: 30.0000 chunk 69 optimal weight: 7.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 ASN ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN I 274 HIS B 188 HIS B 230 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20935 Z= 0.178 Angle : 0.512 8.948 28509 Z= 0.265 Chirality : 0.040 0.142 3094 Planarity : 0.004 0.057 3683 Dihedral : 13.022 149.973 3497 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.50 % Allowed : 20.71 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.98 (0.15), residues: 2610 helix: -0.66 (0.19), residues: 727 sheet: -1.35 (0.26), residues: 424 loop : -3.01 (0.14), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 329 HIS 0.014 0.001 HIS I 274 PHE 0.013 0.001 PHE G 165 TYR 0.017 0.001 TYR D 132 ARG 0.006 0.000 ARG D 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 173 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6334 (pm20) cc_final: 0.5777 (pm20) REVERT: C 147 TRP cc_start: 0.6549 (OUTLIER) cc_final: 0.6173 (t60) REVERT: C 151 ARG cc_start: 0.8546 (pmt170) cc_final: 0.8209 (ptt-90) REVERT: C 171 LYS cc_start: 0.9354 (tptt) cc_final: 0.8964 (tppt) REVERT: C 262 TYR cc_start: 0.9036 (m-10) cc_final: 0.8770 (m-10) REVERT: D 248 GLU cc_start: 0.7589 (tp30) cc_final: 0.7012 (tp30) REVERT: D 280 ASN cc_start: 0.8699 (t0) cc_final: 0.8438 (t0) REVERT: D 317 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7977 (mmtm) REVERT: D 328 ASN cc_start: 0.8547 (p0) cc_final: 0.8283 (p0) REVERT: D 347 ASN cc_start: 0.9259 (t0) cc_final: 0.8805 (t0) REVERT: F 37 ASP cc_start: 0.8141 (t70) cc_final: 0.7676 (p0) REVERT: F 43 MET cc_start: 0.8379 (mtt) cc_final: 0.8144 (mtt) REVERT: G 93 ASN cc_start: 0.8621 (p0) cc_final: 0.8362 (p0) REVERT: H 248 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: I 228 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7953 (tt) REVERT: I 298 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8122 (mp) REVERT: I 323 TYR cc_start: 0.7876 (t80) cc_final: 0.7560 (t80) REVERT: A 42 VAL cc_start: 0.8854 (t) cc_final: 0.8624 (p) REVERT: A 45 LYS cc_start: 0.7559 (mtmm) cc_final: 0.6593 (pptt) REVERT: A 46 GLU cc_start: 0.8545 (mm-30) cc_final: 0.7707 (tp30) REVERT: A 51 ASN cc_start: 0.8690 (m110) cc_final: 0.8340 (m-40) REVERT: B 210 ARG cc_start: 0.8006 (mtp180) cc_final: 0.7618 (mtp180) REVERT: B 219 ARG cc_start: 0.8337 (tpm170) cc_final: 0.7368 (ptm-80) outliers start: 67 outliers final: 41 residues processed: 221 average time/residue: 0.3220 time to fit residues: 111.5060 Evaluate side-chains 211 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 165 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 287 THR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 240 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 213 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 229 optimal weight: 30.0000 chunk 64 optimal weight: 0.0000 overall best weight: 3.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 HIS ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN I 159 ASN I 274 HIS B 188 HIS B 225 GLN B 230 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20935 Z= 0.331 Angle : 0.570 7.850 28509 Z= 0.295 Chirality : 0.041 0.149 3094 Planarity : 0.004 0.056 3683 Dihedral : 13.035 151.159 3497 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 4.96 % Allowed : 20.24 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.87 (0.16), residues: 2610 helix: -0.51 (0.20), residues: 728 sheet: -1.31 (0.26), residues: 423 loop : -2.97 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 329 HIS 0.009 0.001 HIS I 274 PHE 0.017 0.002 PHE G 165 TYR 0.022 0.002 TYR B 179 ARG 0.005 0.000 ARG D 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 160 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6452 (pm20) cc_final: 0.5926 (pm20) REVERT: C 147 TRP cc_start: 0.6677 (OUTLIER) cc_final: 0.6183 (t60) REVERT: C 151 ARG cc_start: 0.8568 (pmt170) cc_final: 0.8236 (ptt-90) REVERT: C 171 LYS cc_start: 0.9350 (tptt) cc_final: 0.8959 (tppt) REVERT: C 262 TYR cc_start: 0.9061 (m-10) cc_final: 0.8798 (m-10) REVERT: D 317 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7995 (mmtm) REVERT: D 328 ASN cc_start: 0.8574 (p0) cc_final: 0.8312 (p0) REVERT: D 347 ASN cc_start: 0.9292 (t0) cc_final: 0.8794 (t0) REVERT: E 132 TYR cc_start: 0.8835 (t80) cc_final: 0.8566 (t80) REVERT: E 192 TRP cc_start: 0.8858 (OUTLIER) cc_final: 0.6841 (m-90) REVERT: F 37 ASP cc_start: 0.8263 (t70) cc_final: 0.7788 (p0) REVERT: G 40 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8273 (t0) REVERT: G 93 ASN cc_start: 0.8640 (p0) cc_final: 0.8345 (p0) REVERT: H 133 ARG cc_start: 0.9348 (ttp80) cc_final: 0.9015 (mtm110) REVERT: H 248 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: I 228 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8061 (tt) REVERT: I 298 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8212 (mp) REVERT: A 46 GLU cc_start: 0.8512 (mm-30) cc_final: 0.7886 (tp30) REVERT: A 51 ASN cc_start: 0.8637 (m110) cc_final: 0.8332 (m110) REVERT: B 210 ARG cc_start: 0.8068 (mtp180) cc_final: 0.7812 (mtp180) REVERT: B 219 ARG cc_start: 0.8393 (tpm170) cc_final: 0.7438 (ptm-80) outliers start: 95 outliers final: 66 residues processed: 236 average time/residue: 0.3261 time to fit residues: 118.3492 Evaluate side-chains 226 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 153 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 287 THR Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 269 ASP Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 349 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 240 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 86 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 63 optimal weight: 0.0470 chunk 256 optimal weight: 0.9980 chunk 212 optimal weight: 6.9990 chunk 118 optimal weight: 0.0170 chunk 21 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN H 347 ASN I 101 ASN I 274 HIS B 188 HIS B 230 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 20935 Z= 0.123 Angle : 0.485 7.918 28509 Z= 0.250 Chirality : 0.039 0.150 3094 Planarity : 0.003 0.054 3683 Dihedral : 12.868 150.362 3497 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.34 % Allowed : 21.91 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.46 (0.16), residues: 2610 helix: -0.08 (0.21), residues: 719 sheet: -1.05 (0.26), residues: 406 loop : -2.75 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 329 HIS 0.017 0.001 HIS I 274 PHE 0.015 0.001 PHE B 232 TYR 0.017 0.001 TYR D 132 ARG 0.004 0.000 ARG D 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 198 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6377 (pm20) cc_final: 0.5908 (pm20) REVERT: C 156 ASN cc_start: 0.8743 (p0) cc_final: 0.8487 (p0) REVERT: C 171 LYS cc_start: 0.9348 (tptt) cc_final: 0.8969 (tppt) REVERT: D 33 GLU cc_start: 0.8266 (tt0) cc_final: 0.8053 (pm20) REVERT: D 328 ASN cc_start: 0.8592 (p0) cc_final: 0.8354 (p0) REVERT: D 347 ASN cc_start: 0.9264 (t0) cc_final: 0.8789 (t0) REVERT: E 132 TYR cc_start: 0.8853 (t80) cc_final: 0.8596 (t80) REVERT: E 192 TRP cc_start: 0.8718 (OUTLIER) cc_final: 0.6761 (m-90) REVERT: F 37 ASP cc_start: 0.8142 (t70) cc_final: 0.7736 (t70) REVERT: G 40 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8246 (t0) REVERT: G 93 ASN cc_start: 0.8597 (p0) cc_final: 0.8351 (p0) REVERT: G 273 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7235 (mt) REVERT: I 323 TYR cc_start: 0.7856 (t80) cc_final: 0.7644 (t80) REVERT: A 46 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7829 (tp30) REVERT: A 51 ASN cc_start: 0.8712 (m110) cc_final: 0.8402 (m110) REVERT: A 83 GLU cc_start: 0.7108 (tp30) cc_final: 0.6786 (tp30) REVERT: B 210 ARG cc_start: 0.8051 (mtp180) cc_final: 0.7625 (mtp180) REVERT: B 219 ARG cc_start: 0.8336 (tpm170) cc_final: 0.7377 (ptm-80) outliers start: 64 outliers final: 41 residues processed: 249 average time/residue: 0.3275 time to fit residues: 125.6711 Evaluate side-chains 216 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 172 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 262 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 247 optimal weight: 50.0000 chunk 28 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 187 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 215 optimal weight: 0.0270 chunk 143 optimal weight: 6.9990 chunk 255 optimal weight: 8.9990 chunk 159 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 overall best weight: 3.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN I 274 HIS B 230 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20935 Z= 0.288 Angle : 0.553 8.277 28509 Z= 0.283 Chirality : 0.041 0.159 3094 Planarity : 0.004 0.054 3683 Dihedral : 12.886 151.502 3497 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 4.28 % Allowed : 22.64 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.46 (0.16), residues: 2610 helix: -0.07 (0.21), residues: 723 sheet: -0.91 (0.27), residues: 406 loop : -2.80 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 329 HIS 0.009 0.001 HIS I 274 PHE 0.029 0.002 PHE E 322 TYR 0.019 0.001 TYR B 179 ARG 0.004 0.000 ARG D 268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 159 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6431 (pm20) cc_final: 0.5714 (pm20) REVERT: C 106 GLU cc_start: 0.6342 (tt0) cc_final: 0.5905 (mt-10) REVERT: C 147 TRP cc_start: 0.5125 (OUTLIER) cc_final: 0.4774 (t60) REVERT: C 171 LYS cc_start: 0.9342 (tptt) cc_final: 0.8958 (tppt) REVERT: D 317 LYS cc_start: 0.8452 (mmtm) cc_final: 0.8182 (mmtm) REVERT: D 328 ASN cc_start: 0.8669 (p0) cc_final: 0.8388 (p0) REVERT: D 347 ASN cc_start: 0.9309 (t0) cc_final: 0.8800 (t0) REVERT: E 132 TYR cc_start: 0.8832 (t80) cc_final: 0.8616 (t80) REVERT: E 192 TRP cc_start: 0.8753 (OUTLIER) cc_final: 0.6789 (m-90) REVERT: E 265 TYR cc_start: 0.8986 (t80) cc_final: 0.8507 (t80) REVERT: E 321 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7095 (p0) REVERT: F 43 MET cc_start: 0.8409 (mtt) cc_final: 0.8174 (mtt) REVERT: G 40 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8352 (t0) REVERT: G 93 ASN cc_start: 0.8643 (p0) cc_final: 0.8373 (p0) REVERT: G 247 GLN cc_start: 0.8934 (mt0) cc_final: 0.8570 (mt0) REVERT: G 273 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7292 (mt) REVERT: A 46 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7841 (tp30) REVERT: A 51 ASN cc_start: 0.8637 (m110) cc_final: 0.8332 (m110) REVERT: B 188 HIS cc_start: 0.7052 (OUTLIER) cc_final: 0.6807 (m170) REVERT: B 210 ARG cc_start: 0.8087 (mtp180) cc_final: 0.7644 (mtp180) REVERT: B 219 ARG cc_start: 0.8389 (tpm170) cc_final: 0.7446 (ptm-80) outliers start: 82 outliers final: 61 residues processed: 225 average time/residue: 0.3373 time to fit residues: 117.1146 Evaluate side-chains 223 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 156 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 287 THR Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 269 ASP Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 349 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 240 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 158 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 162 optimal weight: 0.1980 chunk 174 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN I 274 HIS B 230 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20935 Z= 0.235 Angle : 0.539 11.933 28509 Z= 0.274 Chirality : 0.040 0.194 3094 Planarity : 0.003 0.054 3683 Dihedral : 12.878 151.196 3497 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 4.17 % Allowed : 23.16 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.35 (0.16), residues: 2610 helix: 0.04 (0.21), residues: 718 sheet: -0.88 (0.27), residues: 408 loop : -2.72 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 329 HIS 0.007 0.001 HIS I 274 PHE 0.022 0.001 PHE E 322 TYR 0.019 0.001 TYR D 132 ARG 0.004 0.000 ARG H 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 168 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6430 (pm20) cc_final: 0.5726 (pm20) REVERT: C 106 GLU cc_start: 0.6409 (tt0) cc_final: 0.6018 (mt-10) REVERT: C 171 LYS cc_start: 0.9347 (tptt) cc_final: 0.8969 (tppt) REVERT: D 317 LYS cc_start: 0.8444 (mmtm) cc_final: 0.8068 (mmtm) REVERT: D 328 ASN cc_start: 0.8651 (p0) cc_final: 0.8375 (p0) REVERT: D 347 ASN cc_start: 0.9287 (t0) cc_final: 0.8781 (t0) REVERT: E 132 TYR cc_start: 0.8840 (t80) cc_final: 0.8618 (t80) REVERT: E 192 TRP cc_start: 0.8790 (OUTLIER) cc_final: 0.6756 (m-90) REVERT: E 265 TYR cc_start: 0.8961 (t80) cc_final: 0.8570 (t80) REVERT: F 43 MET cc_start: 0.8362 (mtt) cc_final: 0.8128 (mtt) REVERT: G 40 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8162 (t0) REVERT: G 93 ASN cc_start: 0.8628 (p0) cc_final: 0.8350 (p0) REVERT: G 273 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7267 (mt) REVERT: H 248 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: A 46 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7828 (tp30) REVERT: A 51 ASN cc_start: 0.8498 (m110) cc_final: 0.7938 (m-40) REVERT: B 210 ARG cc_start: 0.8099 (mtp180) cc_final: 0.7618 (mtp-110) REVERT: B 219 ARG cc_start: 0.8415 (tpm170) cc_final: 0.7456 (ptm-80) outliers start: 80 outliers final: 65 residues processed: 235 average time/residue: 0.3397 time to fit residues: 122.3664 Evaluate side-chains 229 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 160 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 287 THR Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 269 ASP Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain B residue 200 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 232 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 223 optimal weight: 50.0000 chunk 238 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 186 optimal weight: 0.0370 chunk 73 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 225 optimal weight: 0.0170 chunk 237 optimal weight: 0.0980 overall best weight: 2.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN I 274 HIS B 188 HIS B 225 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20935 Z= 0.199 Angle : 0.526 12.743 28509 Z= 0.267 Chirality : 0.040 0.184 3094 Planarity : 0.003 0.054 3683 Dihedral : 12.841 150.890 3497 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.02 % Allowed : 23.63 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.23 (0.16), residues: 2610 helix: 0.17 (0.21), residues: 716 sheet: -0.69 (0.27), residues: 398 loop : -2.70 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 329 HIS 0.009 0.001 HIS I 274 PHE 0.012 0.001 PHE G 165 TYR 0.019 0.001 TYR D 132 ARG 0.006 0.000 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 167 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6385 (pm20) cc_final: 0.5839 (pm20) REVERT: C 106 GLU cc_start: 0.6454 (tt0) cc_final: 0.5997 (mt-10) REVERT: C 171 LYS cc_start: 0.9353 (tptt) cc_final: 0.8976 (tppt) REVERT: D 317 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8169 (mmtm) REVERT: D 328 ASN cc_start: 0.8646 (p0) cc_final: 0.8369 (p0) REVERT: D 347 ASN cc_start: 0.9274 (t0) cc_final: 0.8771 (t0) REVERT: E 132 TYR cc_start: 0.8842 (t80) cc_final: 0.8621 (t80) REVERT: E 192 TRP cc_start: 0.8770 (OUTLIER) cc_final: 0.6845 (m-90) REVERT: E 265 TYR cc_start: 0.8947 (t80) cc_final: 0.8638 (t80) REVERT: G 40 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8277 (t0) REVERT: G 93 ASN cc_start: 0.8638 (p0) cc_final: 0.8354 (p0) REVERT: G 273 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7274 (mt) REVERT: H 248 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: A 46 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7826 (tp30) REVERT: A 51 ASN cc_start: 0.8454 (m110) cc_final: 0.7888 (m-40) REVERT: B 210 ARG cc_start: 0.8085 (mtp180) cc_final: 0.7605 (mtp-110) REVERT: B 219 ARG cc_start: 0.8407 (tpm170) cc_final: 0.7461 (ptm-80) outliers start: 77 outliers final: 65 residues processed: 229 average time/residue: 0.3266 time to fit residues: 115.0446 Evaluate side-chains 232 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 162 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 287 THR Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 269 ASP Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 225 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 156 optimal weight: 2.9990 chunk 251 optimal weight: 50.0000 chunk 153 optimal weight: 5.9990 chunk 119 optimal weight: 0.0970 chunk 174 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 242 optimal weight: 50.0000 chunk 210 optimal weight: 0.0020 chunk 21 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 20935 Z= 0.239 Angle : 0.739 59.188 28509 Z= 0.426 Chirality : 0.042 0.516 3094 Planarity : 0.006 0.208 3683 Dihedral : 12.839 150.849 3497 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.81 % Favored : 91.15 % Rotamer: Outliers : 4.23 % Allowed : 23.32 % Favored : 72.46 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.22 (0.16), residues: 2610 helix: 0.19 (0.21), residues: 716 sheet: -0.68 (0.27), residues: 398 loop : -2.70 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 329 HIS 0.307 0.006 HIS B 188 PHE 0.039 0.001 PHE D 244 TYR 0.019 0.001 TYR D 132 ARG 0.005 0.000 ARG H 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 161 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6384 (pm20) cc_final: 0.5798 (pm20) REVERT: C 106 GLU cc_start: 0.6450 (tt0) cc_final: 0.5994 (mt-10) REVERT: C 171 LYS cc_start: 0.9353 (tptt) cc_final: 0.8976 (tppt) REVERT: D 317 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8168 (mmtm) REVERT: D 328 ASN cc_start: 0.8645 (p0) cc_final: 0.8369 (p0) REVERT: D 347 ASN cc_start: 0.9279 (t0) cc_final: 0.8771 (t0) REVERT: E 132 TYR cc_start: 0.8842 (t80) cc_final: 0.8621 (t80) REVERT: E 192 TRP cc_start: 0.8770 (OUTLIER) cc_final: 0.6845 (m-90) REVERT: E 265 TYR cc_start: 0.8950 (t80) cc_final: 0.8648 (t80) REVERT: E 321 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7038 (p0) REVERT: E 322 PHE cc_start: 0.8586 (t80) cc_final: 0.8274 (t80) REVERT: G 40 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8275 (t0) REVERT: G 93 ASN cc_start: 0.8638 (p0) cc_final: 0.8352 (p0) REVERT: G 273 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7273 (mt) REVERT: H 248 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: A 46 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7826 (tp30) REVERT: A 51 ASN cc_start: 0.8454 (m110) cc_final: 0.7889 (m-40) REVERT: A 83 GLU cc_start: 0.7133 (tp30) cc_final: 0.6760 (tp30) REVERT: B 210 ARG cc_start: 0.8082 (mtp180) cc_final: 0.7601 (mtp-110) REVERT: B 219 ARG cc_start: 0.8407 (tpm170) cc_final: 0.7461 (ptm-80) outliers start: 81 outliers final: 68 residues processed: 228 average time/residue: 0.3320 time to fit residues: 116.3105 Evaluate side-chains 236 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 162 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 350 ARG Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 287 THR Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 269 ASP Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 307 THR Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain B residue 200 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 166 optimal weight: 5.9990 chunk 223 optimal weight: 0.0570 chunk 64 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 216 optimal weight: 0.0010 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.6108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.108752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.078725 restraints weight = 45556.772| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 4.49 r_work: 0.3002 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 20935 Z= 0.239 Angle : 0.739 59.188 28509 Z= 0.426 Chirality : 0.042 0.516 3094 Planarity : 0.006 0.208 3683 Dihedral : 12.839 150.849 3497 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.81 % Favored : 91.15 % Rotamer: Outliers : 3.86 % Allowed : 23.58 % Favored : 72.56 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.22 (0.16), residues: 2610 helix: 0.19 (0.21), residues: 716 sheet: -0.68 (0.27), residues: 398 loop : -2.70 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 329 HIS 0.307 0.006 HIS B 188 PHE 0.039 0.001 PHE D 244 TYR 0.019 0.001 TYR D 132 ARG 0.005 0.000 ARG H 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4228.80 seconds wall clock time: 77 minutes 37.18 seconds (4657.18 seconds total)