Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 15:46:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/04_2023/6vqw_21359.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/04_2023/6vqw_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_21359/04_2023/6vqw_21359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/04_2023/6vqw_21359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/04_2023/6vqw_21359.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/04_2023/6vqw_21359.pdb" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 10.80, per 1000 atoms: 0.53 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: 7.97 Conformation dependent library (CDL) restraints added in 2.9 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: 4.93 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: 6.18 Time building geometry restraints manager: 8.57 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: 11681 30.14 - 60.28: 426 60.28 - 90.42: 50 90.42 - 120.55: 1 120.55 - 150.69: 1 Dihedral angle restraints: 12159 sinusoidal: 4963 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 12156 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.270 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 53.560 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.400 ------------------------------------------------------------------------------- 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 : 15.462 150.693 7655 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 % 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 *********************** 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 : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 226 average time/residue: 0.3703 time to fit residues: 124.1915 Evaluate side-chains 161 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 156 time to evaluate : 2.452 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1806 time to fit residues: 4.8702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 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: 0.9990 chunk 240 optimal weight: 9.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 A 51 ASN B 188 HIS B 230 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 20935 Z= 0.155 Angle : 0.519 7.589 28509 Z= 0.274 Chirality : 0.039 0.169 3094 Planarity : 0.004 0.062 3683 Dihedral : 9.803 147.641 3347 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 1.83 % 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: -3.88 (0.14), residues: 2610 helix: -2.06 (0.16), residues: 737 sheet: -1.64 (0.25), residues: 418 loop : -3.28 (0.13), residues: 1455 *********************** 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 233 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 198 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 15 residues processed: 222 average time/residue: 0.3320 time to fit residues: 113.8245 Evaluate side-chains 183 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 168 time to evaluate : 2.338 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1874 time to fit residues: 8.3818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 200 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 241 optimal weight: 20.0000 chunk 260 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 chunk 239 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 D 347 ASN E 147 GLN E 347 ASN F 162 ASN ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 ASN H 347 ASN A 51 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.081 20935 Z= 0.471 Angle : 0.683 7.072 28509 Z= 0.353 Chirality : 0.044 0.188 3094 Planarity : 0.005 0.059 3683 Dihedral : 10.130 149.584 3347 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer Outliers : 3.60 % 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: -3.52 (0.15), residues: 2610 helix: -1.33 (0.18), residues: 728 sheet: -1.59 (0.25), residues: 416 loop : -3.24 (0.14), residues: 1466 *********************** 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 228 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 159 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 42 residues processed: 216 average time/residue: 0.3355 time to fit residues: 112.6044 Evaluate side-chains 191 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 149 time to evaluate : 2.471 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2036 time to fit residues: 18.8127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 125 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 20.0000 chunk 256 optimal weight: 0.0270 chunk 126 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- 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** ** D 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN E 347 ASN ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1835 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= 0.187 Angle : 0.527 12.356 28509 Z= 0.273 Chirality : 0.040 0.150 3094 Planarity : 0.004 0.059 3683 Dihedral : 9.664 149.493 3347 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 1.83 % 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: -2.93 (0.15), residues: 2610 helix: -0.69 (0.19), residues: 729 sheet: -1.21 (0.27), residues: 394 loop : -2.96 (0.14), residues: 1487 *********************** 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 210 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 9 residues processed: 199 average time/residue: 0.3255 time to fit residues: 101.8572 Evaluate side-chains 171 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 2.341 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2227 time to fit residues: 6.6218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 213 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 chunk 105 optimal weight: 0.0570 chunk 218 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 229 optimal weight: 30.0000 chunk 64 optimal weight: 3.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- 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** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 20935 Z= 0.264 Angle : 0.554 11.384 28509 Z= 0.286 Chirality : 0.041 0.162 3094 Planarity : 0.004 0.061 3683 Dihedral : 9.694 150.389 3347 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer Outliers : 2.30 % 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: -2.74 (0.16), residues: 2610 helix: -0.43 (0.20), residues: 728 sheet: -1.07 (0.27), residues: 396 loop : -2.91 (0.15), residues: 1486 *********************** 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 204 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 160 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 20 residues processed: 193 average time/residue: 0.3644 time to fit residues: 108.2357 Evaluate side-chains 171 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 2.556 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2012 time to fit residues: 10.5823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 86 optimal weight: 9.9990 chunk 230 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 0.0070 chunk 256 optimal weight: 30.0000 chunk 212 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 84 optimal weight: 0.0370 chunk 134 optimal weight: 9.9990 overall best weight: 2.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2061 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= 0.233 Angle : 0.539 10.662 28509 Z= 0.278 Chirality : 0.040 0.154 3094 Planarity : 0.004 0.056 3683 Dihedral : 9.623 150.718 3347 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer Outliers : 1.67 % 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: -2.54 (0.16), residues: 2610 helix: -0.21 (0.20), residues: 719 sheet: -0.92 (0.27), residues: 407 loop : -2.81 (0.15), residues: 1484 *********************** 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 199 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 194 average time/residue: 0.3362 time to fit residues: 100.4006 Evaluate side-chains 170 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 155 time to evaluate : 2.306 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2016 time to fit residues: 8.5130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 146 optimal weight: 3.9990 chunk 187 optimal weight: 0.0370 chunk 145 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 274 HIS A 51 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 20935 Z= 0.182 Angle : 0.518 11.913 28509 Z= 0.265 Chirality : 0.040 0.138 3094 Planarity : 0.003 0.059 3683 Dihedral : 9.482 150.755 3347 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer Outliers : 1.20 % 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: -2.34 (0.16), residues: 2610 helix: 0.03 (0.21), residues: 718 sheet: -0.83 (0.27), residues: 409 loop : -2.72 (0.15), residues: 1483 *********************** 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 189 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 182 average time/residue: 0.3627 time to fit residues: 101.0514 Evaluate side-chains 164 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 2.189 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.2458 time to fit residues: 7.6955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 158 optimal weight: 7.9990 chunk 101 optimal weight: 0.0270 chunk 152 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 I 101 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 20935 Z= 0.129 Angle : 0.501 13.304 28509 Z= 0.254 Chirality : 0.039 0.153 3094 Planarity : 0.003 0.054 3683 Dihedral : 9.277 150.819 3347 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 0.94 % 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: -2.08 (0.16), residues: 2610 helix: 0.32 (0.21), residues: 713 sheet: -0.54 (0.27), residues: 387 loop : -2.62 (0.15), residues: 1510 *********************** 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 218 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 200 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 215 average time/residue: 0.3487 time to fit residues: 117.1371 Evaluate side-chains 186 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 180 time to evaluate : 2.265 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1900 time to fit residues: 5.3075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 232 optimal weight: 8.9990 chunk 244 optimal weight: 30.0000 chunk 223 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 103 optimal weight: 0.0370 chunk 186 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 237 optimal weight: 0.8980 overall best weight: 3.3864 ------------------------------------------------------------------------------- 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** G 247 GLN ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 20935 Z= 0.293 Angle : 0.583 11.805 28509 Z= 0.297 Chirality : 0.041 0.175 3094 Planarity : 0.004 0.056 3683 Dihedral : 9.528 150.464 3347 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer Outliers : 0.89 % 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: -2.18 (0.16), residues: 2610 helix: 0.14 (0.21), residues: 715 sheet: -0.53 (0.27), residues: 394 loop : -2.66 (0.15), residues: 1501 *********************** 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 176 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 171 average time/residue: 0.3813 time to fit residues: 101.9265 Evaluate side-chains 163 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 2.444 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2413 time to fit residues: 7.0705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 156 optimal weight: 6.9990 chunk 251 optimal weight: 50.0000 chunk 153 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 174 optimal weight: 0.0670 chunk 264 optimal weight: 10.0000 chunk 242 optimal weight: 30.0000 chunk 210 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- 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 ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 20935 Z= 0.292 Angle : 0.587 11.367 28509 Z= 0.299 Chirality : 0.042 0.160 3094 Planarity : 0.004 0.054 3683 Dihedral : 9.654 151.167 3347 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer Outliers : 0.52 % 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: -2.19 (0.16), residues: 2610 helix: 0.11 (0.21), residues: 716 sheet: -0.63 (0.28), residues: 376 loop : -2.60 (0.15), residues: 1518 ********************** 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 171 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 169 average time/residue: 0.3379 time to fit residues: 88.8602 Evaluate side-chains 158 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 2.386 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1885 time to fit residues: 4.2193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 166 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 216 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** ** 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** ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.106460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.076375 restraints weight = 46293.210| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 4.43 r_work: 0.2957 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 20935 Z= 0.338 Angle : 0.614 10.613 28509 Z= 0.312 Chirality : 0.042 0.160 3094 Planarity : 0.004 0.051 3683 Dihedral : 9.784 151.103 3347 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer Outliers : 0.52 % 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: -2.26 (0.16), residues: 2610 helix: 0.05 (0.21), residues: 716 sheet: -0.74 (0.27), residues: 386 loop : -2.63 (0.15), residues: 1508 =============================================================================== Job complete usr+sys time: 3777.34 seconds wall clock time: 69 minutes 51.65 seconds (4191.65 seconds total)