Starting phenix.real_space_refine (version: dev) on Thu Apr 7 01:44:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/04_2022/7jzw_22582.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/04_2022/7jzw_22582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/04_2022/7jzw_22582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/04_2022/7jzw_22582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/04_2022/7jzw_22582.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/04_2022/7jzw_22582.pdb" } resolution = 3.2 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= 0.001 sd= 0.006 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 24266 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3145 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 364 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 192 Chain: "C" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 14, 'TRANS': 171, 'PCIS': 1} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 14, 'TRANS': 171, 'PCIS': 1} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2554 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "J" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 760 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'RNA': 60, 'DNA': 1} Modifications used: {'rna3p_pyr': 14, 'rna2p_pur': 11, 'rna3p_pur': 17, 'rna2p_pyr': 17, '5*END': 1} Link IDs: {'rna3p': 32, 'rna2p': 28} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 14.25, per 1000 atoms: 0.59 Number of scatterers: 24266 At special positions: 0 Unit cell: (130.2, 157.5, 148.05, 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 29 16.00 P 60 15.00 O 4715 8.00 N 4422 7.00 C 15040 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: 10.67 Conformation dependent library (CDL) restraints added in 4.0 seconds 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5548 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 56 sheets defined 32.4% alpha, 22.8% beta 6 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 7.61 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.417A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 60 removed outlier: 3.663A pdb=" N ALA A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.600A pdb=" N GLU A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.500A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.785A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.658A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.819A pdb=" N GLU A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 removed outlier: 4.444A pdb=" N GLN A 273 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 309 removed outlier: 3.515A pdb=" N SER A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 364 through 368 removed outlier: 4.044A pdb=" N ARG A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.590A pdb=" N ARG A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 381' Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.667A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.781A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 431 removed outlier: 4.376A pdb=" N ALA A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.902A pdb=" N LEU C 76 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.889A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'B' and resid 33 through 49 removed outlier: 3.904A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.648A pdb=" N ASP B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.581A pdb=" N LEU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 208 through 223 Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 322 through 331 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 152 through 163 Processing helix chain 'D' and resid 209 through 224 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 322 through 332 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.633A pdb=" N SER F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 209 through 223 removed outlier: 3.588A pdb=" N ALA F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 322 through 332 removed outlier: 3.504A pdb=" N LEU F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 91 Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 209 through 223 removed outlier: 3.565A pdb=" N ALA G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 293 through 297 Processing helix chain 'G' and resid 322 through 331 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.739A pdb=" N SER H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 322 through 331 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 51 through 55 Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 152 through 163 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 5 through 14 removed outlier: 3.539A pdb=" N ILE J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR J 12 " --> pdb=" O ASP J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 78 Processing helix chain 'J' and resid 79 through 100 removed outlier: 3.690A pdb=" N VAL J 83 " --> pdb=" O ARG J 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.211A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.211A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 254 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLY B 285 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY B 287 " --> pdb=" O PRO B 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AA7, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.534A pdb=" N HIS C 3 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.534A pdb=" N HIS C 3 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.509A pdb=" N VAL C 184 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB2, first strand: chain 'B' and resid 54 through 60 removed outlier: 4.079A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.198A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AB5, first strand: chain 'B' and resid 221 through 222 Processing sheet with id=AB6, first strand: chain 'B' and resid 304 through 306 Processing sheet with id=AB7, first strand: chain 'E' and resid 127 through 128 Processing sheet with id=AB8, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.212A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 189 through 192 removed outlier: 6.553A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 63 through 70 Processing sheet with id=AC2, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC3, first strand: chain 'E' and resid 306 through 307 removed outlier: 3.519A pdb=" N VAL E 307 " --> pdb=" O LYS E 312 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS E 312 " --> pdb=" O VAL E 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AC5, first strand: chain 'D' and resid 38 through 39 removed outlier: 4.093A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA D 176 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL D 177 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP D 196 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL D 179 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG D 194 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE D 181 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA D 192 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N HIS D 183 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D 188 " --> pdb=" O ARG D 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'D' and resid 63 through 66 removed outlier: 4.598A pdb=" N ALA D 101 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 248 through 249 removed outlier: 4.603A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AD1, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AD2, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AD3, first strand: chain 'F' and resid 38 through 39 removed outlier: 4.181A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG F 191 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD5, first strand: chain 'F' and resid 63 through 70 removed outlier: 3.671A pdb=" N GLY F 70 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN F 94 " --> pdb=" O GLY F 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD7, first strand: chain 'F' and resid 306 through 307 removed outlier: 3.670A pdb=" N LYS F 312 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 127 through 128 Processing sheet with id=AD9, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.040A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 189 through 192 removed outlier: 3.670A pdb=" N ARG G 191 " --> pdb=" O HIS G 183 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 63 through 70 removed outlier: 3.611A pdb=" N GLY G 70 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AE4, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.569A pdb=" N GLY H 353 " --> pdb=" O PHE H 33 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 38 through 39 removed outlier: 4.142A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 188 through 192 removed outlier: 6.731A pdb=" N HIS H 183 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA H 192 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE H 181 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 63 through 66 removed outlier: 4.576A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 69 through 70 removed outlier: 3.697A pdb=" N GLY H 70 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'H' and resid 248 through 249 removed outlier: 4.702A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AF2, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.653A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AF4, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.528A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL I 177 " --> pdb=" O ASP I 196 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASP I 196 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL I 179 " --> pdb=" O ARG I 194 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG I 194 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE I 181 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA I 192 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N HIS I 183 " --> pdb=" O ALA I 190 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AF6, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.729A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.729A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LYS I 261 " --> pdb=" O LEU I 95 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR I 97 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS I 263 " --> pdb=" O THR I 97 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF9, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.665A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 17 through 21 removed outlier: 12.893A pdb=" N TRP J 28 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N VAL J 47 " --> pdb=" O TRP J 28 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE J 30 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY J 55 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 17 through 21 1050 hydrogen bonds defined for protein. 2925 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 8.76 Time building geometry restraints manager: 11.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5046 1.32 - 1.44: 5968 1.44 - 1.56: 13702 1.56 - 1.68: 120 1.68 - 1.80: 44 Bond restraints: 24880 Sorted by residual: bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.337 1.382 -0.046 9.80e-03 1.04e+04 2.16e+01 bond pdb=" O3' A M 36 " pdb=" P C M 37 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.26e+01 bond pdb=" N LEU A 70 " pdb=" CA LEU A 70 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.32e-02 5.74e+03 8.10e+00 bond pdb=" N GLN H 186 " pdb=" CA GLN H 186 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.19e+00 bond pdb=" CG LEU D 229 " pdb=" CD1 LEU D 229 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.90e+00 ... (remaining 24875 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.35: 993 106.35 - 113.29: 13482 113.29 - 120.23: 9214 120.23 - 127.17: 9946 127.17 - 134.11: 441 Bond angle restraints: 34076 Sorted by residual: angle pdb=" O ARG H 185 " pdb=" C ARG H 185 " pdb=" N GLN H 186 " ideal model delta sigma weight residual 122.23 129.29 -7.06 1.33e+00 5.65e-01 2.82e+01 angle pdb=" C ARG F 185 " pdb=" N GLN F 186 " pdb=" CA GLN F 186 " ideal model delta sigma weight residual 120.82 128.71 -7.89 1.50e+00 4.44e-01 2.77e+01 angle pdb=" C GLN A 124 " pdb=" N TYR A 125 " pdb=" CA TYR A 125 " ideal model delta sigma weight residual 120.79 127.65 -6.86 1.39e+00 5.18e-01 2.44e+01 angle pdb=" C ARG I 185 " pdb=" N GLN I 186 " pdb=" CA GLN I 186 " ideal model delta sigma weight residual 120.38 126.93 -6.55 1.37e+00 5.33e-01 2.28e+01 angle pdb=" C ARG H 185 " pdb=" N GLN H 186 " pdb=" CA GLN H 186 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.25e+01 ... (remaining 34071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 14400 35.59 - 71.19: 365 71.19 - 106.78: 24 106.78 - 142.37: 1 142.37 - 177.96: 5 Dihedral angle restraints: 14795 sinusoidal: 6203 harmonic: 8592 Sorted by residual: dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 53.90 146.10 1 1.50e+01 4.44e-03 7.81e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 65.69 134.31 1 1.50e+01 4.44e-03 7.25e+01 dihedral pdb=" O4' C M 38 " pdb=" C1' C M 38 " pdb=" N1 C M 38 " pdb=" C2 C M 38 " ideal model delta sinusoidal sigma weight residual -128.00 49.96 -177.96 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 14792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3034 0.063 - 0.127: 682 0.127 - 0.190: 113 0.190 - 0.254: 6 0.254 - 0.317: 4 Chirality restraints: 3839 Sorted by residual: chirality pdb=" CB THR B 318 " pdb=" CA THR B 318 " pdb=" OG1 THR B 318 " pdb=" CG2 THR B 318 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE B 219 " pdb=" CA ILE B 219 " pdb=" CG1 ILE B 219 " pdb=" CG2 ILE B 219 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C1' U M 33 " pdb=" O4' U M 33 " pdb=" C2' U M 33 " pdb=" N1 U M 33 " both_signs ideal model delta sigma weight residual False 2.47 2.21 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3836 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.053 5.00e-02 4.00e+02 7.88e-02 9.95e+00 pdb=" N PRO A 72 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 73 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO C 74 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 103 " 0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO D 104 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 104 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 104 " 0.038 5.00e-02 4.00e+02 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4954 2.77 - 3.30: 21528 3.30 - 3.83: 42348 3.83 - 4.37: 51903 4.37 - 4.90: 87079 Nonbonded interactions: 207812 Sorted by model distance: nonbonded pdb=" OH TYR F 324 " pdb=" O SER G 73 " model vdw 2.237 2.440 nonbonded pdb=" OH TYR E 324 " pdb=" O SER F 73 " model vdw 2.237 2.440 nonbonded pdb=" OH TYR G 324 " pdb=" O SER H 73 " model vdw 2.255 2.440 nonbonded pdb=" OH TYR H 324 " pdb=" O SER I 73 " model vdw 2.256 2.440 nonbonded pdb=" O SER E 73 " pdb=" OH TYR D 324 " model vdw 2.266 2.440 ... (remaining 207807 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' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 29 5.16 5 C 15040 2.51 5 N 4422 2.21 5 O 4715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 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: 0.860 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: 0.020 Extract box with map and model: 5.840 Check model and map are aligned: 0.380 Convert atoms to be neutral: 0.220 Process input model: 72.310 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 24880 Z= 0.635 Angle : 0.973 10.119 34076 Z= 0.541 Chirality : 0.055 0.317 3839 Planarity : 0.007 0.079 4272 Dihedral : 16.209 177.963 9247 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.93 % Favored : 93.04 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -3.86 (0.12), residues: 2959 helix: -2.82 (0.11), residues: 933 sheet: -1.31 (0.22), residues: 482 loop : -2.85 (0.12), residues: 1544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 285 time to evaluate : 2.964 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 288 average time/residue: 0.4873 time to fit residues: 198.8708 Evaluate side-chains 204 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 2.655 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1981 time to fit residues: 4.4157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 174 optimal weight: 0.5980 chunk 271 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN C 29 HIS ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 24880 Z= 0.191 Angle : 0.559 11.082 34076 Z= 0.295 Chirality : 0.040 0.205 3839 Planarity : 0.004 0.055 4272 Dihedral : 12.077 179.954 3987 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.75 % Favored : 94.22 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -2.41 (0.13), residues: 2959 helix: -0.91 (0.15), residues: 950 sheet: -0.52 (0.23), residues: 460 loop : -2.46 (0.13), residues: 1549 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 229 time to evaluate : 2.824 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 248 average time/residue: 0.4791 time to fit residues: 171.7764 Evaluate side-chains 217 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 203 time to evaluate : 2.704 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3016 time to fit residues: 10.4850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 225 optimal weight: 0.9990 chunk 184 optimal weight: 0.3980 chunk 74 optimal weight: 7.9990 chunk 272 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN D 102 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN G 148 GLN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 319 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.111 24880 Z= 0.191 Angle : 0.536 11.480 34076 Z= 0.278 Chirality : 0.039 0.188 3839 Planarity : 0.004 0.061 4272 Dihedral : 11.808 179.268 3987 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.22 % Favored : 93.75 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.65 (0.14), residues: 2959 helix: 0.11 (0.16), residues: 954 sheet: -0.26 (0.23), residues: 472 loop : -2.24 (0.14), residues: 1533 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 212 time to evaluate : 2.597 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 234 average time/residue: 0.4444 time to fit residues: 153.1148 Evaluate side-chains 204 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 2.677 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2714 time to fit residues: 9.3108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 0.0870 chunk 204 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN C 154 HIS E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN D 102 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.114 24880 Z= 0.286 Angle : 0.558 12.436 34076 Z= 0.288 Chirality : 0.041 0.188 3839 Planarity : 0.004 0.092 4272 Dihedral : 11.740 178.691 3987 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.39 % Favored : 93.58 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.33 (0.15), residues: 2959 helix: 0.54 (0.16), residues: 956 sheet: -0.19 (0.23), residues: 476 loop : -2.14 (0.14), residues: 1527 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 211 time to evaluate : 2.770 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 225 average time/residue: 0.4605 time to fit residues: 153.8533 Evaluate side-chains 214 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 3.104 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3375 time to fit residues: 12.2150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 147 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS E 91 GLN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN D 102 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.134 24880 Z= 0.244 Angle : 0.532 12.286 34076 Z= 0.275 Chirality : 0.040 0.186 3839 Planarity : 0.004 0.081 4272 Dihedral : 11.657 178.706 3987 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.39 % Favored : 93.58 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.06 (0.15), residues: 2959 helix: 0.84 (0.17), residues: 961 sheet: -0.14 (0.23), residues: 486 loop : -2.01 (0.14), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 212 time to evaluate : 2.588 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 227 average time/residue: 0.4569 time to fit residues: 153.7034 Evaluate side-chains 205 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 194 time to evaluate : 2.751 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2298 time to fit residues: 8.4965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 289 optimal weight: 6.9990 chunk 240 optimal weight: 0.0070 chunk 133 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.143 24880 Z= 0.290 Angle : 0.560 12.474 34076 Z= 0.289 Chirality : 0.041 0.186 3839 Planarity : 0.004 0.065 4272 Dihedral : 11.649 178.322 3987 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.63 % Favored : 93.34 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.96 (0.15), residues: 2959 helix: 0.98 (0.17), residues: 956 sheet: -0.12 (0.23), residues: 480 loop : -1.97 (0.15), residues: 1523 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 2.891 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 209 average time/residue: 0.4923 time to fit residues: 151.9079 Evaluate side-chains 193 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 184 time to evaluate : 2.757 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2513 time to fit residues: 7.7806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 211 optimal weight: 0.6980 chunk 163 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 288 optimal weight: 0.8980 chunk 180 optimal weight: 0.7980 chunk 175 optimal weight: 0.0050 chunk 133 optimal weight: 3.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.150 24880 Z= 0.182 Angle : 0.517 13.647 34076 Z= 0.268 Chirality : 0.039 0.180 3839 Planarity : 0.004 0.062 4272 Dihedral : 11.495 179.474 3987 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.91 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.70 (0.15), residues: 2959 helix: 1.26 (0.17), residues: 960 sheet: 0.07 (0.23), residues: 474 loop : -1.87 (0.15), residues: 1525 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 2.536 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 224 average time/residue: 0.4735 time to fit residues: 155.6547 Evaluate side-chains 196 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 189 time to evaluate : 2.845 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3828 time to fit residues: 7.7839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 183 optimal weight: 0.0270 chunk 196 optimal weight: 0.6980 chunk 142 optimal weight: 0.0030 chunk 26 optimal weight: 0.5980 chunk 226 optimal weight: 4.9990 overall best weight: 0.4048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 HIS ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN I 96 GLN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.183 24880 Z= 0.174 Angle : 0.521 16.932 34076 Z= 0.273 Chirality : 0.038 0.177 3839 Planarity : 0.004 0.057 4272 Dihedral : 11.319 179.495 3987 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.61 % Favored : 94.35 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.48 (0.15), residues: 2959 helix: 1.53 (0.17), residues: 957 sheet: 0.18 (0.23), residues: 474 loop : -1.80 (0.15), residues: 1528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 203 time to evaluate : 2.674 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 212 average time/residue: 0.4768 time to fit residues: 148.6500 Evaluate side-chains 190 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 2.910 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2555 time to fit residues: 4.8932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 0.7980 chunk 276 optimal weight: 2.9990 chunk 251 optimal weight: 0.5980 chunk 268 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 210 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 242 optimal weight: 3.9990 chunk 253 optimal weight: 0.9980 chunk 267 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN D 348 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.183 24880 Z= 0.191 Angle : 0.520 15.281 34076 Z= 0.272 Chirality : 0.039 0.178 3839 Planarity : 0.004 0.139 4272 Dihedral : 11.293 179.072 3987 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.49 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.40 (0.15), residues: 2959 helix: 1.61 (0.17), residues: 957 sheet: 0.17 (0.23), residues: 486 loop : -1.74 (0.15), residues: 1516 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 2.817 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 193 average time/residue: 0.4767 time to fit residues: 135.0816 Evaluate side-chains 186 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 184 time to evaluate : 3.014 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2027 time to fit residues: 4.3556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 0.7980 chunk 283 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 197 optimal weight: 0.0070 chunk 297 optimal weight: 10.0000 chunk 274 optimal weight: 0.0270 chunk 237 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.241 24880 Z= 0.182 Angle : 0.506 17.343 34076 Z= 0.264 Chirality : 0.038 0.227 3839 Planarity : 0.004 0.090 4272 Dihedral : 11.230 179.680 3987 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.41 % Favored : 94.56 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.31 (0.15), residues: 2959 helix: 1.70 (0.17), residues: 959 sheet: 0.07 (0.23), residues: 496 loop : -1.65 (0.15), residues: 1504 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 2.576 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 199 average time/residue: 0.5166 time to fit residues: 150.6444 Evaluate side-chains 183 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 2.756 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.8551 time to fit residues: 4.7737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 218 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 237 optimal weight: 0.6980 chunk 99 optimal weight: 0.0470 chunk 243 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 43 optimal weight: 0.0370 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.125235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.095622 restraints weight = 48843.077| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.56 r_work: 0.3164 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work: 0.3111 rms_B_bonded: 2.45 restraints_weight: 0.1250 r_work: 0.3080 rms_B_bonded: 2.74 restraints_weight: 0.0625 r_work: 0.3042 rms_B_bonded: 3.19 restraints_weight: 0.0312 r_work: 0.2994 rms_B_bonded: 3.84 restraints_weight: 0.0156 r_work: 0.2933 rms_B_bonded: 4.78 restraints_weight: 0.0078 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.382 24880 Z= 0.292 Angle : 0.617 52.857 34076 Z= 0.306 Chirality : 0.039 0.233 3839 Planarity : 0.004 0.105 4272 Dihedral : 11.196 179.709 3987 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.24 (0.15), residues: 2959 helix: 1.79 (0.17), residues: 956 sheet: 0.13 (0.23), residues: 496 loop : -1.63 (0.15), residues: 1507 =============================================================================== Job complete usr+sys time: 4251.65 seconds wall clock time: 78 minutes 44.69 seconds (4724.69 seconds total)