Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 19:22:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uhc_20770/08_2023/6uhc_20770_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uhc_20770/08_2023/6uhc_20770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uhc_20770/08_2023/6uhc_20770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uhc_20770/08_2023/6uhc_20770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uhc_20770/08_2023/6uhc_20770_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uhc_20770/08_2023/6uhc_20770_neut_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.088 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 72 5.16 5 C 9320 2.51 5 N 2540 2.21 5 O 2740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "G GLU 115": "OE1" <-> "OE2" Residue "H GLU 500": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 14680 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3099 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 26, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2587 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 16, 'TRANS': 357} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 438 Unresolved non-hydrogen angles: 558 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 5, 'GLU:plan': 15, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 242 Chain: "C" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2681 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 339} Chain breaks: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2240 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 273} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1344 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 160} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1346 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 161} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 996 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 20} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 161 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 23} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.67, per 1000 atoms: 0.52 Number of scatterers: 14680 At special positions: 0 Unit cell: (94.468, 130.416, 147.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 6 15.00 Mg 2 11.99 O 2740 8.00 N 2540 7.00 C 9320 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: 5.93 Conformation dependent library (CDL) restraints added in 2.4 seconds 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 19 sheets defined 37.5% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.527A pdb=" N ALA A 66 " --> pdb=" O GLY A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 125 through 131 removed outlier: 4.184A pdb=" N ILE A 129 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N MET A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 removed outlier: 4.020A pdb=" N LEU A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TRP A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 217 through 231 removed outlier: 4.969A pdb=" N LEU A 221 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 222 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 223 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 225 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 230 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 231 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.686A pdb=" N ILE A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 282' Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 296 through 306 Processing helix chain 'A' and resid 309 through 316 removed outlier: 5.600A pdb=" N ARG A 313 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 331 through 352 removed outlier: 5.056A pdb=" N ASP A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 386 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.597A pdb=" N VAL B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 147 No H-bonds generated for 'chain 'B' and resid 144 through 147' Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 186 through 199 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 227 through 236 removed outlier: 3.757A pdb=" N LYS B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 265 removed outlier: 3.648A pdb=" N GLU B 260 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA B 261 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Proline residue: B 262 - end of helix Processing helix chain 'B' and resid 278 through 288 Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.642A pdb=" N SER B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 313 through 328 Processing helix chain 'B' and resid 335 through 338 No H-bonds generated for 'chain 'B' and resid 335 through 338' Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 375 through 380 removed outlier: 3.568A pdb=" N GLU B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 64 through 70 removed outlier: 3.703A pdb=" N HIS D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 79 Processing helix chain 'D' and resid 106 through 114 Processing helix chain 'D' and resid 116 through 134 removed outlier: 3.590A pdb=" N CYS D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.781A pdb=" N VAL D 176 " --> pdb=" O ASP D 172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 185 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU D 187 " --> pdb=" O GLN D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 232 No H-bonds generated for 'chain 'D' and resid 229 through 232' Processing helix chain 'D' and resid 234 through 280 removed outlier: 3.745A pdb=" N ARG D 237 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP D 238 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN D 239 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 241 " --> pdb=" O ASP D 238 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE D 244 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N HIS D 245 " --> pdb=" O ASN D 242 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ARG D 248 " --> pdb=" O HIS D 245 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR D 253 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS D 257 " --> pdb=" O HIS D 254 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG D 267 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS D 269 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR D 270 " --> pdb=" O ARG D 267 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 274 " --> pdb=" O SER D 271 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS D 275 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL D 276 " --> pdb=" O PHE D 273 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU D 277 " --> pdb=" O LEU D 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 54 removed outlier: 4.632A pdb=" N LYS E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ALA E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 84 removed outlier: 3.534A pdb=" N THR E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS E 84 " --> pdb=" O LYS E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 100 Processing helix chain 'E' and resid 124 through 148 removed outlier: 3.705A pdb=" N GLU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 163 removed outlier: 5.595A pdb=" N PHE E 163 " --> pdb=" O TRP E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'F' and resid 5 through 19 Processing helix chain 'F' and resid 37 through 40 No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 44 through 46 No H-bonds generated for 'chain 'F' and resid 44 through 46' Processing helix chain 'F' and resid 81 through 96 removed outlier: 3.553A pdb=" N PHE F 93 " --> pdb=" O LYS F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 128 through 167 removed outlier: 3.817A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 48 removed outlier: 3.630A pdb=" N CYS G 45 " --> pdb=" O GLU G 41 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 58 Processing helix chain 'G' and resid 69 through 85 removed outlier: 3.558A pdb=" N VAL G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 95 removed outlier: 4.978A pdb=" N GLU G 92 " --> pdb=" O ASN G 89 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS G 93 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 115 removed outlier: 3.505A pdb=" N MET G 107 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS G 108 " --> pdb=" O ASP G 104 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 146 removed outlier: 3.665A pdb=" N GLN G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL G 138 " --> pdb=" O ALA G 134 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLY G 139 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE G 141 " --> pdb=" O GLY G 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL G 144 " --> pdb=" O SER G 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 466 No H-bonds generated for 'chain 'H' and resid 463 through 466' Processing helix chain 'H' and resid 472 through 477 removed outlier: 3.680A pdb=" N LYS H 476 " --> pdb=" O GLN H 472 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA H 477 " --> pdb=" O LYS H 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 472 through 477' Processing helix chain 'I' and resid 460 through 474 removed outlier: 3.556A pdb=" N GLU I 469 " --> pdb=" O GLY I 465 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN I 472 " --> pdb=" O MET I 468 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS I 473 " --> pdb=" O GLU I 469 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 139 through 143 removed outlier: 6.553A pdb=" N PHE A 110 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA A 142 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 112 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N CYS A 8 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N THR A 113 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N VAL A 10 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= C, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.310A pdb=" N THR A 166 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N SER A 322 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE A 168 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 175 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 254 through 259 removed outlier: 3.567A pdb=" N TYR A 256 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 10 through 13 Processing sheet with id= F, first strand: chain 'B' and resid 36 through 39 Processing sheet with id= G, first strand: chain 'B' and resid 106 through 111 removed outlier: 6.616A pdb=" N GLY B 135 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU B 109 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR B 137 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU B 111 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA B 139 " --> pdb=" O GLU B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 301 through 304 removed outlier: 6.498A pdb=" N VAL B 155 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N SER B 304 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL B 157 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 242 through 245 Processing sheet with id= J, first strand: chain 'C' and resid 2 through 5 removed outlier: 4.026A pdb=" N GLY C 353 " --> pdb=" O GLY C 349 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP C 357 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE C 345 " --> pdb=" O TRP C 357 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 14 through 16 removed outlier: 5.999A pdb=" N GLU C 36 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS C 44 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N SER C 38 " --> pdb=" O TRP C 42 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 85 through 91 removed outlier: 3.982A pdb=" N ALA C 76 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 102 through 104 removed outlier: 3.540A pdb=" N PHE C 111 " --> pdb=" O CYS C 123 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.164A pdb=" N GLY C 160 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU C 148 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA C 158 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TRP C 150 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU C 156 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C 169 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 159 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG C 167 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER C 170 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 194 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 236 through 241 removed outlier: 3.763A pdb=" N ALA C 236 " --> pdb=" O ASP C 230 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 230 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY C 207 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 247 through 252 removed outlier: 6.667A pdb=" N ALA C 261 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU C 250 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 259 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE C 252 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER C 257 " --> pdb=" O PHE C 252 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR C 271 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N PHE C 281 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP C 273 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU C 279 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 32 through 37 removed outlier: 3.732A pdb=" N VAL D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 142 through 144 Processing sheet with id= S, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.734A pdb=" N SER F 69 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE F 114 " --> pdb=" O ILE F 74 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.83 Time building geometry restraints manager: 6.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 2443 1.26 - 1.40: 3663 1.40 - 1.54: 8264 1.54 - 1.68: 505 1.68 - 1.82: 112 Bond restraints: 14987 Sorted by residual: bond pdb=" C PRO A 116 " pdb=" N LEU A 117 " ideal model delta sigma weight residual 1.331 1.462 -0.130 1.14e-02 7.69e+03 1.30e+02 bond pdb=" N PRO B 347 " pdb=" CD PRO B 347 " ideal model delta sigma weight residual 1.473 1.615 -0.142 1.40e-02 5.10e+03 1.03e+02 bond pdb=" C ALA A 196 " pdb=" N GLY A 197 " ideal model delta sigma weight residual 1.331 1.470 -0.139 1.46e-02 4.69e+03 9.11e+01 bond pdb=" N PRO C 180 " pdb=" CD PRO C 180 " ideal model delta sigma weight residual 1.473 1.602 -0.129 1.40e-02 5.10e+03 8.52e+01 bond pdb=" C PRO A 6 " pdb=" O PRO A 6 " ideal model delta sigma weight residual 1.232 1.116 0.117 1.27e-02 6.20e+03 8.43e+01 ... (remaining 14982 not shown) Histogram of bond angle deviations from ideal: 96.89 - 105.29: 361 105.29 - 113.69: 8164 113.69 - 122.09: 8501 122.09 - 130.49: 3231 130.49 - 138.89: 87 Bond angle restraints: 20344 Sorted by residual: angle pdb=" PB ATP B 502 " pdb=" O3B ATP B 502 " pdb=" PG ATP B 502 " ideal model delta sigma weight residual 139.87 121.93 17.94 1.00e+00 1.00e+00 3.22e+02 angle pdb=" PB ATP A 502 " pdb=" O3B ATP A 502 " pdb=" PG ATP A 502 " ideal model delta sigma weight residual 139.87 123.50 16.37 1.00e+00 1.00e+00 2.68e+02 angle pdb=" PA ATP B 502 " pdb=" O3A ATP B 502 " pdb=" PB ATP B 502 " ideal model delta sigma weight residual 136.83 121.29 15.54 1.00e+00 1.00e+00 2.42e+02 angle pdb=" PA ATP A 502 " pdb=" O3A ATP A 502 " pdb=" PB ATP A 502 " ideal model delta sigma weight residual 136.83 124.22 12.61 1.00e+00 1.00e+00 1.59e+02 angle pdb=" N PHE D 121 " pdb=" CA PHE D 121 " pdb=" C PHE D 121 " ideal model delta sigma weight residual 113.19 127.71 -14.52 1.19e+00 7.06e-01 1.49e+02 ... (remaining 20339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 8171 17.34 - 34.68: 583 34.68 - 52.02: 125 52.02 - 69.36: 37 69.36 - 86.70: 17 Dihedral angle restraints: 8933 sinusoidal: 3307 harmonic: 5626 Sorted by residual: dihedral pdb=" N TYR A 375 " pdb=" C TYR A 375 " pdb=" CA TYR A 375 " pdb=" CB TYR A 375 " ideal model delta harmonic sigma weight residual 122.80 138.51 -15.71 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" N LYS F 107 " pdb=" C LYS F 107 " pdb=" CA LYS F 107 " pdb=" CB LYS F 107 " ideal model delta harmonic sigma weight residual 122.80 108.54 14.26 0 2.50e+00 1.60e-01 3.25e+01 dihedral pdb=" N ASP I 497 " pdb=" C ASP I 497 " pdb=" CA ASP I 497 " pdb=" CB ASP I 497 " ideal model delta harmonic sigma weight residual 122.80 136.21 -13.41 0 2.50e+00 1.60e-01 2.88e+01 ... (remaining 8930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 2064 0.130 - 0.260: 189 0.260 - 0.390: 25 0.390 - 0.520: 5 0.520 - 0.650: 3 Chirality restraints: 2286 Sorted by residual: chirality pdb=" CA TYR A 375 " pdb=" N TYR A 375 " pdb=" C TYR A 375 " pdb=" CB TYR A 375 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CA TYR A 184 " pdb=" N TYR A 184 " pdb=" C TYR A 184 " pdb=" CB TYR A 184 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.63 2.00e-01 2.50e+01 9.77e+00 chirality pdb=" CA ASP I 497 " pdb=" N ASP I 497 " pdb=" C ASP I 497 " pdb=" CB ASP I 497 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.34e+00 ... (remaining 2283 not shown) Planarity restraints: 2628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 112 " -0.033 2.00e-02 2.50e+03 6.50e-02 4.22e+01 pdb=" C ALA C 112 " 0.112 2.00e-02 2.50e+03 pdb=" O ALA C 112 " -0.043 2.00e-02 2.50e+03 pdb=" N VAL C 113 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 155 " 0.034 2.00e-02 2.50e+03 6.41e-02 4.11e+01 pdb=" C SER A 155 " -0.111 2.00e-02 2.50e+03 pdb=" O SER A 155 " 0.041 2.00e-02 2.50e+03 pdb=" N ARG A 156 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 30 " -0.032 2.00e-02 2.50e+03 6.13e-02 3.75e+01 pdb=" C GLY G 30 " 0.106 2.00e-02 2.50e+03 pdb=" O GLY G 30 " -0.039 2.00e-02 2.50e+03 pdb=" N GLY G 31 " -0.035 2.00e-02 2.50e+03 ... (remaining 2625 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 68 2.55 - 3.14: 11388 3.14 - 3.72: 21506 3.72 - 4.31: 31673 4.31 - 4.90: 50685 Nonbonded interactions: 115320 Sorted by model distance: nonbonded pdb=" O SER H 475 " pdb=" N ALA H 477 " model vdw 1.961 2.520 nonbonded pdb=" O GLU B 171 " pdb=" OE1 GLU B 171 " model vdw 1.971 3.040 nonbonded pdb=" OE2 GLU D 126 " pdb=" NE ARG D 237 " model vdw 2.119 2.520 nonbonded pdb=" O ASP C 322 " pdb=" OG SER C 323 " model vdw 2.131 2.440 nonbonded pdb=" O GLU B 171 " pdb=" CD GLU B 171 " model vdw 2.165 3.270 ... (remaining 115315 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 'H' and (resid 462 through 471 or (resid 472 through 474 and (name N or n \ ame CA or name C or name O or name CB )) or resid 475 or (resid 476 through 477 \ and (name N or name CA or name C or name O or name CB )) or resid 498 through 50 \ 0 or (resid 501 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'I' and (resid 462 through 477 or resid 498 through 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 8.030 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 40.220 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.142 14987 Z= 0.612 Angle : 1.464 17.936 20344 Z= 1.003 Chirality : 0.083 0.650 2286 Planarity : 0.007 0.080 2628 Dihedral : 13.864 86.703 5293 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.81 % Favored : 91.61 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -3.16 (0.17), residues: 1908 helix: -2.25 (0.16), residues: 655 sheet: -1.26 (0.26), residues: 366 loop : -2.27 (0.19), residues: 887 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 550 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 551 average time/residue: 0.2841 time to fit residues: 221.4040 Evaluate side-chains 233 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.672 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 173 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS A 371 HIS ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 129 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** E 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 14987 Z= 0.345 Angle : 0.728 8.823 20344 Z= 0.387 Chirality : 0.048 0.162 2286 Planarity : 0.006 0.059 2628 Dihedral : 5.639 76.789 2080 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.46 % Favored : 96.33 % Rotamer Outliers : 5.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -1.60 (0.18), residues: 1908 helix: -0.77 (0.18), residues: 723 sheet: -0.65 (0.26), residues: 370 loop : -1.40 (0.21), residues: 815 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 247 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 49 residues processed: 307 average time/residue: 0.2481 time to fit residues: 118.7450 Evaluate side-chains 237 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 188 time to evaluate : 1.705 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.1283 time to fit residues: 14.0969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 172 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN B 267 GLN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN C 65 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 HIS D 254 HIS ** E 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 14987 Z= 0.356 Angle : 0.680 8.824 20344 Z= 0.362 Chirality : 0.048 0.147 2286 Planarity : 0.005 0.061 2628 Dihedral : 5.460 84.138 2080 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.04 % Favored : 95.70 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -1.16 (0.18), residues: 1908 helix: -0.21 (0.19), residues: 719 sheet: -0.57 (0.25), residues: 372 loop : -1.27 (0.21), residues: 817 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 196 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 24 residues processed: 235 average time/residue: 0.2145 time to fit residues: 79.6795 Evaluate side-chains 189 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.676 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1294 time to fit residues: 8.1116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 174 optimal weight: 8.9990 chunk 184 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 14987 Z= 0.179 Angle : 0.557 8.751 20344 Z= 0.294 Chirality : 0.044 0.199 2286 Planarity : 0.004 0.059 2628 Dihedral : 5.079 88.306 2080 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.09 % Favored : 96.75 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -0.67 (0.19), residues: 1908 helix: 0.22 (0.20), residues: 710 sheet: -0.29 (0.26), residues: 372 loop : -1.01 (0.21), residues: 826 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 211 average time/residue: 0.2667 time to fit residues: 88.9956 Evaluate side-chains 178 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 1.838 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1351 time to fit residues: 5.1364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 46 optimal weight: 50.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN B 379 GLN ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN E 135 GLN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 14987 Z= 0.290 Angle : 0.602 8.294 20344 Z= 0.315 Chirality : 0.046 0.178 2286 Planarity : 0.005 0.057 2628 Dihedral : 5.054 88.930 2080 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.72 % Favored : 96.12 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -0.56 (0.19), residues: 1908 helix: 0.38 (0.20), residues: 709 sheet: -0.29 (0.25), residues: 381 loop : -0.98 (0.21), residues: 818 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 172 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 195 average time/residue: 0.2207 time to fit residues: 67.8800 Evaluate side-chains 179 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 1.623 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1433 time to fit residues: 7.3354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 45 optimal weight: 50.0000 chunk 184 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 HIS ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 ASN F 34 ASN G 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.6729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 14987 Z= 0.285 Angle : 0.595 9.757 20344 Z= 0.311 Chirality : 0.045 0.276 2286 Planarity : 0.004 0.058 2628 Dihedral : 4.964 86.290 2080 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.46 % Favored : 96.44 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -0.51 (0.19), residues: 1908 helix: 0.47 (0.20), residues: 702 sheet: -0.30 (0.25), residues: 385 loop : -0.97 (0.21), residues: 821 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 184 average time/residue: 0.2180 time to fit residues: 64.6678 Evaluate side-chains 176 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 1.797 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1449 time to fit residues: 5.0966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 0.3980 chunk 20 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 134 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 184 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.6975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 14987 Z= 0.259 Angle : 0.593 10.713 20344 Z= 0.307 Chirality : 0.045 0.239 2286 Planarity : 0.004 0.057 2628 Dihedral : 4.816 80.797 2080 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.93 % Favored : 95.96 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -0.51 (0.19), residues: 1908 helix: 0.45 (0.20), residues: 704 sheet: -0.19 (0.26), residues: 380 loop : -1.03 (0.21), residues: 824 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 185 average time/residue: 0.2249 time to fit residues: 65.9385 Evaluate side-chains 176 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 1.757 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1305 time to fit residues: 5.0818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 144 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 HIS ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 HIS E 5 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.7131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 14987 Z= 0.237 Angle : 0.583 12.200 20344 Z= 0.304 Chirality : 0.045 0.222 2286 Planarity : 0.004 0.056 2628 Dihedral : 4.656 73.438 2080 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.38 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.19), residues: 1908 helix: 0.55 (0.20), residues: 700 sheet: -0.10 (0.26), residues: 378 loop : -0.93 (0.21), residues: 830 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 176 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 182 average time/residue: 0.2329 time to fit residues: 66.7388 Evaluate side-chains 173 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 1.804 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1348 time to fit residues: 4.6533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 103 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 155 optimal weight: 0.4980 chunk 162 optimal weight: 0.8980 chunk 170 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 411 ASN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.7219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 14987 Z= 0.161 Angle : 0.555 12.056 20344 Z= 0.288 Chirality : 0.043 0.176 2286 Planarity : 0.004 0.054 2628 Dihedral : 4.308 64.664 2080 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.54 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 1908 helix: 0.65 (0.20), residues: 691 sheet: 0.02 (0.26), residues: 380 loop : -0.75 (0.22), residues: 837 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 188 average time/residue: 0.2381 time to fit residues: 70.8020 Evaluate side-chains 171 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 1.826 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1384 time to fit residues: 3.2639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.7461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.054 14987 Z= 0.438 Angle : 0.705 12.218 20344 Z= 0.371 Chirality : 0.049 0.386 2286 Planarity : 0.005 0.059 2628 Dihedral : 4.758 59.316 2080 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.14 % Favored : 94.76 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -0.55 (0.19), residues: 1908 helix: 0.38 (0.20), residues: 694 sheet: -0.15 (0.26), residues: 378 loop : -1.03 (0.21), residues: 836 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 176 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 179 average time/residue: 0.2303 time to fit residues: 65.6923 Evaluate side-chains 173 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 1.696 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1343 time to fit residues: 4.4351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 7.9990 chunk 161 optimal weight: 0.6980 chunk 46 optimal weight: 50.0000 chunk 139 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 HIS ** E 18 ASN ** 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 = 0.3606 r_free = 0.3606 target = 0.114895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.086663 restraints weight = 29166.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.087261 restraints weight = 22681.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.088811 restraints weight = 17942.416| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.7534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 14987 Z= 0.194 Angle : 0.604 11.945 20344 Z= 0.315 Chirality : 0.044 0.191 2286 Planarity : 0.004 0.057 2628 Dihedral : 4.367 51.305 2080 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.41 % Favored : 96.49 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -0.32 (0.19), residues: 1908 helix: 0.51 (0.20), residues: 689 sheet: 0.05 (0.27), residues: 371 loop : -0.86 (0.21), residues: 848 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2699.29 seconds wall clock time: 50 minutes 15.73 seconds (3015.73 seconds total)