Starting phenix.real_space_refine on Sat Dec 9 13:13:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqo_41510/12_2023/8tqo_41510.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqo_41510/12_2023/8tqo_41510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqo_41510/12_2023/8tqo_41510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqo_41510/12_2023/8tqo_41510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqo_41510/12_2023/8tqo_41510.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqo_41510/12_2023/8tqo_41510.pdb" } resolution = 3.1 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= 0.007 sd= 0.080 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 7047 2.51 5 N 1959 2.21 5 O 2052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 111": "OD1" <-> "OD2" Residue "I TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 301": "OD1" <-> "OD2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 469": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11122 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3200 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "I" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2716 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2472 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2734 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 332} Time building chain proxies: 6.03, per 1000 atoms: 0.54 Number of scatterers: 11122 At special positions: 0 Unit cell: (131.095, 96.025, 129.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2052 8.00 N 1959 7.00 C 7047 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: 4.24 Conformation dependent library (CDL) restraints added in 1.9 seconds 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2722 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 37.2% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.705A pdb=" N TYR A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.648A pdb=" N LYS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.636A pdb=" N ASP A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.806A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 279 removed outlier: 3.515A pdb=" N ASN A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'I' and resid 24 through 27 Processing helix chain 'I' and resid 36 through 44 Processing helix chain 'I' and resid 85 through 93 Processing helix chain 'I' and resid 114 through 124 removed outlier: 3.784A pdb=" N LEU I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 removed outlier: 3.688A pdb=" N LYS I 189 " --> pdb=" O SER I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 218 removed outlier: 4.154A pdb=" N VAL I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP I 213 " --> pdb=" O LYS I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 235 Processing helix chain 'I' and resid 315 through 334 Proline residue: I 327 - end of helix removed outlier: 3.911A pdb=" N ALA I 332 " --> pdb=" O LYS I 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 4.216A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 128 through 146 removed outlier: 4.070A pdb=" N ASN D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.592A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.709A pdb=" N GLU D 299 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 337 through 344 removed outlier: 3.990A pdb=" N SER D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 240 removed outlier: 3.568A pdb=" N CYS E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 267 removed outlier: 4.006A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix removed outlier: 3.504A pdb=" N CYS E 266 " --> pdb=" O PHE E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 312 Processing helix chain 'E' and resid 314 through 325 removed outlier: 4.056A pdb=" N ALA E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 319 " --> pdb=" O ALA E 315 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 351 removed outlier: 3.878A pdb=" N THR E 351 " --> pdb=" O GLN E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 379 removed outlier: 3.986A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 419 through 430 removed outlier: 3.762A pdb=" N LEU E 425 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA E 429 " --> pdb=" O LEU E 425 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS E 430 " --> pdb=" O VAL E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 removed outlier: 3.647A pdb=" N LYS E 442 " --> pdb=" O GLU E 439 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 443 " --> pdb=" O THR E 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 439 through 443' Processing helix chain 'E' and resid 459 through 463 Processing helix chain 'E' and resid 511 through 517 removed outlier: 3.957A pdb=" N VAL E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 124 removed outlier: 6.611A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS A 247 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE A 184 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE A 249 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR A 182 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE A 251 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL A 180 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLN A 286 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET A 181 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE A 287 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A 212 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP A 206 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 204 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 216 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE I 169 " --> pdb=" O GLY I 159 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP I 161 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU I 167 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 225 Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 338 removed outlier: 3.666A pdb=" N ILE A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU A 361 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU A 412 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.526A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 424 " --> pdb=" O LEU A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 6.459A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'I' and resid 76 through 77 removed outlier: 6.426A pdb=" N ALA I 5 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLN I 4 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU I 104 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL I 6 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N HIS I 203 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU I 131 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU I 204 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA I 129 " --> pdb=" O LEU I 204 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU I 128 " --> pdb=" O TYR I 301 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N HIS I 303 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N MET I 130 " --> pdb=" O HIS I 303 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N MET I 305 " --> pdb=" O MET I 130 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET I 132 " --> pdb=" O MET I 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 29 through 30 Processing sheet with id=AA9, first strand: chain 'I' and resid 353 through 354 removed outlier: 4.031A pdb=" N VAL I 354 " --> pdb=" O ILE I 370 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N SER I 369 " --> pdb=" O ILE I 387 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR I 386 " --> pdb=" O ILE I 404 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASN I 403 " --> pdb=" O ILE I 421 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP I 420 " --> pdb=" O LYS I 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'I' and resid 391 through 392 removed outlier: 6.647A pdb=" N LEU I 391 " --> pdb=" O ILE I 409 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL I 408 " --> pdb=" O ILE I 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 414 through 415 removed outlier: 7.350A pdb=" N VAL I 414 " --> pdb=" O ILE I 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 323 through 325 removed outlier: 6.846A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR D 167 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.403A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP E 362 " --> pdb=" O LEU E 386 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR E 336 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY E 404 " --> pdb=" O TYR E 336 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL E 401 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N CYS E 437 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU E 403 " --> pdb=" O CYS E 437 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 407 through 408 removed outlier: 3.604A pdb=" N VAL E 414 " --> pdb=" O THR E 492 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1086 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: 3.11 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3705 1.34 - 1.46: 2234 1.46 - 1.58: 5289 1.58 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 11323 Sorted by residual: bond pdb=" CB GLU D 135 " pdb=" CG GLU D 135 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CG ARG A 145 " pdb=" CD ARG A 145 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CB GLU E 469 " pdb=" CG GLU E 469 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" C PHE D 278 " pdb=" N PRO D 279 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.89e-01 bond pdb=" C VAL I 326 " pdb=" N PRO I 327 " ideal model delta sigma weight residual 1.334 1.347 -0.013 1.51e-02 4.39e+03 7.50e-01 ... (remaining 11318 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.75: 338 106.75 - 113.56: 6428 113.56 - 120.36: 3897 120.36 - 127.17: 4581 127.17 - 133.97: 120 Bond angle restraints: 15364 Sorted by residual: angle pdb=" N VAL D 312 " pdb=" CA VAL D 312 " pdb=" C VAL D 312 " ideal model delta sigma weight residual 112.96 109.83 3.13 1.00e+00 1.00e+00 9.82e+00 angle pdb=" C GLU I 44 " pdb=" N ARG I 45 " pdb=" CA ARG I 45 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.67e+00 angle pdb=" CB GLU D 135 " pdb=" CG GLU D 135 " pdb=" CD GLU D 135 " ideal model delta sigma weight residual 112.60 117.21 -4.61 1.70e+00 3.46e-01 7.36e+00 angle pdb=" CA SER A 60 " pdb=" C SER A 60 " pdb=" N LYS A 61 " ideal model delta sigma weight residual 116.84 121.41 -4.57 1.71e+00 3.42e-01 7.14e+00 angle pdb=" C LEU I 351 " pdb=" N VAL I 352 " pdb=" CA VAL I 352 " ideal model delta sigma weight residual 121.97 126.76 -4.79 1.80e+00 3.09e-01 7.08e+00 ... (remaining 15359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5906 17.82 - 35.64: 761 35.64 - 53.45: 196 53.45 - 71.27: 28 71.27 - 89.09: 10 Dihedral angle restraints: 6901 sinusoidal: 2715 harmonic: 4186 Sorted by residual: dihedral pdb=" CA PHE A 57 " pdb=" C PHE A 57 " pdb=" N PRO A 58 " pdb=" CA PRO A 58 " ideal model delta harmonic sigma weight residual 180.00 140.19 39.81 0 5.00e+00 4.00e-02 6.34e+01 dihedral pdb=" CA ARG I 45 " pdb=" C ARG I 45 " pdb=" N VAL I 46 " pdb=" CA VAL I 46 " ideal model delta harmonic sigma weight residual 180.00 159.57 20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP A 147 " pdb=" CB ASP A 147 " pdb=" CG ASP A 147 " pdb=" OD1 ASP A 147 " ideal model delta sinusoidal sigma weight residual -30.00 -89.98 59.98 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 6898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1245 0.035 - 0.070: 362 0.070 - 0.106: 157 0.106 - 0.141: 55 0.141 - 0.176: 3 Chirality restraints: 1822 Sorted by residual: chirality pdb=" CB VAL I 54 " pdb=" CA VAL I 54 " pdb=" CG1 VAL I 54 " pdb=" CG2 VAL I 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CB ILE I 346 " pdb=" CA ILE I 346 " pdb=" CG1 ILE I 346 " pdb=" CG2 ILE I 346 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA ILE I 404 " pdb=" N ILE I 404 " pdb=" C ILE I 404 " pdb=" CB ILE I 404 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 1819 not shown) Planarity restraints: 1963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 57 " 0.077 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO A 58 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 395 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO E 396 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 396 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 396 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " 0.105 9.50e-02 1.11e+02 4.78e-02 2.13e+00 pdb=" NE ARG A 145 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " -0.001 2.00e-02 2.50e+03 ... (remaining 1960 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 803 2.74 - 3.28: 10959 3.28 - 3.82: 18019 3.82 - 4.36: 20823 4.36 - 4.90: 37285 Nonbonded interactions: 87889 Sorted by model distance: nonbonded pdb=" O PRO A 69 " pdb=" OH TYR A 306 " model vdw 2.202 2.440 nonbonded pdb=" OG SER I 402 " pdb=" O ALA I 419 " model vdw 2.214 2.440 nonbonded pdb=" N GLU E 469 " pdb=" OE1 GLU E 469 " model vdw 2.247 2.520 nonbonded pdb=" OG SER I 127 " pdb=" OH TYR I 210 " model vdw 2.253 2.440 nonbonded pdb=" O LEU D 265 " pdb=" OG1 THR D 322 " model vdw 2.254 2.440 ... (remaining 87884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.140 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 30.660 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 0.002 0.038 11323 Z= 0.133 Angle : 0.540 8.139 15364 Z= 0.282 Chirality : 0.043 0.176 1822 Planarity : 0.005 0.119 1963 Dihedral : 16.855 89.091 4179 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.16 % Allowed : 28.68 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.14 (0.23), residues: 1417 helix: 1.64 (0.26), residues: 456 sheet: -0.39 (0.38), residues: 193 loop : -0.72 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 51 HIS 0.011 0.001 HIS I 350 PHE 0.012 0.001 PHE D 177 TYR 0.021 0.001 TYR D 337 ARG 0.015 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.304 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.2181 time to fit residues: 35.7893 Evaluate side-chains 105 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1207 time to fit residues: 1.8543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 5.9990 chunk 107 optimal weight: 0.0970 chunk 59 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN ** I 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 286 HIS E 274 HIS ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11323 Z= 0.343 Angle : 0.595 7.442 15364 Z= 0.309 Chirality : 0.047 0.172 1822 Planarity : 0.005 0.079 1963 Dihedral : 4.334 38.922 1552 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.90 % Allowed : 26.00 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.07 (0.23), residues: 1417 helix: 1.32 (0.25), residues: 484 sheet: -0.71 (0.36), residues: 202 loop : -0.76 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 97 HIS 0.008 0.001 HIS I 350 PHE 0.015 0.002 PHE A 215 TYR 0.027 0.002 TYR I 231 ARG 0.004 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 117 time to evaluate : 1.076 Fit side-chains outliers start: 48 outliers final: 32 residues processed: 155 average time/residue: 0.2328 time to fit residues: 51.9204 Evaluate side-chains 130 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 98 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1096 time to fit residues: 8.4738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 20.0000 chunk 40 optimal weight: 0.0470 chunk 107 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 ASN D 162 ASN D 242 ASN ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11323 Z= 0.220 Angle : 0.533 7.298 15364 Z= 0.273 Chirality : 0.044 0.155 1822 Planarity : 0.004 0.102 1963 Dihedral : 4.200 36.932 1552 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.68 % Allowed : 26.48 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.09 (0.23), residues: 1417 helix: 1.56 (0.25), residues: 479 sheet: -0.61 (0.37), residues: 193 loop : -0.74 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 97 HIS 0.008 0.001 HIS I 350 PHE 0.012 0.001 PHE D 177 TYR 0.021 0.001 TYR I 231 ARG 0.007 0.000 ARG D 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 101 time to evaluate : 1.316 Fit side-chains outliers start: 33 outliers final: 13 residues processed: 129 average time/residue: 0.2310 time to fit residues: 43.4811 Evaluate side-chains 107 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 1.290 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0983 time to fit residues: 4.1671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 0.0770 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 137 optimal weight: 0.0070 chunk 122 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 4 GLN E 347 GLN E 411 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11323 Z= 0.166 Angle : 0.510 7.795 15364 Z= 0.261 Chirality : 0.044 0.163 1822 Planarity : 0.004 0.094 1963 Dihedral : 4.082 38.365 1552 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.52 % Allowed : 25.67 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.26 (0.23), residues: 1417 helix: 1.68 (0.25), residues: 479 sheet: -0.37 (0.37), residues: 187 loop : -0.67 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 97 HIS 0.008 0.001 HIS I 350 PHE 0.012 0.001 PHE D 177 TYR 0.017 0.001 TYR E 214 ARG 0.006 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 100 time to evaluate : 1.529 Fit side-chains outliers start: 31 outliers final: 13 residues processed: 126 average time/residue: 0.2242 time to fit residues: 41.5425 Evaluate side-chains 108 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1101 time to fit residues: 4.3434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11323 Z= 0.317 Angle : 0.568 8.306 15364 Z= 0.292 Chirality : 0.046 0.173 1822 Planarity : 0.005 0.105 1963 Dihedral : 4.327 39.370 1552 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.27 % Allowed : 26.89 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.23), residues: 1417 helix: 1.58 (0.25), residues: 481 sheet: -0.37 (0.38), residues: 188 loop : -0.74 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 97 HIS 0.010 0.001 HIS I 350 PHE 0.016 0.002 PHE A 57 TYR 0.018 0.002 TYR E 214 ARG 0.008 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 1.382 Fit side-chains outliers start: 28 outliers final: 13 residues processed: 113 average time/residue: 0.2581 time to fit residues: 41.3687 Evaluate side-chains 100 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1026 time to fit residues: 4.3274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 80 optimal weight: 30.0000 chunk 33 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 114 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 72 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11323 Z= 0.160 Angle : 0.511 8.109 15364 Z= 0.262 Chirality : 0.044 0.190 1822 Planarity : 0.004 0.114 1963 Dihedral : 4.153 39.542 1552 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.89 % Allowed : 27.46 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.33 (0.23), residues: 1417 helix: 1.72 (0.25), residues: 479 sheet: -0.26 (0.39), residues: 186 loop : -0.63 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 97 HIS 0.007 0.001 HIS I 350 PHE 0.011 0.001 PHE D 177 TYR 0.016 0.001 TYR E 214 ARG 0.007 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 1.265 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 103 average time/residue: 0.2711 time to fit residues: 39.8159 Evaluate side-chains 92 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 1.303 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1107 time to fit residues: 2.6120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 136 optimal weight: 0.6980 chunk 85 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11323 Z= 0.402 Angle : 0.616 9.365 15364 Z= 0.315 Chirality : 0.048 0.179 1822 Planarity : 0.005 0.119 1963 Dihedral : 4.516 42.087 1552 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.19 % Allowed : 27.38 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.09 (0.23), residues: 1417 helix: 1.42 (0.25), residues: 493 sheet: -0.36 (0.39), residues: 191 loop : -0.76 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 97 HIS 0.007 0.001 HIS I 350 PHE 0.013 0.002 PHE D 177 TYR 0.018 0.002 TYR A 128 ARG 0.008 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 1.371 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 20 residues processed: 113 average time/residue: 0.2412 time to fit residues: 39.3274 Evaluate side-chains 104 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1264 time to fit residues: 6.0068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11323 Z= 0.185 Angle : 0.534 9.037 15364 Z= 0.272 Chirality : 0.044 0.164 1822 Planarity : 0.004 0.119 1963 Dihedral : 4.287 40.124 1552 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.41 % Allowed : 28.19 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.30 (0.23), residues: 1417 helix: 1.63 (0.25), residues: 489 sheet: -0.24 (0.39), residues: 186 loop : -0.64 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 97 HIS 0.009 0.001 HIS I 350 PHE 0.012 0.001 PHE D 177 TYR 0.011 0.001 TYR E 385 ARG 0.008 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 1.384 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 94 average time/residue: 0.2733 time to fit residues: 36.5795 Evaluate side-chains 90 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1071 time to fit residues: 2.6043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 55 optimal weight: 0.0170 chunk 100 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11323 Z= 0.229 Angle : 0.549 9.090 15364 Z= 0.278 Chirality : 0.045 0.190 1822 Planarity : 0.005 0.123 1963 Dihedral : 4.250 40.895 1552 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.41 % Allowed : 28.76 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.28 (0.23), residues: 1417 helix: 1.60 (0.25), residues: 489 sheet: -0.26 (0.39), residues: 191 loop : -0.64 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 97 HIS 0.008 0.001 HIS I 350 PHE 0.012 0.001 PHE D 177 TYR 0.015 0.001 TYR I 319 ARG 0.007 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 1.239 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 91 average time/residue: 0.2458 time to fit residues: 32.1253 Evaluate side-chains 87 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0993 time to fit residues: 1.9763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.2980 chunk 63 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 141 optimal weight: 0.0020 chunk 130 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11323 Z= 0.139 Angle : 0.520 8.567 15364 Z= 0.265 Chirality : 0.043 0.165 1822 Planarity : 0.004 0.121 1963 Dihedral : 4.077 38.295 1552 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.16 % Allowed : 28.84 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.42 (0.23), residues: 1417 helix: 1.86 (0.25), residues: 471 sheet: -0.30 (0.37), residues: 196 loop : -0.57 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 111 HIS 0.008 0.001 HIS I 350 PHE 0.011 0.001 PHE D 177 TYR 0.017 0.001 TYR E 214 ARG 0.008 0.000 ARG A 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 1.383 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 95 average time/residue: 0.2571 time to fit residues: 35.0066 Evaluate side-chains 87 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 1.337 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1211 time to fit residues: 2.0379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 115 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.111740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.077760 restraints weight = 18222.794| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.34 r_work: 0.2873 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11323 Z= 0.195 Angle : 0.546 8.834 15364 Z= 0.277 Chirality : 0.044 0.181 1822 Planarity : 0.005 0.121 1963 Dihedral : 4.066 39.387 1552 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.08 % Allowed : 29.16 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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 (0.23), residues: 1417 helix: 1.86 (0.25), residues: 478 sheet: -0.20 (0.38), residues: 191 loop : -0.55 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 97 HIS 0.008 0.001 HIS I 350 PHE 0.012 0.001 PHE D 177 TYR 0.010 0.001 TYR A 128 ARG 0.007 0.000 ARG A 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2192.02 seconds wall clock time: 40 minutes 36.16 seconds (2436.16 seconds total)