Starting phenix.real_space_refine on Wed Feb 14 05:36:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zds_14668/02_2024/7zds_14668_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zds_14668/02_2024/7zds_14668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zds_14668/02_2024/7zds_14668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zds_14668/02_2024/7zds_14668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zds_14668/02_2024/7zds_14668_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zds_14668/02_2024/7zds_14668_neut.pdb" } resolution = 3.26 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 5600 2.51 5 N 1538 2.21 5 O 1569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ASP 126": "OD1" <-> "OD2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 374": "NH1" <-> "NH2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "C ASP 401": "OD1" <-> "OD2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C ARG 431": "NH1" <-> "NH2" Residue "C ASP 443": "OD1" <-> "OD2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C ARG 481": "NH1" <-> "NH2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "C GLU 519": "OE1" <-> "OE2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C ARG 538": "NH1" <-> "NH2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 546": "OD1" <-> "OD2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D ASP 306": "OD1" <-> "OD2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D ASP 441": "OD1" <-> "OD2" Residue "D GLU 452": "OE1" <-> "OE2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D ARG 485": "NH1" <-> "NH2" Residue "D ARG 493": "NH1" <-> "NH2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "D ASP 549": "OD1" <-> "OD2" Residue "D ASP 551": "OD1" <-> "OD2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D GLU 563": "OE1" <-> "OE2" Residue "D ARG 566": "NH1" <-> "NH2" Residue "D TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8736 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4319 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 18, 'TRANS': 545} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 4417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4417 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 26, 'TRANS': 538} Time building chain proxies: 5.19, per 1000 atoms: 0.59 Number of scatterers: 8736 At special positions: 0 Unit cell: (122.202, 86.211, 105.462, 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 29 16.00 O 1569 8.00 N 1538 7.00 C 5600 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: 3.30 Conformation dependent library (CDL) restraints added in 1.7 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 4 sheets defined 64.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'C' and resid 4 through 12 removed outlier: 3.629A pdb=" N ALA C 9 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 50 removed outlier: 3.630A pdb=" N ALA C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 104 removed outlier: 3.506A pdb=" N ARG C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.746A pdb=" N ARG C 113 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 131 removed outlier: 3.767A pdb=" N ASN C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 137 through 156 Processing helix chain 'C' and resid 159 through 175 removed outlier: 3.845A pdb=" N THR C 165 " --> pdb=" O THR C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 185 through 208 removed outlier: 3.538A pdb=" N GLY C 189 " --> pdb=" O GLY C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 removed outlier: 3.868A pdb=" N ILE C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 269 removed outlier: 3.707A pdb=" N GLN C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 226 " --> pdb=" O TYR C 222 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 244 " --> pdb=" O GLN C 240 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 269 " --> pdb=" O MET C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 290 removed outlier: 3.658A pdb=" N LEU C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 316 removed outlier: 3.900A pdb=" N GLN C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 387 removed outlier: 3.786A pdb=" N LEU C 382 " --> pdb=" O GLY C 378 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 383 " --> pdb=" O LYS C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 415 removed outlier: 4.020A pdb=" N GLN C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 442 through 454 removed outlier: 3.525A pdb=" N SER C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C 454 " --> pdb=" O LEU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 492 Processing helix chain 'C' and resid 506 through 521 removed outlier: 3.590A pdb=" N MET C 520 " --> pdb=" O LEU C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 539 removed outlier: 4.556A pdb=" N SER C 537 " --> pdb=" O ARG C 534 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 538 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 17 Processing helix chain 'D' and resid 22 through 54 removed outlier: 3.509A pdb=" N SER D 27 " --> pdb=" O TRP D 23 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 62 through 115 removed outlier: 3.612A pdb=" N LEU D 71 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU D 84 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG D 85 " --> pdb=" O TRP D 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 118 through 127 removed outlier: 3.849A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 133 through 138 removed outlier: 3.728A pdb=" N TYR D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 159 removed outlier: 4.159A pdb=" N VAL D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Proline residue: D 151 - end of helix Processing helix chain 'D' and resid 164 through 194 removed outlier: 3.784A pdb=" N LEU D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Proline residue: D 174 - end of helix Proline residue: D 177 - end of helix removed outlier: 3.971A pdb=" N GLY D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 203 removed outlier: 4.098A pdb=" N GLY D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 210 Processing helix chain 'D' and resid 211 through 218 removed outlier: 3.607A pdb=" N LEU D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE D 218 " --> pdb=" O THR D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 274 removed outlier: 3.786A pdb=" N SER D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG D 244 " --> pdb=" O MET D 240 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 311 removed outlier: 3.816A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Proline residue: D 298 - end of helix removed outlier: 3.880A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 311 through 330 removed outlier: 3.728A pdb=" N ALA D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 323 " --> pdb=" O GLY D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 398 Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 438 through 444 removed outlier: 3.697A pdb=" N VAL D 443 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 462 removed outlier: 3.617A pdb=" N ASN D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA D 462 " --> pdb=" O ALA D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 477 removed outlier: 4.071A pdb=" N ASP D 476 " --> pdb=" O GLN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 501 removed outlier: 3.702A pdb=" N ARG D 493 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 495 " --> pdb=" O ALA D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 529 removed outlier: 3.748A pdb=" N ARG D 523 " --> pdb=" O HIS D 519 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.219A pdb=" N ILE C 359 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP C 343 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU C 396 " --> pdb=" O ARG C 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 419 removed outlier: 6.741A pdb=" N VAL C 496 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL C 529 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU C 498 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE C 369 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR C 530 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE C 371 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN C 541 " --> pdb=" O HIS C 368 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASP C 546 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE C 550 " --> pdb=" O ASP C 546 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 364 through 373 removed outlier: 6.523A pdb=" N LEU D 365 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N THR D 358 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLY D 367 " --> pdb=" O PHE D 356 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE D 356 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU D 369 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU D 354 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ALA D 352 " --> pdb=" O ARG D 407 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ARG D 407 " --> pdb=" O ALA D 352 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU D 354 " --> pdb=" O SER D 405 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER D 405 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER D 401 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 425 through 428 removed outlier: 6.329A pdb=" N SER D 426 " --> pdb=" O LEU D 508 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ASP D 510 " --> pdb=" O SER D 426 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL D 428 " --> pdb=" O ASP D 510 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU D 507 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL D 540 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU D 509 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL D 380 " --> pdb=" O TRP D 554 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET D 556 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL D 382 " --> pdb=" O MET D 556 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU D 563 " --> pdb=" O VAL D 555 " (cutoff:3.500A) 491 hydrogen bonds defined for protein. 1455 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: 2.52 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1836 1.33 - 1.45: 1933 1.45 - 1.57: 5083 1.57 - 1.69: 1 1.69 - 1.81: 55 Bond restraints: 8908 Sorted by residual: bond pdb=" N VAL C 344 " pdb=" CA VAL C 344 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.99e+00 bond pdb=" N GLU C 460 " pdb=" CA GLU C 460 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.19e-02 7.06e+03 7.88e+00 bond pdb=" N SER C 466 " pdb=" CA SER C 466 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.25e-02 6.40e+03 7.21e+00 bond pdb=" C PRO C 178 " pdb=" O PRO C 178 " ideal model delta sigma weight residual 1.240 1.210 0.030 1.12e-02 7.97e+03 7.20e+00 bond pdb=" N ARG C 332 " pdb=" CA ARG C 332 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.86e+00 ... (remaining 8903 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.26: 227 106.26 - 113.22: 4900 113.22 - 120.19: 3338 120.19 - 127.15: 3538 127.15 - 134.12: 104 Bond angle restraints: 12107 Sorted by residual: angle pdb=" CA PRO D 432 " pdb=" N PRO D 432 " pdb=" CD PRO D 432 " ideal model delta sigma weight residual 112.00 104.84 7.16 1.40e+00 5.10e-01 2.62e+01 angle pdb=" N VAL C 312 " pdb=" CA VAL C 312 " pdb=" C VAL C 312 " ideal model delta sigma weight residual 112.96 109.00 3.96 1.00e+00 1.00e+00 1.57e+01 angle pdb=" C GLU C 460 " pdb=" CA GLU C 460 " pdb=" CB GLU C 460 " ideal model delta sigma weight residual 110.88 116.68 -5.80 1.57e+00 4.06e-01 1.36e+01 angle pdb=" CA GLN C 354 " pdb=" C GLN C 354 " pdb=" O GLN C 354 " ideal model delta sigma weight residual 122.14 117.63 4.51 1.24e+00 6.50e-01 1.32e+01 angle pdb=" CA ALA C 355 " pdb=" C ALA C 355 " pdb=" O ALA C 355 " ideal model delta sigma weight residual 120.63 116.77 3.86 1.08e+00 8.57e-01 1.27e+01 ... (remaining 12102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 4790 17.54 - 35.08: 432 35.08 - 52.62: 69 52.62 - 70.16: 17 70.16 - 87.69: 11 Dihedral angle restraints: 5319 sinusoidal: 2080 harmonic: 3239 Sorted by residual: dihedral pdb=" CA GLU D 84 " pdb=" C GLU D 84 " pdb=" N ARG D 85 " pdb=" CA ARG D 85 " ideal model delta harmonic sigma weight residual 180.00 156.24 23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" C GLU C 460 " pdb=" N GLU C 460 " pdb=" CA GLU C 460 " pdb=" CB GLU C 460 " ideal model delta harmonic sigma weight residual -122.60 -132.30 9.70 0 2.50e+00 1.60e-01 1.51e+01 dihedral pdb=" CA PHE C 291 " pdb=" C PHE C 291 " pdb=" N GLU C 292 " pdb=" CA GLU C 292 " ideal model delta harmonic sigma weight residual 180.00 161.24 18.76 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1135 0.051 - 0.103: 239 0.103 - 0.154: 37 0.154 - 0.206: 2 0.206 - 0.257: 2 Chirality restraints: 1415 Sorted by residual: chirality pdb=" CA LEU C 425 " pdb=" N LEU C 425 " pdb=" C LEU C 425 " pdb=" CB LEU C 425 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA GLU C 460 " pdb=" N GLU C 460 " pdb=" C GLU C 460 " pdb=" CB GLU C 460 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA PHE C 426 " pdb=" N PHE C 426 " pdb=" C PHE C 426 " pdb=" CB PHE C 426 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1412 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 431 " -0.073 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO D 432 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO D 432 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 432 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 295 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.30e+00 pdb=" N PRO C 296 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 296 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 296 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 341 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.10e+00 pdb=" C LEU C 341 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU C 341 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG C 342 " 0.012 2.00e-02 2.50e+03 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 56 2.59 - 3.17: 7352 3.17 - 3.75: 13456 3.75 - 4.32: 18944 4.32 - 4.90: 31727 Nonbonded interactions: 71535 Sorted by model distance: nonbonded pdb=" OG SER C 427 " pdb=" OD2 ASP D 207 " model vdw 2.017 2.440 nonbonded pdb=" OG SER C 438 " pdb=" OG SER C 441 " model vdw 2.161 2.440 nonbonded pdb=" OG SER D 417 " pdb=" OG SER D 420 " model vdw 2.178 2.440 nonbonded pdb=" O SER C 427 " pdb=" OG SER C 427 " model vdw 2.210 2.440 nonbonded pdb=" O PHE C 426 " pdb=" OD2 ASP D 207 " model vdw 2.230 3.040 ... (remaining 71530 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: 0.010 Normalize map: mean=0, sd=1: 1.110 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: 5.350 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.640 Find NCS groups from input model: 0.300 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:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 : 0.005 0.126 8908 Z= 0.338 Angle : 0.737 7.720 12107 Z= 0.458 Chirality : 0.044 0.257 1415 Planarity : 0.005 0.106 1550 Dihedral : 14.062 87.694 3229 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.23), residues: 1125 helix: -1.95 (0.18), residues: 654 sheet: -1.10 (0.69), residues: 57 loop : -1.11 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 463 HIS 0.004 0.001 HIS C 491 PHE 0.011 0.001 PHE C 426 TYR 0.012 0.001 TYR C 7 ARG 0.013 0.001 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.056 Fit side-chains REVERT: C 517 LEU cc_start: 0.8199 (tt) cc_final: 0.7661 (mp) REVERT: C 521 MET cc_start: 0.8904 (mtm) cc_final: 0.8495 (mtt) REVERT: D 54 MET cc_start: 0.8788 (mmm) cc_final: 0.8582 (mmp) REVERT: D 377 GLN cc_start: 0.7846 (mt0) cc_final: 0.7527 (tt0) REVERT: D 558 ASP cc_start: 0.6614 (t70) cc_final: 0.6349 (t0) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2577 time to fit residues: 37.7230 Evaluate side-chains 91 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 GLN C 121 ASN C 512 GLN D 16 GLN D 89 HIS D 191 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8908 Z= 0.220 Angle : 0.613 8.289 12107 Z= 0.310 Chirality : 0.041 0.162 1415 Planarity : 0.005 0.043 1550 Dihedral : 4.487 21.988 1228 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.32 % Allowed : 6.82 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.24), residues: 1125 helix: -0.13 (0.20), residues: 653 sheet: -0.77 (0.66), residues: 65 loop : -1.02 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 463 HIS 0.006 0.001 HIS C 556 PHE 0.015 0.001 PHE C 164 TYR 0.015 0.001 TYR D 88 ARG 0.004 0.000 ARG D 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.082 Fit side-chains REVERT: C 517 LEU cc_start: 0.8140 (tt) cc_final: 0.7758 (mp) REVERT: C 521 MET cc_start: 0.8839 (mtm) cc_final: 0.8386 (mtt) REVERT: D 94 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8919 (mp) REVERT: D 234 ASP cc_start: 0.7830 (t0) cc_final: 0.7581 (m-30) REVERT: D 377 GLN cc_start: 0.7815 (mt0) cc_final: 0.7497 (tt0) REVERT: D 566 ARG cc_start: 0.5639 (ttp80) cc_final: 0.5307 (mtp180) outliers start: 12 outliers final: 7 residues processed: 111 average time/residue: 0.2221 time to fit residues: 33.6955 Evaluate side-chains 101 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 540 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 100 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN D 89 HIS D 93 HIS ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8908 Z= 0.177 Angle : 0.537 8.224 12107 Z= 0.268 Chirality : 0.040 0.137 1415 Planarity : 0.004 0.036 1550 Dihedral : 4.144 16.547 1228 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.21 % Allowed : 10.23 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1125 helix: 0.78 (0.21), residues: 656 sheet: -0.65 (0.65), residues: 65 loop : -0.99 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 463 HIS 0.004 0.001 HIS D 134 PHE 0.010 0.001 PHE C 181 TYR 0.014 0.001 TYR D 88 ARG 0.003 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.004 Fit side-chains REVERT: C 11 TYR cc_start: 0.8711 (m-80) cc_final: 0.8508 (m-80) REVERT: C 490 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8351 (mm) REVERT: C 517 LEU cc_start: 0.8079 (tt) cc_final: 0.7753 (mp) REVERT: C 520 MET cc_start: 0.7791 (mtt) cc_final: 0.7546 (mtt) REVERT: D 94 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8918 (mp) REVERT: D 377 GLN cc_start: 0.7705 (mt0) cc_final: 0.7400 (tt0) outliers start: 11 outliers final: 5 residues processed: 117 average time/residue: 0.2418 time to fit residues: 38.1792 Evaluate side-chains 99 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 540 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 0.2980 chunk 53 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN D 89 HIS D 93 HIS ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8908 Z= 0.202 Angle : 0.541 8.267 12107 Z= 0.266 Chirality : 0.040 0.135 1415 Planarity : 0.004 0.037 1550 Dihedral : 4.077 16.018 1228 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.42 % Allowed : 11.77 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1125 helix: 1.06 (0.20), residues: 662 sheet: -0.54 (0.66), residues: 65 loop : -0.98 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 463 HIS 0.004 0.001 HIS D 134 PHE 0.012 0.001 PHE C 426 TYR 0.015 0.001 TYR D 88 ARG 0.003 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 0.934 Fit side-chains REVERT: C 362 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7474 (tm-30) REVERT: C 490 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8328 (mm) REVERT: C 517 LEU cc_start: 0.8081 (tt) cc_final: 0.7778 (mp) REVERT: D 94 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8903 (mp) REVERT: D 370 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7748 (t0) REVERT: D 377 GLN cc_start: 0.7668 (mt0) cc_final: 0.7354 (tt0) REVERT: D 459 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7936 (mp) REVERT: D 463 TRP cc_start: 0.7545 (m-10) cc_final: 0.7207 (m-10) outliers start: 22 outliers final: 11 residues processed: 117 average time/residue: 0.2172 time to fit residues: 35.0273 Evaluate side-chains 107 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 540 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.0010 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 0.0670 chunk 36 optimal weight: 5.9990 overall best weight: 0.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 HIS D 93 HIS ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8908 Z= 0.171 Angle : 0.520 9.317 12107 Z= 0.255 Chirality : 0.039 0.132 1415 Planarity : 0.003 0.039 1550 Dihedral : 3.983 15.295 1228 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.31 % Allowed : 13.31 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1125 helix: 1.28 (0.20), residues: 665 sheet: -0.41 (0.67), residues: 65 loop : -0.95 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 41 HIS 0.004 0.001 HIS D 134 PHE 0.009 0.001 PHE C 426 TYR 0.014 0.001 TYR D 88 ARG 0.002 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 1.028 Fit side-chains REVERT: C 362 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7528 (tm-30) REVERT: C 490 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8249 (mm) REVERT: C 517 LEU cc_start: 0.8113 (tt) cc_final: 0.7869 (mp) REVERT: D 45 MET cc_start: 0.9204 (mtp) cc_final: 0.8845 (mtp) REVERT: D 94 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8888 (mp) REVERT: D 370 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7768 (t0) REVERT: D 377 GLN cc_start: 0.7602 (mt0) cc_final: 0.7297 (tt0) REVERT: D 459 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7955 (mp) REVERT: D 463 TRP cc_start: 0.7586 (m-10) cc_final: 0.7238 (m-10) outliers start: 21 outliers final: 15 residues processed: 108 average time/residue: 0.2263 time to fit residues: 33.5567 Evaluate side-chains 111 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 540 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 HIS D 93 HIS ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8908 Z= 0.234 Angle : 0.547 8.442 12107 Z= 0.267 Chirality : 0.041 0.133 1415 Planarity : 0.004 0.040 1550 Dihedral : 4.009 15.605 1228 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.53 % Allowed : 14.08 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1125 helix: 1.35 (0.20), residues: 663 sheet: -0.41 (0.66), residues: 65 loop : -0.94 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 463 HIS 0.004 0.001 HIS D 134 PHE 0.010 0.001 PHE C 181 TYR 0.015 0.001 TYR D 88 ARG 0.003 0.000 ARG C 452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.003 Fit side-chains REVERT: C 362 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7527 (tm-30) REVERT: C 490 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8341 (mm) REVERT: C 517 LEU cc_start: 0.8161 (tt) cc_final: 0.7899 (mp) REVERT: D 94 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8916 (mp) REVERT: D 370 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7782 (t0) REVERT: D 459 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8016 (mp) REVERT: D 463 TRP cc_start: 0.7632 (m-10) cc_final: 0.7268 (m-10) outliers start: 23 outliers final: 17 residues processed: 110 average time/residue: 0.2293 time to fit residues: 34.4094 Evaluate side-chains 114 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 540 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 67 optimal weight: 0.0040 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 HIS D 93 HIS ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8908 Z= 0.165 Angle : 0.520 8.639 12107 Z= 0.254 Chirality : 0.039 0.164 1415 Planarity : 0.003 0.040 1550 Dihedral : 3.908 15.031 1228 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.64 % Allowed : 14.52 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1125 helix: 1.55 (0.20), residues: 662 sheet: -0.31 (0.65), residues: 65 loop : -0.88 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 122 HIS 0.004 0.001 HIS D 134 PHE 0.009 0.001 PHE C 426 TYR 0.014 0.001 TYR D 88 ARG 0.003 0.000 ARG C 452 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.987 Fit side-chains REVERT: C 362 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7545 (tm-30) REVERT: C 490 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8287 (mm) REVERT: C 517 LEU cc_start: 0.8135 (tt) cc_final: 0.7874 (mp) REVERT: D 370 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7810 (t0) REVERT: D 459 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8011 (mp) REVERT: D 463 TRP cc_start: 0.7595 (m-10) cc_final: 0.7228 (m-10) outliers start: 24 outliers final: 16 residues processed: 114 average time/residue: 0.2093 time to fit residues: 33.3693 Evaluate side-chains 110 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 540 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 HIS D 93 HIS ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8908 Z= 0.174 Angle : 0.538 9.842 12107 Z= 0.259 Chirality : 0.039 0.131 1415 Planarity : 0.003 0.040 1550 Dihedral : 3.873 13.848 1228 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.20 % Allowed : 15.07 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1125 helix: 1.64 (0.20), residues: 662 sheet: -0.19 (0.66), residues: 65 loop : -0.81 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 463 HIS 0.003 0.001 HIS D 134 PHE 0.009 0.001 PHE C 181 TYR 0.014 0.001 TYR D 88 ARG 0.002 0.000 ARG C 452 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.055 Fit side-chains REVERT: C 362 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7565 (tm-30) REVERT: C 490 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8290 (mm) REVERT: C 517 LEU cc_start: 0.8114 (tt) cc_final: 0.7882 (mp) REVERT: D 63 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8529 (mp) REVERT: D 370 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7820 (t0) REVERT: D 377 GLN cc_start: 0.7555 (mt0) cc_final: 0.7313 (tt0) REVERT: D 459 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8028 (mp) outliers start: 20 outliers final: 16 residues processed: 109 average time/residue: 0.2230 time to fit residues: 33.7256 Evaluate side-chains 114 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 540 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.0010 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 0.0020 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 HIS D 93 HIS ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8908 Z= 0.171 Angle : 0.530 9.301 12107 Z= 0.256 Chirality : 0.040 0.257 1415 Planarity : 0.003 0.039 1550 Dihedral : 3.847 13.279 1228 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.42 % Allowed : 14.63 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1125 helix: 1.72 (0.20), residues: 662 sheet: -0.20 (0.65), residues: 65 loop : -0.76 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 463 HIS 0.003 0.001 HIS D 134 PHE 0.012 0.001 PHE C 181 TYR 0.015 0.001 TYR D 88 ARG 0.002 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 0.936 Fit side-chains REVERT: C 362 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7612 (tm-30) REVERT: C 490 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8295 (mm) REVERT: C 517 LEU cc_start: 0.8109 (tt) cc_final: 0.7874 (mp) REVERT: D 63 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8520 (mp) REVERT: D 377 GLN cc_start: 0.7558 (mt0) cc_final: 0.7311 (tt0) REVERT: D 459 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8027 (mp) outliers start: 22 outliers final: 16 residues processed: 110 average time/residue: 0.2157 time to fit residues: 33.2949 Evaluate side-chains 114 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 540 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 111 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 HIS D 93 HIS D 162 ASN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8908 Z= 0.200 Angle : 0.559 9.660 12107 Z= 0.267 Chirality : 0.040 0.139 1415 Planarity : 0.004 0.039 1550 Dihedral : 3.871 13.643 1228 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.53 % Allowed : 14.96 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1125 helix: 1.69 (0.20), residues: 662 sheet: -0.03 (0.67), residues: 63 loop : -0.76 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 463 HIS 0.004 0.001 HIS D 134 PHE 0.011 0.001 PHE C 181 TYR 0.014 0.001 TYR D 88 ARG 0.002 0.000 ARG D 523 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 0.931 Fit side-chains REVERT: C 362 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 490 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8304 (mm) REVERT: C 517 LEU cc_start: 0.8127 (tt) cc_final: 0.7893 (mp) REVERT: D 117 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7902 (pttt) REVERT: D 377 GLN cc_start: 0.7582 (mt0) cc_final: 0.7363 (tt0) REVERT: D 459 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8041 (mp) outliers start: 23 outliers final: 16 residues processed: 114 average time/residue: 0.2207 time to fit residues: 34.7103 Evaluate side-chains 115 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 540 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 0.0370 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 HIS D 93 HIS D 162 ASN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.141557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.106715 restraints weight = 9909.143| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.36 r_work: 0.2961 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8908 Z= 0.174 Angle : 0.552 9.221 12107 Z= 0.263 Chirality : 0.040 0.140 1415 Planarity : 0.004 0.038 1550 Dihedral : 3.845 13.023 1228 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.09 % Allowed : 15.40 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1125 helix: 1.77 (0.20), residues: 662 sheet: -0.15 (0.66), residues: 65 loop : -0.76 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 463 HIS 0.003 0.001 HIS D 134 PHE 0.011 0.001 PHE C 181 TYR 0.015 0.001 TYR D 88 ARG 0.010 0.000 ARG D 244 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2036.96 seconds wall clock time: 37 minutes 29.17 seconds (2249.17 seconds total)