Starting phenix.real_space_refine on Wed Feb 14 11:12:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj2_33869/02_2024/7yj2_33869_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj2_33869/02_2024/7yj2_33869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj2_33869/02_2024/7yj2_33869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj2_33869/02_2024/7yj2_33869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj2_33869/02_2024/7yj2_33869_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yj2_33869/02_2024/7yj2_33869_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 50 5.16 5 C 5878 2.51 5 N 1542 2.21 5 O 1653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 57": "NH1" <-> "NH2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 344": "OD1" <-> "OD2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B ASP 369": "OD1" <-> "OD2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B ASP 465": "OD1" <-> "OD2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ASP 522": "OD1" <-> "OD2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "E GLU 19": "OE1" <-> "OE2" Residue "E TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 76": "OD1" <-> "OD2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A ASP 76": "OD1" <-> "OD2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ASP 301": "OD1" <-> "OD2" Residue "A ASP 326": "OD1" <-> "OD2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9124 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3953 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 483} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 298 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1162 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "C" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 411 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "A" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3285 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.14, per 1000 atoms: 0.56 Number of scatterers: 9124 At special positions: 0 Unit cell: (93.96, 86.4, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 1 15.00 O 1653 8.00 N 1542 7.00 C 5878 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.7 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 5 sheets defined 42.9% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'B' and resid 68 through 94 removed outlier: 3.612A pdb=" N TYR B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 76 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 82 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TRP B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 127 through 130 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.778A pdb=" N GLU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 4.091A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 243 " --> pdb=" O PHE B 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 238 through 243' Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.629A pdb=" N GLU B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 334 Processing helix chain 'B' and resid 359 through 362 No H-bonds generated for 'chain 'B' and resid 359 through 362' Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 392 through 401 removed outlier: 4.033A pdb=" N THR B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 426 Processing helix chain 'B' and resid 434 through 456 removed outlier: 3.631A pdb=" N LEU B 442 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 489 removed outlier: 4.162A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 487 " --> pdb=" O GLY B 483 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 489 " --> pdb=" O GLU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 500 No H-bonds generated for 'chain 'B' and resid 498 through 500' Processing helix chain 'B' and resid 518 through 535 removed outlier: 3.819A pdb=" N GLU B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 17 removed outlier: 3.580A pdb=" N LEU E 17 " --> pdb=" O MET E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 25 No H-bonds generated for 'chain 'E' and resid 22 through 25' Processing helix chain 'E' and resid 27 through 38 removed outlier: 3.763A pdb=" N ILE E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 18 No H-bonds generated for 'chain 'D' and resid 16 through 18' Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.593A pdb=" N ALA D 29 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 30 " --> pdb=" O TYR D 26 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 33 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 65 removed outlier: 3.566A pdb=" N ASN D 53 " --> pdb=" O TRP D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 removed outlier: 6.021A pdb=" N ASP D 90 " --> pdb=" O TRP D 86 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 115 removed outlier: 3.675A pdb=" N LEU D 102 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) Proline residue: D 106 - end of helix removed outlier: 3.705A pdb=" N LEU D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE D 115 " --> pdb=" O PHE D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 136 removed outlier: 3.717A pdb=" N LEU D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL D 129 " --> pdb=" O VAL D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'C' and resid 10 through 23 removed outlier: 3.715A pdb=" N PHE C 16 " --> pdb=" O GLN C 12 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR C 17 " --> pdb=" O MET C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 49 removed outlier: 3.630A pdb=" N ILE C 44 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 54 No H-bonds generated for 'chain 'C' and resid 51 through 54' Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.512A pdb=" N ALA A 119 " --> pdb=" O PRO A 115 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 169 through 178 removed outlier: 3.780A pdb=" N ILE A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.578A pdb=" N GLN A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.571A pdb=" N TYR A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 322 through 329 removed outlier: 4.755A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.560A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 368 removed outlier: 3.673A pdb=" N PHE A 363 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 364 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 365 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 373 No H-bonds generated for 'chain 'A' and resid 370 through 373' Processing helix chain 'A' and resid 405 through 422 removed outlier: 3.981A pdb=" N GLU A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG A 422 " --> pdb=" O GLN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 468 removed outlier: 3.673A pdb=" N ALA A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.626A pdb=" N ALA B 231 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 255 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU B 313 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 257 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLU B 315 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N ASP B 259 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR B 276 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER B 258 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG B 278 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.965A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 92 through 95 Processing sheet with id= D, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.604A pdb=" N GLY A 316 " --> pdb=" O TYR A 164 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 184 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL A 243 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE A 186 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP A 205 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 187 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS A 207 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 383 through 386 280 hydrogen bonds defined for protein. 810 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: 2.39 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2853 1.33 - 1.45: 1327 1.45 - 1.57: 5060 1.57 - 1.69: 1 1.69 - 1.81: 83 Bond restraints: 9324 Sorted by residual: bond pdb=" C2 PLP B 601 " pdb=" C3 PLP B 601 " ideal model delta sigma weight residual 1.390 1.484 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C4 PLP B 601 " pdb=" C5 PLP B 601 " ideal model delta sigma weight residual 1.390 1.482 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C3 PLP B 601 " pdb=" C4 PLP B 601 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C VAL B 469 " pdb=" N PRO B 470 " ideal model delta sigma weight residual 1.335 1.319 0.016 8.70e-03 1.32e+04 3.26e+00 bond pdb=" C6 PLP B 601 " pdb=" N1 PLP B 601 " ideal model delta sigma weight residual 1.380 1.345 0.035 2.00e-02 2.50e+03 3.15e+00 ... (remaining 9319 not shown) Histogram of bond angle deviations from ideal: 98.04 - 105.31: 176 105.31 - 112.57: 4649 112.57 - 119.83: 3418 119.83 - 127.09: 4291 127.09 - 134.35: 88 Bond angle restraints: 12622 Sorted by residual: angle pdb=" N ILE A 300 " pdb=" CA ILE A 300 " pdb=" C ILE A 300 " ideal model delta sigma weight residual 111.91 118.22 -6.31 8.90e-01 1.26e+00 5.03e+01 angle pdb=" N PRO A 78 " pdb=" CA PRO A 78 " pdb=" CB PRO A 78 " ideal model delta sigma weight residual 103.25 109.64 -6.39 1.05e+00 9.07e-01 3.71e+01 angle pdb=" CA PRO A 135 " pdb=" C PRO A 135 " pdb=" N ARG A 136 " ideal model delta sigma weight residual 116.45 121.20 -4.75 8.50e-01 1.38e+00 3.13e+01 angle pdb=" CA PRO A 135 " pdb=" C PRO A 135 " pdb=" O PRO A 135 " ideal model delta sigma weight residual 121.38 117.36 4.02 7.70e-01 1.69e+00 2.72e+01 angle pdb=" N ASP B 117 " pdb=" CA ASP B 117 " pdb=" C ASP B 117 " ideal model delta sigma weight residual 111.75 118.21 -6.46 1.28e+00 6.10e-01 2.54e+01 ... (remaining 12617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4874 17.91 - 35.82: 475 35.82 - 53.72: 169 53.72 - 71.63: 42 71.63 - 89.54: 12 Dihedral angle restraints: 5572 sinusoidal: 2230 harmonic: 3342 Sorted by residual: dihedral pdb=" CA LEU B 473 " pdb=" C LEU B 473 " pdb=" N TYR B 474 " pdb=" CA TYR B 474 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA PRO A 135 " pdb=" C PRO A 135 " pdb=" N ARG A 136 " pdb=" CA ARG A 136 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TYR B 461 " pdb=" C TYR B 461 " pdb=" N GLY B 462 " pdb=" CA GLY B 462 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 960 0.058 - 0.116: 352 0.116 - 0.174: 71 0.174 - 0.231: 23 0.231 - 0.289: 7 Chirality restraints: 1413 Sorted by residual: chirality pdb=" CA GLU A 400 " pdb=" N GLU A 400 " pdb=" C GLU A 400 " pdb=" CB GLU A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA ARG A 181 " pdb=" N ARG A 181 " pdb=" C ARG A 181 " pdb=" CB ARG A 181 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA ASP B 117 " pdb=" N ASP B 117 " pdb=" C ASP B 117 " pdb=" CB ASP B 117 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1410 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 111 " -0.011 2.00e-02 2.50e+03 2.06e-02 7.43e+00 pdb=" CG PHE B 111 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE B 111 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE B 111 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 111 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 111 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 116 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C GLN B 116 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN B 116 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP B 117 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 413 " -0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C GLN A 413 " 0.037 2.00e-02 2.50e+03 pdb=" O GLN A 413 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU A 414 " -0.013 2.00e-02 2.50e+03 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 219 2.67 - 3.23: 8156 3.23 - 3.79: 13044 3.79 - 4.34: 18816 4.34 - 4.90: 31209 Nonbonded interactions: 71444 Sorted by model distance: nonbonded pdb=" O THR B 66 " pdb=" NH1 ARG D 20 " model vdw 2.119 2.520 nonbonded pdb=" O TRP B 134 " pdb=" O GLY A 137 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR A 178 " pdb=" O VAL A 324 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR A 53 " pdb=" OE1 GLU A 56 " model vdw 2.206 2.440 nonbonded pdb=" OD2 ASP B 132 " pdb=" ND2 ASN B 157 " model vdw 2.212 2.520 ... (remaining 71439 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=0.80 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: 0.720 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: 4.130 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 26.530 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.094 9324 Z= 0.633 Angle : 1.029 10.177 12622 Z= 0.629 Chirality : 0.065 0.289 1413 Planarity : 0.006 0.051 1602 Dihedral : 17.033 89.539 3434 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.08 % Favored : 92.31 % Rotamer: Outliers : 8.32 % Allowed : 4.93 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.22), residues: 1144 helix: -2.04 (0.21), residues: 524 sheet: -1.36 (0.45), residues: 125 loop : -2.47 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 32 HIS 0.008 0.002 HIS D 65 PHE 0.044 0.003 PHE B 111 TYR 0.029 0.003 TYR B 93 ARG 0.007 0.001 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 129 time to evaluate : 1.101 Fit side-chains REVERT: B 68 MET cc_start: 0.8554 (tpp) cc_final: 0.8325 (tpt) REVERT: B 92 ARG cc_start: 0.7234 (ttp-110) cc_final: 0.7015 (ttp-110) REVERT: B 117 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7755 (t0) REVERT: B 161 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8082 (mttm) REVERT: B 183 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7890 (ptm160) REVERT: B 209 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: E 42 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7373 (mtpp) REVERT: D 15 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6329 (mtp85) REVERT: D 17 MET cc_start: 0.7093 (tpt) cc_final: 0.6860 (mmt) REVERT: D 132 MET cc_start: 0.8513 (mmp) cc_final: 0.8144 (mmp) REVERT: D 141 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8608 (mm-40) REVERT: C 11 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.6519 (tmmt) REVERT: C 12 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: A 62 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: A 428 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8197 (tt0) outliers start: 81 outliers final: 39 residues processed: 195 average time/residue: 1.4077 time to fit residues: 290.0975 Evaluate side-chains 158 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 108 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 465 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 0.0770 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN B 189 GLN B 440 GLN B 441 GLN D 18 ASN A 224 GLN A 229 GLN A 469 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9324 Z= 0.174 Angle : 0.595 13.222 12622 Z= 0.304 Chirality : 0.044 0.228 1413 Planarity : 0.004 0.039 1602 Dihedral : 10.390 87.929 1395 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 4.11 % Allowed : 12.85 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.24), residues: 1144 helix: -0.85 (0.23), residues: 527 sheet: -1.02 (0.45), residues: 128 loop : -1.99 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 32 HIS 0.006 0.001 HIS E 24 PHE 0.051 0.001 PHE D 42 TYR 0.019 0.001 TYR E 44 ARG 0.005 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.210 Fit side-chains REVERT: B 130 ILE cc_start: 0.8804 (pt) cc_final: 0.8518 (pt) REVERT: B 290 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7956 (ttpp) REVERT: E 37 ARG cc_start: 0.7446 (tpt170) cc_final: 0.7106 (tmt90) REVERT: D 15 ARG cc_start: 0.7089 (mtp180) cc_final: 0.6274 (mtp85) REVERT: D 17 MET cc_start: 0.7093 (tpt) cc_final: 0.6804 (mmt) REVERT: D 141 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8707 (mm-40) REVERT: C 11 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.6941 (mppt) REVERT: A 229 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7637 (mt0) outliers start: 40 outliers final: 16 residues processed: 153 average time/residue: 1.2699 time to fit residues: 207.2582 Evaluate side-chains 135 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 402 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 0.0170 chunk 111 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9324 Z= 0.165 Angle : 0.531 7.600 12622 Z= 0.274 Chirality : 0.043 0.197 1413 Planarity : 0.004 0.038 1602 Dihedral : 7.139 85.671 1308 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 3.80 % Allowed : 15.52 % Favored : 80.68 % 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: -1.52 (0.25), residues: 1144 helix: -0.27 (0.24), residues: 522 sheet: -0.77 (0.46), residues: 124 loop : -1.83 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.005 0.001 HIS E 24 PHE 0.029 0.001 PHE D 42 TYR 0.011 0.001 TYR E 44 ARG 0.004 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 116 time to evaluate : 1.004 Fit side-chains REVERT: B 130 ILE cc_start: 0.8720 (pt) cc_final: 0.8458 (pt) REVERT: B 189 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7390 (mp10) REVERT: B 475 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8111 (mtt) REVERT: E 37 ARG cc_start: 0.7486 (tpt170) cc_final: 0.7160 (tmt90) REVERT: D 15 ARG cc_start: 0.7037 (mtp180) cc_final: 0.6228 (mtp85) REVERT: D 17 MET cc_start: 0.7123 (tpt) cc_final: 0.6800 (mmt) REVERT: D 132 MET cc_start: 0.8686 (tpp) cc_final: 0.8019 (mmt) REVERT: C 11 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.6991 (mppt) REVERT: A 229 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.6894 (mp10) REVERT: A 239 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8034 (mtt180) REVERT: A 284 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7416 (tm-30) outliers start: 37 outliers final: 20 residues processed: 142 average time/residue: 1.3805 time to fit residues: 208.0911 Evaluate side-chains 132 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.0010 overall best weight: 1.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9324 Z= 0.240 Angle : 0.578 7.965 12622 Z= 0.295 Chirality : 0.045 0.190 1413 Planarity : 0.004 0.039 1602 Dihedral : 6.279 63.798 1293 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 3.91 % Allowed : 16.75 % Favored : 79.34 % 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: -1.39 (0.25), residues: 1144 helix: -0.12 (0.24), residues: 522 sheet: -0.88 (0.44), residues: 130 loop : -1.77 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.005 0.001 HIS E 24 PHE 0.028 0.002 PHE D 42 TYR 0.015 0.001 TYR B 342 ARG 0.003 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 111 time to evaluate : 1.114 Fit side-chains REVERT: B 117 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7707 (t0) REVERT: B 130 ILE cc_start: 0.8781 (pt) cc_final: 0.8514 (pt) REVERT: B 189 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7405 (mp10) REVERT: B 290 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7968 (ttpp) REVERT: B 436 LYS cc_start: 0.7860 (ttmm) cc_final: 0.7506 (ttmm) REVERT: B 475 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8144 (mtt) REVERT: E 37 ARG cc_start: 0.7551 (tpt170) cc_final: 0.7201 (tmt90) REVERT: D 15 ARG cc_start: 0.7028 (mtp180) cc_final: 0.6285 (mtp85) REVERT: D 17 MET cc_start: 0.7135 (tpt) cc_final: 0.6864 (mmt) REVERT: D 132 MET cc_start: 0.8675 (tpp) cc_final: 0.7979 (mmt) REVERT: C 11 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6952 (mppt) REVERT: A 229 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6779 (mp10) REVERT: A 239 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8090 (mtt180) outliers start: 38 outliers final: 21 residues processed: 140 average time/residue: 1.3972 time to fit residues: 207.6952 Evaluate side-chains 136 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 0.0670 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9324 Z= 0.162 Angle : 0.518 7.602 12622 Z= 0.267 Chirality : 0.043 0.200 1413 Planarity : 0.004 0.038 1602 Dihedral : 5.847 60.317 1289 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 3.80 % Allowed : 17.68 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.25), residues: 1144 helix: 0.23 (0.24), residues: 520 sheet: -0.68 (0.45), residues: 126 loop : -1.62 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.004 0.000 HIS E 24 PHE 0.030 0.001 PHE D 42 TYR 0.011 0.001 TYR B 342 ARG 0.002 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 116 time to evaluate : 1.090 Fit side-chains REVERT: B 117 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7640 (t0) REVERT: B 120 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7410 (p0) REVERT: B 130 ILE cc_start: 0.8690 (pt) cc_final: 0.8433 (pt) REVERT: B 189 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7400 (mp10) REVERT: B 290 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7939 (ttpp) REVERT: B 399 ARG cc_start: 0.8735 (mtp85) cc_final: 0.8521 (mtp180) REVERT: B 436 LYS cc_start: 0.7833 (ttmm) cc_final: 0.7472 (ttmm) REVERT: B 475 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8099 (mtt) REVERT: B 530 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7185 (mt-10) REVERT: E 37 ARG cc_start: 0.7502 (tpt170) cc_final: 0.7275 (tmt90) REVERT: D 15 ARG cc_start: 0.6972 (mtp180) cc_final: 0.6243 (mtp85) REVERT: D 17 MET cc_start: 0.7101 (tpt) cc_final: 0.6830 (mmt) REVERT: D 132 MET cc_start: 0.8674 (tpp) cc_final: 0.8028 (mmt) REVERT: A 239 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8057 (mtt180) outliers start: 37 outliers final: 19 residues processed: 142 average time/residue: 1.3411 time to fit residues: 202.3529 Evaluate side-chains 133 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 0.0040 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS A 83 ASN A 229 GLN A 407 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9324 Z= 0.251 Angle : 0.574 8.466 12622 Z= 0.294 Chirality : 0.045 0.211 1413 Planarity : 0.004 0.041 1602 Dihedral : 5.061 59.745 1277 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.67 % Rotamer: Outliers : 4.32 % Allowed : 17.16 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.25), residues: 1144 helix: 0.20 (0.24), residues: 523 sheet: -0.85 (0.45), residues: 130 loop : -1.58 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 32 HIS 0.006 0.001 HIS E 24 PHE 0.034 0.002 PHE D 42 TYR 0.015 0.001 TYR B 342 ARG 0.003 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 109 time to evaluate : 1.136 Fit side-chains REVERT: B 117 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7653 (t0) REVERT: B 124 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7641 (ptt90) REVERT: B 189 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7429 (mp10) REVERT: B 209 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: B 290 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7936 (ttpp) REVERT: B 436 LYS cc_start: 0.7832 (ttmm) cc_final: 0.7472 (ttmm) REVERT: B 456 MET cc_start: 0.8085 (mtt) cc_final: 0.7869 (mtp) REVERT: B 475 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8137 (mtt) REVERT: E 37 ARG cc_start: 0.7546 (tpt170) cc_final: 0.7321 (tmt90) REVERT: D 15 ARG cc_start: 0.6982 (mtp180) cc_final: 0.6257 (mtp85) REVERT: D 17 MET cc_start: 0.7141 (tpt) cc_final: 0.6868 (mmt) REVERT: D 132 MET cc_start: 0.8644 (tpp) cc_final: 0.8035 (mmt) REVERT: A 150 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: A 239 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8007 (mtt180) REVERT: A 411 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8193 (tt) REVERT: A 428 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8177 (tt0) outliers start: 42 outliers final: 23 residues processed: 143 average time/residue: 1.4062 time to fit residues: 213.6515 Evaluate side-chains 138 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 106 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 443 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 79 optimal weight: 0.0370 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 0.0670 chunk 50 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9324 Z= 0.146 Angle : 0.497 8.202 12622 Z= 0.256 Chirality : 0.042 0.231 1413 Planarity : 0.003 0.038 1602 Dihedral : 4.709 58.751 1277 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 3.39 % Allowed : 18.09 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.25), residues: 1144 helix: 0.51 (0.24), residues: 525 sheet: -0.51 (0.45), residues: 124 loop : -1.47 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.002 0.000 HIS B 47 PHE 0.007 0.001 PHE D 124 TYR 0.010 0.001 TYR B 342 ARG 0.002 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 1.062 Fit side-chains REVERT: B 120 ASN cc_start: 0.7962 (p0) cc_final: 0.7368 (p0) REVERT: B 126 LEU cc_start: 0.8693 (mp) cc_final: 0.8143 (tt) REVERT: B 189 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7472 (mp10) REVERT: B 290 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7918 (ttpp) REVERT: B 399 ARG cc_start: 0.8724 (mtp85) cc_final: 0.8505 (mtp180) REVERT: B 436 LYS cc_start: 0.7836 (ttmm) cc_final: 0.7452 (ttmm) REVERT: B 456 MET cc_start: 0.7979 (mtt) cc_final: 0.7772 (mtp) REVERT: B 475 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8072 (mtt) REVERT: E 37 ARG cc_start: 0.7500 (tpt170) cc_final: 0.7274 (tmt90) REVERT: D 15 ARG cc_start: 0.7043 (mtp180) cc_final: 0.6341 (mtp85) REVERT: D 132 MET cc_start: 0.8631 (tpp) cc_final: 0.8042 (mmt) REVERT: A 150 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: A 154 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8277 (mptm) REVERT: A 239 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8011 (mtt180) outliers start: 33 outliers final: 13 residues processed: 134 average time/residue: 1.4521 time to fit residues: 206.2728 Evaluate side-chains 123 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 367 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.0170 chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9324 Z= 0.140 Angle : 0.492 8.341 12622 Z= 0.253 Chirality : 0.042 0.232 1413 Planarity : 0.003 0.038 1602 Dihedral : 4.537 59.550 1277 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 2.88 % Allowed : 18.81 % Favored : 78.31 % 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: -0.47 (0.25), residues: 1144 helix: 0.74 (0.24), residues: 522 sheet: -0.56 (0.45), residues: 126 loop : -1.36 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.002 0.000 HIS B 47 PHE 0.008 0.001 PHE C 55 TYR 0.009 0.001 TYR B 235 ARG 0.002 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 0.907 Fit side-chains REVERT: B 117 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7772 (t0) REVERT: B 189 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7470 (mp10) REVERT: B 221 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: B 290 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7924 (ttpp) REVERT: B 399 ARG cc_start: 0.8713 (mtp85) cc_final: 0.8497 (mtp180) REVERT: B 436 LYS cc_start: 0.7868 (ttmm) cc_final: 0.7463 (ttmm) REVERT: B 490 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8159 (m-40) REVERT: E 37 ARG cc_start: 0.7481 (tpt170) cc_final: 0.7257 (tmt90) REVERT: D 15 ARG cc_start: 0.6962 (mtp180) cc_final: 0.6265 (mtp85) REVERT: D 116 TYR cc_start: 0.8909 (m-80) cc_final: 0.8292 (m-80) REVERT: D 132 MET cc_start: 0.8625 (tpp) cc_final: 0.8050 (mmt) REVERT: A 150 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: A 154 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8272 (mptm) REVERT: A 239 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8046 (mtt180) outliers start: 28 outliers final: 13 residues processed: 130 average time/residue: 1.3881 time to fit residues: 191.2077 Evaluate side-chains 125 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 367 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 61 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN A 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9324 Z= 0.245 Angle : 0.572 9.137 12622 Z= 0.295 Chirality : 0.045 0.251 1413 Planarity : 0.004 0.042 1602 Dihedral : 4.838 59.723 1273 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 3.19 % Allowed : 19.01 % Favored : 77.80 % 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: -0.68 (0.25), residues: 1144 helix: 0.48 (0.24), residues: 528 sheet: -0.57 (0.46), residues: 126 loop : -1.43 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 32 HIS 0.003 0.001 HIS E 24 PHE 0.013 0.002 PHE B 280 TYR 0.015 0.001 TYR B 342 ARG 0.002 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 1.001 Fit side-chains REVERT: B 117 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7685 (t0) REVERT: B 189 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7475 (mp10) REVERT: B 290 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7964 (ttpp) REVERT: B 436 LYS cc_start: 0.7871 (ttmm) cc_final: 0.7492 (ttmm) REVERT: B 490 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8158 (m-40) REVERT: E 37 ARG cc_start: 0.7503 (tpt170) cc_final: 0.7283 (tmt90) REVERT: D 15 ARG cc_start: 0.7059 (mtp180) cc_final: 0.6337 (mtp85) REVERT: D 132 MET cc_start: 0.8597 (tpp) cc_final: 0.7961 (mmt) REVERT: A 150 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7383 (m-30) REVERT: A 239 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8003 (mtt180) REVERT: A 411 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8143 (tt) outliers start: 31 outliers final: 17 residues processed: 130 average time/residue: 1.3723 time to fit residues: 189.6397 Evaluate side-chains 126 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9324 Z= 0.319 Angle : 0.623 9.733 12622 Z= 0.320 Chirality : 0.047 0.277 1413 Planarity : 0.004 0.046 1602 Dihedral : 5.142 59.663 1273 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 3.08 % Allowed : 19.12 % Favored : 77.80 % 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: -0.98 (0.25), residues: 1144 helix: 0.20 (0.23), residues: 530 sheet: -0.77 (0.45), residues: 130 loop : -1.52 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 32 HIS 0.004 0.001 HIS B 100 PHE 0.016 0.002 PHE B 280 TYR 0.017 0.002 TYR B 342 ARG 0.002 0.000 ARG B 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 1.195 Fit side-chains REVERT: B 109 LYS cc_start: 0.8911 (pmtt) cc_final: 0.8479 (mtmt) REVERT: B 117 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7744 (t0) REVERT: B 290 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7946 (ttpp) REVERT: B 436 LYS cc_start: 0.7888 (ttmm) cc_final: 0.7538 (ttmm) REVERT: B 490 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8361 (m-40) REVERT: E 37 ARG cc_start: 0.7492 (tpt170) cc_final: 0.7263 (tmt90) REVERT: D 15 ARG cc_start: 0.7023 (mtp180) cc_final: 0.6314 (mtp85) REVERT: D 132 MET cc_start: 0.8527 (tpp) cc_final: 0.8020 (mmt) REVERT: A 150 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7419 (m-30) REVERT: A 239 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8003 (mtt180) REVERT: A 411 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8135 (tt) outliers start: 30 outliers final: 18 residues processed: 130 average time/residue: 1.3506 time to fit residues: 186.9356 Evaluate side-chains 127 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 64 optimal weight: 0.0020 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.118747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.095726 restraints weight = 11908.011| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.84 r_work: 0.2883 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9324 Z= 0.197 Angle : 0.544 9.415 12622 Z= 0.280 Chirality : 0.044 0.279 1413 Planarity : 0.004 0.043 1602 Dihedral : 4.871 59.387 1273 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.76 % Rotamer: Outliers : 2.67 % Allowed : 19.53 % Favored : 77.80 % 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: -0.76 (0.25), residues: 1144 helix: 0.39 (0.24), residues: 532 sheet: -0.53 (0.46), residues: 126 loop : -1.46 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.003 0.001 HIS E 24 PHE 0.009 0.001 PHE B 280 TYR 0.013 0.001 TYR B 342 ARG 0.002 0.000 ARG B 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3728.20 seconds wall clock time: 66 minutes 47.43 seconds (4007.43 seconds total)