Starting phenix.real_space_refine on Thu Feb 15 21:01:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxu_30238/02_2024/7bxu_30238.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxu_30238/02_2024/7bxu_30238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxu_30238/02_2024/7bxu_30238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxu_30238/02_2024/7bxu_30238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxu_30238/02_2024/7bxu_30238.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxu_30238/02_2024/7bxu_30238.pdb" } resolution = 3.7 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= 0.001 sd= 0.007 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 84 5.16 5 C 8704 2.51 5 N 2242 2.21 5 O 2414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 110": "NH1" <-> "NH2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A ARG 561": "NH1" <-> "NH2" Residue "A ARG 639": "NH1" <-> "NH2" Residue "A ARG 640": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 674": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B ARG 561": "NH1" <-> "NH2" Residue "B ARG 639": "NH1" <-> "NH2" Residue "B ARG 640": "NH1" <-> "NH2" Residue "B ARG 641": "NH1" <-> "NH2" Residue "B ARG 674": "NH1" <-> "NH2" Residue "B ARG 717": "NH1" <-> "NH2" Residue "B PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 767": "NH1" <-> "NH2" Residue "B ARG 775": "NH1" <-> "NH2" Residue "B ARG 789": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13444 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1552 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5072 Classifications: {'peptide': 673} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 29, 'TRANS': 643} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1552 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5072 Classifications: {'peptide': 673} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 29, 'TRANS': 643} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.90, per 1000 atoms: 0.51 Number of scatterers: 13444 At special positions: 0 Unit cell: (104.76, 98.28, 140.4, 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 84 16.00 O 2414 8.00 N 2242 7.00 C 8704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 115 " distance=2.05 Simple disulfide: pdb=" SG CYS C 112 " - pdb=" SG CYS C 171 " distance=1.54 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 115 " distance=2.05 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 171 " distance=1.54 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 Links applied NAG-ASN " NAG C 401 " - " ASN C 93 " " NAG C 402 " - " ASN C 263 " " NAG C 403 " - " ASN C 163 " " NAG C 404 " - " ASN C 184 " " NAG C 405 " - " ASN C 194 " " NAG C 406 " - " ASN C 216 " " NAG C 407 " - " ASN C 128 " " NAG D 401 " - " ASN D 93 " " NAG D 402 " - " ASN D 263 " " NAG D 403 " - " ASN D 163 " " NAG D 404 " - " ASN D 184 " " NAG D 405 " - " ASN D 194 " " NAG D 406 " - " ASN D 216 " " NAG D 407 " - " ASN D 128 " Time building additional restraints: 5.22 Conformation dependent library (CDL) restraints added in 2.4 seconds 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3284 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 6 sheets defined 61.1% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'C' and resid 84 through 105 removed outlier: 3.635A pdb=" N GLU C 97 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 116 through 131 removed outlier: 4.050A pdb=" N GLN C 120 " --> pdb=" O TYR C 116 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 123 " --> pdb=" O PHE C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 153 through 170 Processing helix chain 'C' and resid 184 through 203 removed outlier: 3.991A pdb=" N PHE C 200 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 removed outlier: 4.157A pdb=" N LYS C 222 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 242 removed outlier: 4.458A pdb=" N THR C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 271 removed outlier: 3.562A pdb=" N THR C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 271 " --> pdb=" O LYS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 293 removed outlier: 4.339A pdb=" N SER C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 305 removed outlier: 3.898A pdb=" N LEU C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 removed outlier: 3.658A pdb=" N ARG A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 163 removed outlier: 3.934A pdb=" N VAL A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY A 134 " --> pdb=" O CYS A 130 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 159 " --> pdb=" O LYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.941A pdb=" N LEU A 178 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 249 through 257 removed outlier: 3.948A pdb=" N ILE A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.780A pdb=" N ILE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 262' Processing helix chain 'A' and resid 284 through 294 removed outlier: 3.783A pdb=" N ALA A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 303 through 315 removed outlier: 3.552A pdb=" N GLY A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 335 removed outlier: 3.637A pdb=" N THR A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 329 " --> pdb=" O TRP A 325 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.675A pdb=" N ILE A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 374 through 388 removed outlier: 3.593A pdb=" N ILE A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 407 removed outlier: 3.968A pdb=" N ALA A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR A 397 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A 402 " --> pdb=" O TRP A 398 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 434 removed outlier: 3.772A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE A 415 " --> pdb=" O CYS A 411 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 Processing helix chain 'A' and resid 488 through 505 removed outlier: 3.727A pdb=" N VAL A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 532 removed outlier: 4.563A pdb=" N ILE A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 560 removed outlier: 4.222A pdb=" N TYR A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 573 removed outlier: 3.783A pdb=" N VAL A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 593 removed outlier: 3.881A pdb=" N ILE A 583 " --> pdb=" O TYR A 579 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 592 " --> pdb=" O MET A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 597 Processing helix chain 'A' and resid 600 through 608 removed outlier: 3.535A pdb=" N MET A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 681 through 690 Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.959A pdb=" N ARG A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 753 through 764 removed outlier: 3.550A pdb=" N LEU A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 789 removed outlier: 3.755A pdb=" N LEU A 787 " --> pdb=" O THR A 783 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 789 " --> pdb=" O LYS A 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 105 removed outlier: 3.635A pdb=" N GLU D 97 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER D 105 " --> pdb=" O CYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 116 through 131 removed outlier: 4.049A pdb=" N GLN D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN D 121 " --> pdb=" O PRO D 117 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D 123 " --> pdb=" O PHE D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 153 through 170 Processing helix chain 'D' and resid 184 through 203 removed outlier: 3.992A pdb=" N PHE D 200 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 223 removed outlier: 4.158A pdb=" N LYS D 222 " --> pdb=" O GLU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 242 removed outlier: 4.458A pdb=" N THR D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 271 removed outlier: 3.562A pdb=" N THR D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 271 " --> pdb=" O LYS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 293 removed outlier: 4.338A pdb=" N SER D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 305 removed outlier: 3.898A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 115 removed outlier: 3.658A pdb=" N ARG B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 163 removed outlier: 3.934A pdb=" N VAL B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY B 134 " --> pdb=" O CYS B 130 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 196 removed outlier: 3.941A pdb=" N LEU B 178 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 249 through 257 removed outlier: 3.949A pdb=" N ILE B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.780A pdb=" N ILE B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 257 through 262' Processing helix chain 'B' and resid 284 through 294 removed outlier: 3.783A pdb=" N ALA B 291 " --> pdb=" O ASP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 303 through 315 removed outlier: 3.552A pdb=" N GLY B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 308 " --> pdb=" O PRO B 304 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 335 removed outlier: 3.636A pdb=" N THR B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE B 329 " --> pdb=" O TRP B 325 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 333 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 removed outlier: 3.675A pdb=" N ILE B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 374 through 388 removed outlier: 3.592A pdb=" N ILE B 379 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 407 removed outlier: 3.968A pdb=" N ALA B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 395 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN B 396 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR B 397 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE B 402 " --> pdb=" O TRP B 398 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 434 removed outlier: 3.771A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 414 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE B 415 " --> pdb=" O CYS B 411 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 428 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 480 Processing helix chain 'B' and resid 488 through 505 removed outlier: 3.726A pdb=" N VAL B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 532 removed outlier: 4.563A pdb=" N ILE B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 532 " --> pdb=" O PHE B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 560 removed outlier: 4.222A pdb=" N TYR B 547 " --> pdb=" O ASP B 543 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA B 554 " --> pdb=" O MET B 550 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 573 removed outlier: 3.783A pdb=" N VAL B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 573 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.880A pdb=" N ILE B 583 " --> pdb=" O TYR B 579 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 592 " --> pdb=" O MET B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 600 through 608 removed outlier: 3.535A pdb=" N MET B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE B 606 " --> pdb=" O TYR B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 652 Processing helix chain 'B' and resid 681 through 690 Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.960A pdb=" N ARG B 712 " --> pdb=" O LEU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 724 Processing helix chain 'B' and resid 753 through 764 removed outlier: 3.549A pdb=" N LEU B 764 " --> pdb=" O LEU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 789 removed outlier: 3.755A pdb=" N LEU B 787 " --> pdb=" O THR B 783 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 789 " --> pdb=" O LYS B 785 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 440 Processing sheet with id=AA2, first strand: chain 'A' and resid 660 through 662 Processing sheet with id=AA3, first strand: chain 'A' and resid 747 through 749 removed outlier: 3.831A pdb=" N GLY A 780 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 438 through 440 Processing sheet with id=AA5, first strand: chain 'B' and resid 660 through 662 Processing sheet with id=AA6, first strand: chain 'B' and resid 747 through 749 removed outlier: 3.831A pdb=" N GLY B 780 " --> pdb=" O VAL B 771 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 5.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4161 1.34 - 1.46: 3322 1.46 - 1.58: 6119 1.58 - 1.71: 0 1.71 - 1.83: 128 Bond restraints: 13730 Sorted by residual: bond pdb=" CA GLU B 313 " pdb=" C GLU B 313 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.27e-02 6.20e+03 5.15e+00 bond pdb=" CA GLU A 313 " pdb=" C GLU A 313 " ideal model delta sigma weight residual 1.524 1.495 0.028 1.27e-02 6.20e+03 5.01e+00 bond pdb=" CA ALA D 106 " pdb=" C ALA D 106 " ideal model delta sigma weight residual 1.533 1.523 0.010 5.60e-03 3.19e+04 3.50e+00 bond pdb=" CA ALA C 106 " pdb=" C ALA C 106 " ideal model delta sigma weight residual 1.533 1.523 0.010 5.60e-03 3.19e+04 3.42e+00 bond pdb=" CA ASP D 257 " pdb=" C ASP D 257 " ideal model delta sigma weight residual 1.524 1.547 -0.024 1.29e-02 6.01e+03 3.39e+00 ... (remaining 13725 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.52: 310 105.52 - 112.79: 7255 112.79 - 120.06: 5458 120.06 - 127.34: 5527 127.34 - 134.61: 128 Bond angle restraints: 18678 Sorted by residual: angle pdb=" N ARG A 762 " pdb=" CA ARG A 762 " pdb=" C ARG A 762 " ideal model delta sigma weight residual 111.36 118.98 -7.62 1.09e+00 8.42e-01 4.89e+01 angle pdb=" N ARG B 762 " pdb=" CA ARG B 762 " pdb=" C ARG B 762 " ideal model delta sigma weight residual 111.36 118.93 -7.57 1.09e+00 8.42e-01 4.83e+01 angle pdb=" N PRO A 355 " pdb=" CA PRO A 355 " pdb=" CB PRO A 355 " ideal model delta sigma weight residual 103.51 109.92 -6.41 9.60e-01 1.09e+00 4.46e+01 angle pdb=" N PRO B 355 " pdb=" CA PRO B 355 " pdb=" CB PRO B 355 " ideal model delta sigma weight residual 103.51 109.92 -6.41 9.60e-01 1.09e+00 4.45e+01 angle pdb=" N PRO B 672 " pdb=" CA PRO B 672 " pdb=" CB PRO B 672 " ideal model delta sigma weight residual 103.00 110.30 -7.30 1.10e+00 8.26e-01 4.41e+01 ... (remaining 18673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7750 17.83 - 35.67: 434 35.67 - 53.50: 58 53.50 - 71.33: 12 71.33 - 89.16: 8 Dihedral angle restraints: 8262 sinusoidal: 3196 harmonic: 5066 Sorted by residual: dihedral pdb=" CB CYS C 112 " pdb=" SG CYS C 112 " pdb=" SG CYS C 171 " pdb=" CB CYS C 171 " ideal model delta sinusoidal sigma weight residual -86.00 -175.16 89.16 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS D 112 " pdb=" SG CYS D 112 " pdb=" SG CYS D 171 " pdb=" CB CYS D 171 " ideal model delta sinusoidal sigma weight residual -86.00 -175.11 89.11 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS D 84 " pdb=" SG CYS D 84 " pdb=" SG CYS D 142 " pdb=" CB CYS D 142 " ideal model delta sinusoidal sigma weight residual -86.00 -161.81 75.81 1 1.00e+01 1.00e-02 7.25e+01 ... (remaining 8259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1811 0.077 - 0.154: 361 0.154 - 0.232: 58 0.232 - 0.309: 17 0.309 - 0.386: 7 Chirality restraints: 2254 Sorted by residual: chirality pdb=" CA VAL A 221 " pdb=" N VAL A 221 " pdb=" C VAL A 221 " pdb=" CB VAL A 221 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA VAL B 221 " pdb=" N VAL B 221 " pdb=" C VAL B 221 " pdb=" CB VAL B 221 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA ARG A 762 " pdb=" N ARG A 762 " pdb=" C ARG A 762 " pdb=" CB ARG A 762 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 2251 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " -0.044 2.00e-02 2.50e+03 3.65e-02 1.66e+01 pdb=" C7 NAG C 401 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 404 " 0.044 2.00e-02 2.50e+03 3.64e-02 1.65e+01 pdb=" C7 NAG C 404 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C 404 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG C 404 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG C 404 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 402 " 0.044 2.00e-02 2.50e+03 3.64e-02 1.65e+01 pdb=" C7 NAG D 402 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG D 402 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG D 402 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG D 402 " -0.008 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3584 2.79 - 3.32: 12390 3.32 - 3.85: 20377 3.85 - 4.37: 22351 4.37 - 4.90: 40193 Nonbonded interactions: 98895 Sorted by model distance: nonbonded pdb=" O ASN C 173 " pdb=" OG SER C 183 " model vdw 2.267 2.440 nonbonded pdb=" O ASN D 173 " pdb=" OG SER D 183 " model vdw 2.267 2.440 nonbonded pdb=" O4 NAG D 402 " pdb=" O6 NAG D 402 " model vdw 2.302 2.440 nonbonded pdb=" O4 NAG C 402 " pdb=" O6 NAG C 402 " model vdw 2.303 2.440 nonbonded pdb=" NH2 ARG B 640 " pdb=" OE1 GLN B 676 " model vdw 2.364 2.520 ... (remaining 98890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 2.380 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 35.840 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.008 0.069 13730 Z= 0.529 Angle : 1.170 11.542 18678 Z= 0.662 Chirality : 0.069 0.386 2254 Planarity : 0.009 0.072 2326 Dihedral : 11.207 75.404 4960 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.43 % Allowed : 6.81 % Favored : 92.75 % Cbeta Deviations : 0.12 % 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: -4.33 (0.16), residues: 1708 helix: -2.63 (0.13), residues: 1004 sheet: None (None), residues: 0 loop : -3.12 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP B 179 HIS 0.005 0.001 HIS A 658 PHE 0.047 0.003 PHE A 478 TYR 0.019 0.003 TYR A 156 ARG 0.007 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 259 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9319 (p0) cc_final: 0.8994 (p0) REVERT: C 262 MET cc_start: 0.8715 (tpp) cc_final: 0.8359 (mmm) REVERT: A 332 MET cc_start: 0.8927 (tpp) cc_final: 0.8647 (tpp) REVERT: A 404 ILE cc_start: 0.8962 (tt) cc_final: 0.8507 (mt) REVERT: A 441 LEU cc_start: 0.8240 (pt) cc_final: 0.8023 (tp) REVERT: A 623 HIS cc_start: 0.6532 (t-90) cc_final: 0.6176 (t70) REVERT: A 685 ILE cc_start: 0.9211 (pp) cc_final: 0.8984 (mt) REVERT: D 121 GLN cc_start: 0.7979 (pt0) cc_final: 0.7721 (mt0) REVERT: D 195 HIS cc_start: 0.7977 (t70) cc_final: 0.7717 (t-170) REVERT: B 102 SER cc_start: 0.8762 (m) cc_final: 0.8403 (p) REVERT: B 124 ILE cc_start: 0.9596 (tp) cc_final: 0.9390 (tp) REVERT: B 198 GLU cc_start: 0.8317 (pm20) cc_final: 0.8037 (pm20) REVERT: B 404 ILE cc_start: 0.8914 (tt) cc_final: 0.8449 (mt) REVERT: B 441 LEU cc_start: 0.8154 (pt) cc_final: 0.7908 (tp) outliers start: 6 outliers final: 4 residues processed: 265 average time/residue: 0.2682 time to fit residues: 102.4658 Evaluate side-chains 201 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 197 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain B residue 213 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 0.2980 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 101 optimal weight: 0.0970 chunk 158 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN C 191 ASN A 252 HIS A 460 ASN A 576 ASN A 657 ASN ** A 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN B 252 HIS B 460 ASN B 576 ASN B 623 HIS B 657 ASN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13730 Z= 0.163 Angle : 0.625 7.869 18678 Z= 0.325 Chirality : 0.041 0.179 2254 Planarity : 0.006 0.049 2326 Dihedral : 5.688 43.491 2156 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.16 % Allowed : 12.68 % Favored : 86.16 % 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: -3.11 (0.18), residues: 1708 helix: -1.44 (0.15), residues: 1026 sheet: -3.76 (0.93), residues: 20 loop : -2.94 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 179 HIS 0.012 0.001 HIS B 623 PHE 0.029 0.001 PHE C 119 TYR 0.011 0.001 TYR B 397 ARG 0.004 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 222 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9206 (p0) cc_final: 0.8888 (p0) REVERT: C 152 MET cc_start: 0.7871 (ttm) cc_final: 0.7632 (ttm) REVERT: C 225 ARG cc_start: 0.8925 (tpp-160) cc_final: 0.8704 (ttm-80) REVERT: C 262 MET cc_start: 0.8550 (tpp) cc_final: 0.8100 (mmm) REVERT: A 102 SER cc_start: 0.8698 (m) cc_final: 0.8380 (p) REVERT: A 332 MET cc_start: 0.8962 (tpp) cc_final: 0.8740 (tpp) REVERT: A 337 THR cc_start: 0.9215 (p) cc_final: 0.8904 (t) REVERT: A 404 ILE cc_start: 0.8971 (tt) cc_final: 0.8568 (mt) REVERT: A 441 LEU cc_start: 0.8182 (pt) cc_final: 0.7964 (tp) REVERT: A 560 VAL cc_start: 0.8637 (t) cc_final: 0.8354 (m) REVERT: A 741 MET cc_start: 0.8157 (ptt) cc_final: 0.7943 (ptt) REVERT: D 150 ASP cc_start: 0.8956 (p0) cc_final: 0.8521 (p0) REVERT: D 195 HIS cc_start: 0.7735 (t70) cc_final: 0.7392 (t-170) REVERT: D 262 MET cc_start: 0.8406 (tpp) cc_final: 0.8074 (mmm) REVERT: B 102 SER cc_start: 0.8797 (m) cc_final: 0.8431 (p) REVERT: B 124 ILE cc_start: 0.9394 (tp) cc_final: 0.9056 (tp) REVERT: B 404 ILE cc_start: 0.8922 (tt) cc_final: 0.8469 (mt) REVERT: B 441 LEU cc_start: 0.8075 (pt) cc_final: 0.7809 (tp) REVERT: B 560 VAL cc_start: 0.8593 (t) cc_final: 0.8292 (m) outliers start: 16 outliers final: 8 residues processed: 232 average time/residue: 0.2634 time to fit residues: 87.8802 Evaluate side-chains 197 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 753 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 131 optimal weight: 0.1980 chunk 107 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN C 242 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN A 623 HIS ** A 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN B 413 GLN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13730 Z= 0.148 Angle : 0.559 6.975 18678 Z= 0.286 Chirality : 0.040 0.172 2254 Planarity : 0.004 0.042 2326 Dihedral : 4.712 19.775 2150 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.67 % Allowed : 14.78 % Favored : 83.55 % 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: -2.31 (0.19), residues: 1708 helix: -0.68 (0.16), residues: 1030 sheet: -3.73 (1.00), residues: 20 loop : -2.83 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 524 HIS 0.013 0.001 HIS A 623 PHE 0.032 0.001 PHE D 119 TYR 0.011 0.001 TYR A 397 ARG 0.003 0.000 ARG B 762 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 207 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9182 (p0) cc_final: 0.8810 (p0) REVERT: C 152 MET cc_start: 0.7878 (ttm) cc_final: 0.7606 (ttm) REVERT: C 225 ARG cc_start: 0.8920 (tpp-160) cc_final: 0.8668 (ttm-80) REVERT: C 262 MET cc_start: 0.8534 (tpp) cc_final: 0.8136 (mmm) REVERT: A 102 SER cc_start: 0.8748 (m) cc_final: 0.8385 (p) REVERT: A 198 GLU cc_start: 0.8348 (pm20) cc_final: 0.8105 (pm20) REVERT: A 337 THR cc_start: 0.9173 (p) cc_final: 0.8901 (t) REVERT: A 404 ILE cc_start: 0.8905 (tt) cc_final: 0.8408 (mt) REVERT: D 121 GLN cc_start: 0.8053 (pt0) cc_final: 0.7777 (mt0) REVERT: D 150 ASP cc_start: 0.9035 (p0) cc_final: 0.8449 (p0) REVERT: D 195 HIS cc_start: 0.7669 (t70) cc_final: 0.7311 (t-170) REVERT: D 203 ASN cc_start: 0.8380 (m-40) cc_final: 0.8129 (t0) REVERT: D 262 MET cc_start: 0.8388 (tpp) cc_final: 0.8097 (mmm) REVERT: D 285 VAL cc_start: 0.9007 (m) cc_final: 0.8802 (t) REVERT: B 102 SER cc_start: 0.8851 (m) cc_final: 0.8465 (p) REVERT: B 441 LEU cc_start: 0.8113 (pt) cc_final: 0.7875 (tp) REVERT: B 560 VAL cc_start: 0.8569 (t) cc_final: 0.8287 (m) REVERT: B 687 LEU cc_start: 0.9272 (mp) cc_final: 0.8980 (mp) REVERT: B 741 MET cc_start: 0.8220 (ptt) cc_final: 0.7871 (ptt) outliers start: 23 outliers final: 12 residues processed: 225 average time/residue: 0.2360 time to fit residues: 79.0990 Evaluate side-chains 203 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 191 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 753 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 4.9990 chunk 119 optimal weight: 0.0970 chunk 82 optimal weight: 0.0370 chunk 17 optimal weight: 20.0000 chunk 75 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.2860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13730 Z= 0.183 Angle : 0.583 12.458 18678 Z= 0.300 Chirality : 0.041 0.184 2254 Planarity : 0.004 0.039 2326 Dihedral : 4.471 19.053 2150 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.75 % Allowed : 15.43 % Favored : 81.81 % 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: -1.79 (0.20), residues: 1708 helix: -0.20 (0.16), residues: 1032 sheet: -3.78 (1.03), residues: 20 loop : -2.71 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 524 HIS 0.012 0.001 HIS B 623 PHE 0.015 0.001 PHE D 119 TYR 0.009 0.001 TYR A 397 ARG 0.002 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 194 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9194 (p0) cc_final: 0.8818 (p0) REVERT: C 262 MET cc_start: 0.8591 (tpp) cc_final: 0.8194 (mmm) REVERT: A 198 GLU cc_start: 0.8371 (pm20) cc_final: 0.8116 (pm20) REVERT: A 562 MET cc_start: 0.8419 (mtm) cc_final: 0.8055 (mtm) REVERT: A 616 TRP cc_start: 0.7955 (OUTLIER) cc_final: 0.5640 (p-90) REVERT: A 741 MET cc_start: 0.8469 (ptt) cc_final: 0.8267 (ptt) REVERT: D 150 ASP cc_start: 0.9049 (p0) cc_final: 0.8589 (p0) REVERT: D 152 MET cc_start: 0.7776 (ttm) cc_final: 0.7381 (ttm) REVERT: D 195 HIS cc_start: 0.7654 (t70) cc_final: 0.7284 (t-170) REVERT: D 203 ASN cc_start: 0.8324 (m-40) cc_final: 0.8104 (t0) REVERT: D 262 MET cc_start: 0.8406 (tpp) cc_final: 0.8141 (mmm) REVERT: B 198 GLU cc_start: 0.8424 (pm20) cc_final: 0.8155 (pm20) REVERT: B 278 TYR cc_start: 0.8289 (t80) cc_final: 0.8057 (t80) REVERT: B 616 TRP cc_start: 0.8053 (OUTLIER) cc_final: 0.5757 (p-90) REVERT: B 628 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8176 (ttp80) REVERT: B 687 LEU cc_start: 0.9324 (mp) cc_final: 0.9038 (mp) outliers start: 38 outliers final: 19 residues processed: 222 average time/residue: 0.2920 time to fit residues: 95.8893 Evaluate side-chains 210 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 616 TRP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 753 SER Chi-restraints excluded: chain B residue 778 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 HIS C 242 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13730 Z= 0.330 Angle : 0.676 11.579 18678 Z= 0.344 Chirality : 0.045 0.189 2254 Planarity : 0.004 0.041 2326 Dihedral : 4.708 20.561 2150 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.91 % Allowed : 16.23 % Favored : 79.86 % 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: -1.69 (0.20), residues: 1708 helix: -0.09 (0.16), residues: 1030 sheet: -3.95 (1.01), residues: 20 loop : -2.71 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 179 HIS 0.004 0.001 HIS C 195 PHE 0.019 0.002 PHE B 581 TYR 0.011 0.001 TYR D 188 ARG 0.004 0.001 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 178 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9294 (p0) cc_final: 0.8896 (p0) REVERT: A 416 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: A 616 TRP cc_start: 0.8226 (OUTLIER) cc_final: 0.5501 (p-90) REVERT: D 83 GLU cc_start: 0.7454 (mp0) cc_final: 0.7191 (mp0) REVERT: D 150 ASP cc_start: 0.9094 (p0) cc_final: 0.8543 (p0) REVERT: D 152 MET cc_start: 0.7969 (ttm) cc_final: 0.7549 (ttm) REVERT: D 195 HIS cc_start: 0.7690 (t70) cc_final: 0.7362 (t-170) REVERT: D 203 ASN cc_start: 0.8379 (m-40) cc_final: 0.8061 (t0) REVERT: D 262 MET cc_start: 0.8556 (tpp) cc_final: 0.8256 (tmm) REVERT: B 198 GLU cc_start: 0.8474 (pm20) cc_final: 0.8212 (pm20) REVERT: B 213 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9379 (mt) REVERT: B 416 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: B 616 TRP cc_start: 0.8280 (OUTLIER) cc_final: 0.5559 (p-90) REVERT: B 628 ARG cc_start: 0.8495 (ttp80) cc_final: 0.8249 (ttp80) outliers start: 54 outliers final: 34 residues processed: 219 average time/residue: 0.2468 time to fit residues: 79.3316 Evaluate side-chains 210 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 171 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 616 TRP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 741 MET Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 753 SER Chi-restraints excluded: chain B residue 778 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 41 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 HIS C 242 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13730 Z= 0.196 Angle : 0.595 12.129 18678 Z= 0.303 Chirality : 0.041 0.182 2254 Planarity : 0.004 0.040 2326 Dihedral : 4.419 20.012 2150 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.48 % Allowed : 17.03 % Favored : 79.49 % 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: -1.36 (0.20), residues: 1708 helix: 0.19 (0.17), residues: 1026 sheet: -3.85 (1.02), residues: 20 loop : -2.59 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 524 HIS 0.005 0.001 HIS C 195 PHE 0.012 0.001 PHE D 119 TYR 0.011 0.001 TYR B 397 ARG 0.005 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 191 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9225 (p0) cc_final: 0.8827 (p0) REVERT: C 152 MET cc_start: 0.7950 (ttm) cc_final: 0.7589 (ttm) REVERT: C 262 MET cc_start: 0.8822 (mmm) cc_final: 0.8132 (mmm) REVERT: A 416 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: A 562 MET cc_start: 0.8410 (mtm) cc_final: 0.8048 (mtm) REVERT: A 616 TRP cc_start: 0.8110 (OUTLIER) cc_final: 0.5359 (p-90) REVERT: A 628 ARG cc_start: 0.8411 (ttp80) cc_final: 0.8190 (ttp80) REVERT: D 150 ASP cc_start: 0.9085 (p0) cc_final: 0.8526 (p0) REVERT: D 195 HIS cc_start: 0.7656 (t70) cc_final: 0.7345 (t-170) REVERT: D 203 ASN cc_start: 0.8307 (m-40) cc_final: 0.8034 (t0) REVERT: D 262 MET cc_start: 0.8429 (tpp) cc_final: 0.8177 (mmm) REVERT: B 198 GLU cc_start: 0.8435 (pm20) cc_final: 0.8149 (pm20) REVERT: B 416 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: B 616 TRP cc_start: 0.8090 (OUTLIER) cc_final: 0.5441 (p-90) REVERT: B 628 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8217 (ttm110) outliers start: 48 outliers final: 32 residues processed: 222 average time/residue: 0.2564 time to fit residues: 83.3376 Evaluate side-chains 221 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 616 TRP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 741 MET Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 753 SER Chi-restraints excluded: chain B residue 778 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13730 Z= 0.197 Angle : 0.594 13.281 18678 Z= 0.302 Chirality : 0.041 0.181 2254 Planarity : 0.004 0.039 2326 Dihedral : 4.258 19.119 2150 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.83 % Allowed : 18.84 % Favored : 78.33 % 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 (0.21), residues: 1708 helix: 0.35 (0.17), residues: 1026 sheet: -3.81 (0.99), residues: 20 loop : -2.51 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 524 HIS 0.013 0.001 HIS B 623 PHE 0.010 0.001 PHE D 119 TYR 0.010 0.001 TYR B 397 ARG 0.004 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 184 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9203 (p0) cc_final: 0.8892 (p0) REVERT: C 152 MET cc_start: 0.7981 (ttm) cc_final: 0.7681 (ttm) REVERT: C 262 MET cc_start: 0.8857 (mmm) cc_final: 0.8045 (mmm) REVERT: A 332 MET cc_start: 0.8923 (tpp) cc_final: 0.8598 (mmm) REVERT: A 416 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: A 616 TRP cc_start: 0.8114 (OUTLIER) cc_final: 0.5307 (p-90) REVERT: A 628 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8192 (ttp80) REVERT: D 150 ASP cc_start: 0.9033 (p0) cc_final: 0.8573 (p0) REVERT: D 152 MET cc_start: 0.7955 (ttm) cc_final: 0.7664 (ttm) REVERT: D 195 HIS cc_start: 0.7685 (t70) cc_final: 0.7350 (t-170) REVERT: D 203 ASN cc_start: 0.8251 (m-40) cc_final: 0.8010 (t0) REVERT: D 262 MET cc_start: 0.8380 (tpp) cc_final: 0.8157 (mmm) REVERT: B 416 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: B 616 TRP cc_start: 0.8109 (OUTLIER) cc_final: 0.5401 (p-90) REVERT: B 628 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8098 (ttp80) outliers start: 39 outliers final: 30 residues processed: 211 average time/residue: 0.2611 time to fit residues: 79.9431 Evaluate side-chains 211 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 616 TRP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 741 MET Chi-restraints excluded: chain B residue 753 SER Chi-restraints excluded: chain B residue 778 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 82 optimal weight: 0.0570 chunk 15 optimal weight: 1.9990 chunk 131 optimal weight: 0.0980 chunk 152 optimal weight: 0.4980 chunk 160 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN C 195 HIS A 359 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 13730 Z= 0.142 Angle : 0.565 13.058 18678 Z= 0.288 Chirality : 0.040 0.179 2254 Planarity : 0.004 0.037 2326 Dihedral : 3.937 16.518 2150 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.46 % Allowed : 19.35 % Favored : 78.19 % 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: -0.91 (0.21), residues: 1708 helix: 0.61 (0.17), residues: 1024 sheet: -3.70 (1.01), residues: 20 loop : -2.51 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 524 HIS 0.006 0.001 HIS C 195 PHE 0.012 0.001 PHE A 478 TYR 0.015 0.001 TYR C 188 ARG 0.004 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 206 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 MET cc_start: 0.7855 (ttm) cc_final: 0.7595 (ttm) REVERT: C 262 MET cc_start: 0.8809 (mmm) cc_final: 0.8031 (mmm) REVERT: A 145 ASP cc_start: 0.8390 (t0) cc_final: 0.8142 (t0) REVERT: A 560 VAL cc_start: 0.8354 (t) cc_final: 0.8060 (m) REVERT: A 628 ARG cc_start: 0.8380 (ttp80) cc_final: 0.8160 (ttp80) REVERT: D 195 HIS cc_start: 0.7609 (t70) cc_final: 0.7341 (t-170) REVERT: B 687 LEU cc_start: 0.9167 (mp) cc_final: 0.8954 (mp) outliers start: 34 outliers final: 21 residues processed: 232 average time/residue: 0.2525 time to fit residues: 85.8756 Evaluate side-chains 205 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 184 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 753 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.7980 chunk 160 optimal weight: 0.0770 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 141 optimal weight: 0.2980 chunk 147 optimal weight: 0.9990 chunk 155 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN C 195 HIS ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13730 Z= 0.144 Angle : 0.579 13.434 18678 Z= 0.294 Chirality : 0.040 0.183 2254 Planarity : 0.004 0.038 2326 Dihedral : 3.779 18.915 2150 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.96 % Allowed : 19.93 % Favored : 78.12 % 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: -0.73 (0.21), residues: 1708 helix: 0.75 (0.17), residues: 1028 sheet: -3.73 (0.97), residues: 20 loop : -2.43 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 616 HIS 0.006 0.000 HIS C 195 PHE 0.011 0.001 PHE D 119 TYR 0.022 0.001 TYR B 397 ARG 0.004 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 196 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 MET cc_start: 0.7833 (ttm) cc_final: 0.7557 (ttm) REVERT: C 197 LEU cc_start: 0.8699 (tt) cc_final: 0.8473 (tt) REVERT: C 262 MET cc_start: 0.8843 (mmm) cc_final: 0.8013 (mmm) REVERT: A 145 ASP cc_start: 0.8390 (t0) cc_final: 0.8129 (t0) REVERT: A 560 VAL cc_start: 0.8306 (t) cc_final: 0.8011 (m) REVERT: D 150 ASP cc_start: 0.9156 (p0) cc_final: 0.8924 (p0) REVERT: D 195 HIS cc_start: 0.7629 (t70) cc_final: 0.7307 (t-170) REVERT: D 197 LEU cc_start: 0.8672 (tt) cc_final: 0.8417 (tt) REVERT: B 687 LEU cc_start: 0.9182 (mp) cc_final: 0.8942 (mp) outliers start: 27 outliers final: 23 residues processed: 216 average time/residue: 0.2473 time to fit residues: 78.3257 Evaluate side-chains 210 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 187 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 753 SER Chi-restraints excluded: chain B residue 778 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 7.9990 chunk 78 optimal weight: 0.0770 chunk 114 optimal weight: 5.9990 chunk 173 optimal weight: 0.4980 chunk 159 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 overall best weight: 1.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN C 167 GLN C 195 HIS ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13730 Z= 0.200 Angle : 0.612 13.386 18678 Z= 0.312 Chirality : 0.042 0.184 2254 Planarity : 0.004 0.036 2326 Dihedral : 3.879 19.889 2150 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.96 % Allowed : 20.00 % Favored : 78.04 % 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: -0.71 (0.21), residues: 1708 helix: 0.78 (0.17), residues: 1028 sheet: -3.76 (0.91), residues: 20 loop : -2.45 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 616 HIS 0.006 0.001 HIS C 195 PHE 0.013 0.001 PHE B 429 TYR 0.021 0.001 TYR A 397 ARG 0.004 0.000 ARG D 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 182 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 MET cc_start: 0.7851 (ttm) cc_final: 0.7623 (ttm) REVERT: C 262 MET cc_start: 0.8915 (mmm) cc_final: 0.8077 (mmm) REVERT: A 231 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8859 (p) REVERT: D 150 ASP cc_start: 0.9159 (p0) cc_final: 0.8888 (p0) REVERT: D 195 HIS cc_start: 0.7645 (t70) cc_final: 0.7316 (t-170) REVERT: B 687 LEU cc_start: 0.9211 (mp) cc_final: 0.9004 (mp) outliers start: 27 outliers final: 22 residues processed: 201 average time/residue: 0.2568 time to fit residues: 75.6857 Evaluate side-chains 202 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 753 SER Chi-restraints excluded: chain B residue 778 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN C 195 HIS ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.129566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.097529 restraints weight = 19472.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.100026 restraints weight = 11834.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.101628 restraints weight = 8678.377| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13730 Z= 0.240 Angle : 0.634 13.271 18678 Z= 0.322 Chirality : 0.043 0.185 2254 Planarity : 0.004 0.037 2326 Dihedral : 4.071 18.991 2150 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.45 % Rotamer: Outliers : 1.88 % Allowed : 20.07 % Favored : 78.04 % 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: -0.76 (0.21), residues: 1708 helix: 0.69 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -2.49 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 616 HIS 0.006 0.001 HIS C 195 PHE 0.015 0.001 PHE B 429 TYR 0.018 0.001 TYR B 397 ARG 0.005 0.000 ARG D 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2545.01 seconds wall clock time: 47 minutes 4.93 seconds (2824.93 seconds total)