Starting phenix.real_space_refine on Mon Dec 30 13:00:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mn8_23918/12_2024/7mn8_23918.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mn8_23918/12_2024/7mn8_23918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mn8_23918/12_2024/7mn8_23918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mn8_23918/12_2024/7mn8_23918.map" model { file = "/net/cci-nas-00/data/ceres_data/7mn8_23918/12_2024/7mn8_23918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mn8_23918/12_2024/7mn8_23918.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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 130 5.16 5 C 8055 2.51 5 N 2268 2.21 5 O 2494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12947 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4614 Classifications: {'peptide': 599} Link IDs: {'PTRANS': 39, 'TRANS': 559} Chain breaks: 1 Chain: "H" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain breaks: 1 Chain: "B" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4476 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 540} Chain breaks: 3 Chain: "C" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1649 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "D" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1649 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.51, per 1000 atoms: 0.66 Number of scatterers: 12947 At special positions: 0 Unit cell: (106.752, 126.768, 133.44, 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 130 16.00 O 2494 8.00 N 2268 7.00 C 8055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 56 " distance=2.03 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 218 " distance=2.02 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 235 " distance=2.04 Simple disulfide: pdb=" SG CYS A 231 " - pdb=" SG CYS A 243 " distance=2.02 Simple disulfide: pdb=" SG CYS A 246 " - pdb=" SG CYS A 255 " distance=2.10 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 286 " distance=2.02 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 354 " distance=2.04 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 493 " distance=2.02 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 509 " distance=2.02 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 517 " distance=2.02 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 533 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 573 " distance=2.01 Simple disulfide: pdb=" SG CYS A 576 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 610 " distance=2.04 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 621 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 629 " distance=2.06 Simple disulfide: pdb=" SG CYS H 182 " - pdb=" SG CYS H 196 " distance=2.07 Simple disulfide: pdb=" SG CYS H 190 " - pdb=" SG CYS H 210 " distance=2.02 Simple disulfide: pdb=" SG CYS H 212 " - pdb=" SG CYS H 221 " distance=2.02 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.05 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.05 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.04 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 295 " distance=2.27 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=2.05 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 331 " distance=2.06 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 338 " distance=2.06 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 367 " distance=2.02 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 504 " distance=2.04 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 520 " distance=2.02 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 544 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.02 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.05 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 623 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.11 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A1101 " - " ASN A 408 " " NAG A1102 " - " ASN A 353 " " NAG A1103 " - " ASN A 414 " " NAG B1501 " - " ASN B 530 " " NAG B1502 " - " ASN B 187 " " NAG E 1 " - " ASN A 469 " " NAG F 1 " - " ASN A 250 " " NAG G 1 " - " ASN B 259 " Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 37 sheets defined 14.3% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.076A pdb=" N TRP A 79 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 222 through 226 removed outlier: 4.148A pdb=" N CYS A 226 " --> pdb=" O PRO A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 380 through 390 removed outlier: 3.981A pdb=" N THR A 389 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 423 through 426 Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'H' and resid 185 through 190 removed outlier: 3.507A pdb=" N CYS H 190 " --> pdb=" O LYS H 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 51 removed outlier: 4.652A pdb=" N LEU B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASP B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 77 removed outlier: 4.227A pdb=" N ASP B 76 " --> pdb=" O PHE B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.604A pdb=" N ILE B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 396 through 403 removed outlier: 4.322A pdb=" N THR B 402 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 481 through 485 Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 183 through 188 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 208 through 211 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 7.206A pdb=" N CYS A 29 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 7.184A pdb=" N VAL A 38 " --> pdb=" O CYS H 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.372A pdb=" N LEU A 63 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA A 90 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 65 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 87 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N MET A 120 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 89 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE A 115 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR A 148 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE A 117 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLU A 150 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 119 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL A 147 " --> pdb=" O VAL A 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 235 removed outlier: 3.562A pdb=" N ALA A 245 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLY A 234 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N CYS A 243 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 249 through 251 Processing sheet with id=AA6, first strand: chain 'A' and resid 263 through 266 removed outlier: 3.530A pdb=" N GLN A 271 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 280 through 282 Processing sheet with id=AA8, first strand: chain 'A' and resid 300 through 302 removed outlier: 3.610A pdb=" N VAL A 295 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 363 removed outlier: 4.600A pdb=" N PHE A 428 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TYR A 455 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A 430 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N SER A 457 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE A 432 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 523 through 525 Processing sheet with id=AB3, first strand: chain 'A' and resid 542 through 545 Processing sheet with id=AB4, first strand: chain 'A' and resid 579 through 581 Processing sheet with id=AB5, first strand: chain 'A' and resid 591 through 595 removed outlier: 5.486A pdb=" N HIS A 591 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LYS A 602 " --> pdb=" O HIS A 591 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'B' and resid 25 through 27 removed outlier: 6.823A pdb=" N CYS B 26 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.804A pdb=" N TYR B 112 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU B 154 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 114 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N GLN B 156 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 116 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 153 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 259 through 260 Processing sheet with id=AC1, first strand: chain 'B' and resid 272 through 275 Processing sheet with id=AC2, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AC3, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AC4, first strand: chain 'B' and resid 342 through 343 removed outlier: 6.656A pdb=" N CYS B 342 " --> pdb=" O PHE B 371 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 374 through 376 removed outlier: 5.606A pdb=" N LEU B 465 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N THR B 496 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE B 468 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 553 through 556 Processing sheet with id=AC7, first strand: chain 'B' and resid 590 through 592 Processing sheet with id=AC8, first strand: chain 'B' and resid 615 through 617 Processing sheet with id=AC9, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.527A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.527A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 114 through 118 removed outlier: 3.560A pdb=" N ASN C 138 " --> pdb=" O TYR C 173 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 153 through 154 removed outlier: 4.093A pdb=" N ALA C 193 " --> pdb=" O LYS C 149 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.273A pdb=" N GLY D 10 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR D 33 " --> pdb=" O TRP D 99 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.273A pdb=" N GLY D 10 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 127 through 131 Processing sheet with id=AD9, first strand: chain 'D' and resid 127 through 131 removed outlier: 5.120A pdb=" N ALA D 144 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL D 191 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY D 146 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL D 189 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU D 148 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER D 187 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS D 150 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU D 185 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER D 184 " --> pdb=" O ALA D 175 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA D 175 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 186 " --> pdb=" O PHE D 173 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 158 through 161 340 hydrogen bonds defined for protein. 675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.58 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4016 1.33 - 1.46: 3408 1.46 - 1.60: 5675 1.60 - 1.73: 1 1.73 - 1.87: 149 Bond restraints: 13249 Sorted by residual: bond pdb=" N PRO A 540 " pdb=" CD PRO A 540 " ideal model delta sigma weight residual 1.473 1.583 -0.110 1.40e-02 5.10e+03 6.19e+01 bond pdb=" N PRO H 205 " pdb=" CD PRO H 205 " ideal model delta sigma weight residual 1.473 1.549 -0.076 1.40e-02 5.10e+03 2.93e+01 bond pdb=" N PRO D 209 " pdb=" CD PRO D 209 " ideal model delta sigma weight residual 1.473 1.544 -0.071 1.40e-02 5.10e+03 2.55e+01 bond pdb=" N PRO B 378 " pdb=" CD PRO B 378 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO C 8 " pdb=" CD PRO C 8 " ideal model delta sigma weight residual 1.474 1.419 0.055 1.40e-02 5.10e+03 1.54e+01 ... (remaining 13244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 15741 1.81 - 3.63: 1876 3.63 - 5.44: 256 5.44 - 7.26: 73 7.26 - 9.07: 52 Bond angle restraints: 17998 Sorted by residual: angle pdb=" C PRO A 403 " pdb=" N PRO A 404 " pdb=" CA PRO A 404 " ideal model delta sigma weight residual 119.56 128.53 -8.97 1.02e+00 9.61e-01 7.73e+01 angle pdb=" C ASP A 501 " pdb=" N PRO A 502 " pdb=" CA PRO A 502 " ideal model delta sigma weight residual 119.82 128.32 -8.50 9.80e-01 1.04e+00 7.52e+01 angle pdb=" C GLY B 522 " pdb=" N PRO B 523 " pdb=" CA PRO B 523 " ideal model delta sigma weight residual 119.56 127.98 -8.42 1.01e+00 9.80e-01 6.95e+01 angle pdb=" C LEU A 99 " pdb=" N PRO A 100 " pdb=" CA PRO A 100 " ideal model delta sigma weight residual 119.56 127.97 -8.41 1.01e+00 9.80e-01 6.93e+01 angle pdb=" C GLY A 511 " pdb=" N PRO A 512 " pdb=" CA PRO A 512 " ideal model delta sigma weight residual 119.56 127.84 -8.28 1.01e+00 9.80e-01 6.72e+01 ... (remaining 17993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 7940 21.72 - 43.44: 232 43.44 - 65.17: 56 65.17 - 86.89: 22 86.89 - 108.61: 6 Dihedral angle restraints: 8256 sinusoidal: 3499 harmonic: 4757 Sorted by residual: dihedral pdb=" CB CYS A 290 " pdb=" SG CYS A 290 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 168.21 -75.21 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS B 475 " pdb=" SG CYS B 475 " pdb=" SG CYS B 504 " pdb=" CB CYS B 504 " ideal model delta sinusoidal sigma weight residual 93.00 150.22 -57.22 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 36.01 56.99 1 1.00e+01 1.00e-02 4.37e+01 ... (remaining 8253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1518 0.074 - 0.148: 394 0.148 - 0.221: 70 0.221 - 0.295: 18 0.295 - 0.369: 9 Chirality restraints: 2009 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.72e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.38e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 9.67e+00 ... (remaining 2006 not shown) Planarity restraints: 2361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 280 " 0.096 2.00e-02 2.50e+03 5.00e-02 5.01e+01 pdb=" CG TYR A 280 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR A 280 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR A 280 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 280 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 280 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 280 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 280 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1103 " 0.063 2.00e-02 2.50e+03 5.04e-02 3.18e+01 pdb=" C7 NAG A1103 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG A1103 " 0.049 2.00e-02 2.50e+03 pdb=" N2 NAG A1103 " -0.076 2.00e-02 2.50e+03 pdb=" O7 NAG A1103 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 274 " -0.061 2.00e-02 2.50e+03 3.72e-02 2.77e+01 pdb=" CG TYR B 274 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR B 274 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 274 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR B 274 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR B 274 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 274 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 274 " -0.060 2.00e-02 2.50e+03 ... (remaining 2358 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4342 2.85 - 3.36: 11859 3.36 - 3.88: 22799 3.88 - 4.39: 26715 4.39 - 4.90: 43470 Nonbonded interactions: 109185 Sorted by model distance: nonbonded pdb=" O TYR C 186 " pdb=" OH TYR C 192 " model vdw 2.340 3.040 nonbonded pdb=" OG1 THR D 32 " pdb=" O TRP D 99 " model vdw 2.387 3.040 nonbonded pdb=" NH1 ARG B 552 " pdb=" OG1 THR B 575 " model vdw 2.408 3.120 nonbonded pdb=" OD1 ASP B 30 " pdb=" NZ LYS B 32 " model vdw 2.409 3.120 nonbonded pdb=" OD1 ASP A 581 " pdb=" NZ LYS A 602 " model vdw 2.410 3.120 ... (remaining 109180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.390 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.580 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 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 : 0.012 0.110 13249 Z= 0.813 Angle : 1.324 9.074 17998 Z= 0.929 Chirality : 0.071 0.369 2009 Planarity : 0.007 0.050 2353 Dihedral : 11.569 108.610 5044 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.83 % Favored : 98.05 % Rotamer: Outliers : 0.14 % Allowed : 0.77 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: -0.03 (0.20), residues: 1641 helix: -2.52 (0.43), residues: 89 sheet: -0.11 (0.25), residues: 388 loop : 0.33 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP D 110 HIS 0.007 0.001 HIS B 249 PHE 0.050 0.003 PHE A 351 TYR 0.096 0.003 TYR A 280 ARG 0.006 0.001 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 239 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 211 ASP cc_start: 0.7481 (m-30) cc_final: 0.7067 (m-30) REVERT: C 21 ILE cc_start: 0.4459 (mt) cc_final: 0.4153 (tp) REVERT: C 36 TYR cc_start: 0.6649 (m-80) cc_final: 0.5010 (m-80) REVERT: C 88 CYS cc_start: -0.0651 (t) cc_final: -0.1951 (t) REVERT: C 118 PHE cc_start: 0.3562 (m-80) cc_final: 0.3228 (m-80) REVERT: C 195 GLU cc_start: 0.8171 (tt0) cc_final: 0.7899 (tp30) REVERT: D 29 ILE cc_start: 0.5708 (pt) cc_final: 0.4832 (pt) REVERT: D 83 MET cc_start: 0.8620 (mtm) cc_final: 0.7408 (mtm) REVERT: D 84 ASN cc_start: 0.8884 (m-40) cc_final: 0.8549 (p0) REVERT: D 107 MET cc_start: 0.8307 (mtt) cc_final: 0.7630 (mpp) outliers start: 2 outliers final: 1 residues processed: 241 average time/residue: 0.3243 time to fit residues: 106.1217 Evaluate side-chains 100 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 77 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 GLN B 302 ASN B 320 GLN B 559 HIS C 89 GLN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13249 Z= 0.251 Angle : 0.656 9.000 17998 Z= 0.348 Chirality : 0.046 0.237 2009 Planarity : 0.005 0.052 2353 Dihedral : 6.630 65.325 2057 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.46 % Allowed : 6.56 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.20 (0.20), residues: 1641 helix: -1.87 (0.48), residues: 97 sheet: 0.44 (0.27), residues: 366 loop : 0.30 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 148 HIS 0.007 0.001 HIS A 465 PHE 0.031 0.002 PHE C 118 TYR 0.018 0.002 TYR B 163 ARG 0.007 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 184 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7323 (tp30) REVERT: B 211 ASP cc_start: 0.7599 (m-30) cc_final: 0.7157 (m-30) REVERT: D 27 PHE cc_start: 0.6481 (t80) cc_final: 0.5946 (t80) REVERT: D 83 MET cc_start: 0.8508 (mtm) cc_final: 0.7648 (mtm) REVERT: D 84 ASN cc_start: 0.8972 (m-40) cc_final: 0.8722 (p0) outliers start: 21 outliers final: 9 residues processed: 128 average time/residue: 0.2694 time to fit residues: 50.9773 Evaluate side-chains 89 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 320 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 104 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 100 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 160 optimal weight: 30.0000 chunk 132 optimal weight: 5.9990 chunk 147 optimal weight: 0.0470 chunk 50 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 HIS B 158 ASN B 470 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13249 Z= 0.211 Angle : 0.597 8.646 17998 Z= 0.313 Chirality : 0.045 0.159 2009 Planarity : 0.005 0.063 2353 Dihedral : 5.777 48.404 2055 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.19 % Allowed : 7.39 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.13 (0.21), residues: 1641 helix: -1.78 (0.49), residues: 103 sheet: 0.38 (0.27), residues: 356 loop : 0.25 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 110 HIS 0.009 0.001 HIS A 157 PHE 0.026 0.002 PHE C 139 TYR 0.014 0.001 TYR B 163 ARG 0.005 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.458 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: H 184 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7419 (tp30) REVERT: B 211 ASP cc_start: 0.7671 (m-30) cc_final: 0.7224 (m-30) REVERT: D 84 ASN cc_start: 0.9045 (m-40) cc_final: 0.8796 (p0) outliers start: 17 outliers final: 8 residues processed: 111 average time/residue: 0.2885 time to fit residues: 47.0492 Evaluate side-chains 88 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 9.9990 chunk 111 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 148 optimal weight: 10.0000 chunk 157 optimal weight: 30.0000 chunk 77 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN A 616 ASN B 48 HIS B 88 HIS B 320 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13249 Z= 0.253 Angle : 0.580 7.550 17998 Z= 0.303 Chirality : 0.046 0.167 2009 Planarity : 0.004 0.046 2353 Dihedral : 5.231 29.814 2055 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.67 % Allowed : 7.88 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.11 (0.21), residues: 1641 helix: -1.78 (0.48), residues: 103 sheet: 0.35 (0.27), residues: 348 loop : 0.26 (0.19), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 110 HIS 0.005 0.001 HIS B 469 PHE 0.026 0.002 PHE D 173 TYR 0.013 0.001 TYR B 112 ARG 0.004 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 LYS cc_start: 0.8459 (mttp) cc_final: 0.8179 (pttm) REVERT: H 184 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7446 (tp30) REVERT: B 45 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8109 (ttm) REVERT: B 211 ASP cc_start: 0.7725 (m-30) cc_final: 0.7275 (m-30) REVERT: C 195 GLU cc_start: 0.8178 (tt0) cc_final: 0.7969 (tp30) outliers start: 24 outliers final: 17 residues processed: 116 average time/residue: 0.2978 time to fit residues: 49.6809 Evaluate side-chains 91 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 320 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13249 Z= 0.224 Angle : 0.565 9.222 17998 Z= 0.290 Chirality : 0.046 0.159 2009 Planarity : 0.004 0.044 2353 Dihedral : 5.011 29.256 2055 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.67 % Allowed : 9.07 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.18 (0.21), residues: 1641 helix: -1.39 (0.52), residues: 94 sheet: 0.31 (0.28), residues: 348 loop : 0.28 (0.19), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 614 HIS 0.005 0.001 HIS D 35 PHE 0.026 0.002 PHE C 139 TYR 0.015 0.001 TYR C 92 ARG 0.003 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 LYS cc_start: 0.8479 (mttp) cc_final: 0.8186 (pttm) REVERT: H 184 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7402 (tp30) REVERT: B 45 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8084 (ttm) REVERT: B 211 ASP cc_start: 0.7731 (m-30) cc_final: 0.7290 (m-30) REVERT: C 195 GLU cc_start: 0.8146 (tt0) cc_final: 0.7938 (tp30) outliers start: 24 outliers final: 16 residues processed: 104 average time/residue: 0.2664 time to fit residues: 42.4066 Evaluate side-chains 91 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 20.0000 chunk 141 optimal weight: 30.0000 chunk 31 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 157 optimal weight: 30.0000 chunk 130 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13249 Z= 0.351 Angle : 0.627 9.065 17998 Z= 0.322 Chirality : 0.048 0.158 2009 Planarity : 0.004 0.042 2353 Dihedral : 5.260 26.128 2055 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.39 % Allowed : 9.27 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: -0.02 (0.21), residues: 1641 helix: -1.65 (0.48), residues: 107 sheet: 0.20 (0.27), residues: 360 loop : 0.16 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 148 HIS 0.006 0.001 HIS B 469 PHE 0.023 0.002 PHE C 139 TYR 0.021 0.002 TYR B 112 ARG 0.003 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 184 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7394 (tp30) REVERT: B 45 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8210 (ttm) REVERT: B 211 ASP cc_start: 0.7757 (m-30) cc_final: 0.7330 (m-30) REVERT: B 301 TYR cc_start: 0.7824 (t80) cc_final: 0.7583 (t80) outliers start: 20 outliers final: 16 residues processed: 102 average time/residue: 0.2787 time to fit residues: 42.8680 Evaluate side-chains 91 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 98 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 115 optimal weight: 0.2980 chunk 132 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 157 optimal weight: 40.0000 chunk 98 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13249 Z= 0.227 Angle : 0.570 7.697 17998 Z= 0.292 Chirality : 0.045 0.162 2009 Planarity : 0.004 0.041 2353 Dihedral : 5.013 22.769 2055 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.95 % Allowed : 9.48 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.11 (0.22), residues: 1641 helix: -1.62 (0.50), residues: 100 sheet: 0.26 (0.28), residues: 357 loop : 0.26 (0.20), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 148 HIS 0.003 0.001 HIS B 589 PHE 0.024 0.002 PHE C 118 TYR 0.015 0.001 TYR B 301 ARG 0.003 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 LYS cc_start: 0.8520 (mttp) cc_final: 0.8254 (pttm) REVERT: H 184 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7375 (tp30) REVERT: B 45 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8167 (ttm) REVERT: B 211 ASP cc_start: 0.7756 (m-30) cc_final: 0.7338 (m-30) REVERT: B 282 MET cc_start: 0.8791 (mtm) cc_final: 0.8297 (ptt) REVERT: C 70 ASP cc_start: 0.8269 (m-30) cc_final: 0.7917 (t0) REVERT: C 75 ILE cc_start: 0.2101 (OUTLIER) cc_final: 0.1654 (tt) outliers start: 28 outliers final: 19 residues processed: 103 average time/residue: 0.2534 time to fit residues: 39.0895 Evaluate side-chains 94 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 584 HIS Chi-restraints excluded: chain H residue 197 PHE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 104 PHE Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 0.0670 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 14 optimal weight: 0.0770 chunk 123 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN C 30 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13249 Z= 0.172 Angle : 0.568 9.972 17998 Z= 0.287 Chirality : 0.045 0.166 2009 Planarity : 0.004 0.043 2353 Dihedral : 4.791 22.372 2055 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.60 % Allowed : 10.11 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.14 (0.22), residues: 1641 helix: -1.71 (0.49), residues: 100 sheet: 0.35 (0.28), residues: 345 loop : 0.26 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 148 HIS 0.004 0.001 HIS B 589 PHE 0.023 0.002 PHE A 409 TYR 0.011 0.001 TYR C 36 ARG 0.008 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 SER cc_start: 0.8255 (t) cc_final: 0.8030 (p) REVERT: A 484 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8417 (mm) REVERT: H 184 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7380 (tp30) REVERT: H 215 GLU cc_start: 0.7468 (pm20) cc_final: 0.7263 (pm20) REVERT: B 45 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8110 (ttm) REVERT: B 211 ASP cc_start: 0.7720 (m-30) cc_final: 0.7308 (m-30) REVERT: B 282 MET cc_start: 0.8806 (mtm) cc_final: 0.8336 (ptt) REVERT: C 70 ASP cc_start: 0.8268 (m-30) cc_final: 0.7929 (t0) outliers start: 23 outliers final: 18 residues processed: 101 average time/residue: 0.2399 time to fit residues: 37.0485 Evaluate side-chains 99 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 584 HIS Chi-restraints excluded: chain H residue 197 PHE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 104 PHE Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13249 Z= 0.319 Angle : 0.627 9.833 17998 Z= 0.318 Chirality : 0.047 0.166 2009 Planarity : 0.004 0.045 2353 Dihedral : 5.072 25.543 2055 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.74 % Allowed : 9.90 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.07 (0.22), residues: 1641 helix: -1.53 (0.52), residues: 94 sheet: 0.25 (0.28), residues: 350 loop : 0.20 (0.19), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 452 HIS 0.005 0.001 HIS B 469 PHE 0.029 0.002 PHE B 595 TYR 0.043 0.002 TYR C 36 ARG 0.006 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8476 (mm) REVERT: A 485 LYS cc_start: 0.8525 (mttp) cc_final: 0.8281 (pttm) REVERT: H 184 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7427 (tp30) REVERT: H 198 MET cc_start: 0.7422 (mmm) cc_final: 0.6111 (mtp) REVERT: B 45 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8224 (ttm) REVERT: B 211 ASP cc_start: 0.7739 (m-30) cc_final: 0.7315 (m-30) REVERT: B 282 MET cc_start: 0.8862 (mtm) cc_final: 0.8378 (ptt) REVERT: C 70 ASP cc_start: 0.8222 (m-30) cc_final: 0.7932 (t0) REVERT: D 107 MET cc_start: 0.5955 (mmm) cc_final: 0.5678 (mmm) outliers start: 25 outliers final: 20 residues processed: 99 average time/residue: 0.2502 time to fit residues: 37.6989 Evaluate side-chains 97 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 584 HIS Chi-restraints excluded: chain H residue 197 PHE Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 104 PHE Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 0.4980 chunk 94 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 162 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 79 optimal weight: 0.0980 chunk 102 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13249 Z= 0.167 Angle : 0.568 8.638 17998 Z= 0.288 Chirality : 0.045 0.171 2009 Planarity : 0.004 0.051 2353 Dihedral : 4.780 21.028 2055 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.39 % Allowed : 10.39 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.14 (0.22), residues: 1641 helix: -1.44 (0.52), residues: 93 sheet: 0.23 (0.29), residues: 344 loop : 0.27 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 35 HIS 0.004 0.001 HIS B 559 PHE 0.027 0.002 PHE B 595 TYR 0.023 0.001 TYR C 36 ARG 0.006 0.000 ARG C 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8519 (mp) REVERT: A 485 LYS cc_start: 0.8526 (mttp) cc_final: 0.8222 (pttm) REVERT: H 184 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7379 (tp30) REVERT: B 45 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8158 (ttm) REVERT: B 211 ASP cc_start: 0.7755 (m-30) cc_final: 0.7262 (m-30) REVERT: B 282 MET cc_start: 0.8822 (mtm) cc_final: 0.8348 (ptt) outliers start: 20 outliers final: 16 residues processed: 97 average time/residue: 0.2623 time to fit residues: 38.2908 Evaluate side-chains 94 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 584 HIS Chi-restraints excluded: chain H residue 197 PHE Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 104 PHE Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 30.0000 chunk 39 optimal weight: 0.4980 chunk 119 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.157481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.110877 restraints weight = 24642.601| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 4.29 r_work: 0.3676 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.227 13249 Z= 0.285 Angle : 0.817 59.153 17998 Z= 0.463 Chirality : 0.046 0.429 2009 Planarity : 0.004 0.051 2353 Dihedral : 4.798 20.956 2055 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % Rotamer: Outliers : 1.53 % Allowed : 10.39 % Favored : 88.08 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.83 % 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: 0.13 (0.22), residues: 1641 helix: -1.45 (0.52), residues: 93 sheet: 0.23 (0.29), residues: 344 loop : 0.26 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 35 HIS 0.004 0.001 HIS B 589 PHE 0.023 0.002 PHE B 595 TYR 0.018 0.001 TYR C 36 ARG 0.006 0.000 ARG C 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2686.37 seconds wall clock time: 50 minutes 22.86 seconds (3022.86 seconds total)