Starting phenix.real_space_refine on Fri Jul 3 08:38:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mn8_23918/07_2026/7mn8_23918.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mn8_23918/07_2026/7mn8_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mn8_23918/07_2026/7mn8_23918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mn8_23918/07_2026/7mn8_23918.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mn8_23918/07_2026/7mn8_23918.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mn8_23918/07_2026/7mn8_23918.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mn8_23918/07_2026/7mn8_23918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mn8_23918/07_2026/7mn8_23918.map" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 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 chiralities: 2 Time building chain proxies: 2.38, per 1000 atoms: 0.18 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: 1.29 Conformation dependent library (CDL) restraints added in 571.5 milliseconds 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: 0.35 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: 2.08 Time building geometry restraints manager: 1.71 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 - 17.63: 7577 17.63 - 35.27: 300 35.27 - 52.90: 70 52.90 - 70.53: 27 70.53 - 88.16: 13 Dihedral angle restraints: 7987 sinusoidal: 3230 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 7984 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: 7.200 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: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.610 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.013 0.240 13316 Z= 0.731 Angle : 1.363 15.596 18145 Z= 0.939 Chirality : 0.071 0.369 2009 Planarity : 0.007 0.050 2353 Dihedral : 10.924 88.163 4775 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.001 ARG A 303 TYR 0.096 0.003 TYR A 280 PHE 0.050 0.003 PHE A 351 TRP 0.023 0.004 TRP D 110 HIS 0.007 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.01238 / 0.72 (13249) covalent geometry : angle 1.32449 / 0.93 (17998) SS BOND : bond 0.03771 / 2.74 ( 54) SS BOND : angle 4.28640 / 2.89 ( 108) hydrogen bonds : bond 0.18234 / 11.86 ( 328) hydrogen bonds : angle 8.73276 / 6.09 ( 675) link_ALPHA1-3 : bond 0.05404 / 2.84 ( 1) link_ALPHA1-3 : angle 1.21469 / 0.64 ( 3) link_BETA1-4 : bond 0.04818 / 2.26 ( 4) link_BETA1-4 : angle 1.53193 / 0.87 ( 12) link_NAG-ASN : bond 0.06677 / 3.83 ( 8) link_NAG-ASN : angle 2.34680 / 1.75 ( 24) *********************** 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 : 0.444 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: 0.1200 time to fit residues: 39.5656 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 : 0.325 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 3 GLN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.162800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.119981 restraints weight = 25252.691| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 3.79 r_work: 0.3697 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 13316 Z= 0.166 Angle : 0.683 14.442 18145 Z= 0.362 Chirality : 0.046 0.267 2009 Planarity : 0.005 0.051 2353 Dihedral : 5.215 37.667 1788 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.32 % Allowed : 6.76 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1641 helix: -1.94 (0.47), residues: 98 sheet: 0.45 (0.27), residues: 366 loop : 0.36 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 61 TYR 0.017 0.001 TYR B 163 PHE 0.030 0.002 PHE C 118 TRP 0.021 0.002 TRP C 148 HIS 0.007 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (13249) covalent geometry : angle 0.64865 / 0.35 (17998) SS BOND : bond 0.00453 / 0.30 ( 54) SS BOND : angle 2.71301 / 2.06 ( 108) hydrogen bonds : bond 0.04941 / 3.21 ( 328) hydrogen bonds : angle 6.91266 / 4.84 ( 675) link_ALPHA1-3 : bond 0.01040 / 0.55 ( 1) link_ALPHA1-3 : angle 1.30373 / 0.72 ( 3) link_BETA1-4 : bond 0.00713 / 0.32 ( 4) link_BETA1-4 : angle 1.33454 / 0.73 ( 12) link_NAG-ASN : bond 0.00548 / 0.32 ( 8) link_NAG-ASN : angle 1.58162 / 1.13 ( 24) *********************** 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 133 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 SER cc_start: 0.8014 (t) cc_final: 0.7668 (p) REVERT: A 559 MET cc_start: 0.5048 (mmt) cc_final: 0.4731 (mmt) REVERT: H 184 GLU cc_start: 0.7271 (mm-30) cc_final: 0.7018 (tp30) REVERT: B 211 ASP cc_start: 0.7726 (m-30) cc_final: 0.7220 (m-30) REVERT: B 538 GLN cc_start: 0.7820 (pm20) cc_final: 0.7606 (pm20) REVERT: C 30 ASN cc_start: 0.8870 (m-40) cc_final: 0.8629 (m-40) REVERT: D 27 PHE cc_start: 0.6892 (t80) cc_final: 0.6573 (t80) REVERT: D 83 MET cc_start: 0.8444 (mtm) cc_final: 0.7869 (mtm) REVERT: D 84 ASN cc_start: 0.9171 (m-40) cc_final: 0.8597 (p0) REVERT: D 87 ARG cc_start: 0.8545 (mtt-85) cc_final: 0.8122 (ptp90) outliers start: 19 outliers final: 10 residues processed: 126 average time/residue: 0.1123 time to fit residues: 20.7929 Evaluate side-chains 87 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 3 GLN 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 64 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 HIS B 88 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.153855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.108030 restraints weight = 25053.193| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 4.05 r_work: 0.3536 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13316 Z= 0.199 Angle : 0.653 9.536 18145 Z= 0.339 Chirality : 0.047 0.162 2009 Planarity : 0.005 0.069 2353 Dihedral : 5.183 22.211 1786 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.19 % Allowed : 7.60 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1641 helix: -1.87 (0.48), residues: 103 sheet: 0.39 (0.28), residues: 346 loop : 0.24 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 330 TYR 0.015 0.002 TYR B 163 PHE 0.029 0.002 PHE C 139 TRP 0.016 0.002 TRP D 110 HIS 0.010 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (13249) covalent geometry : angle 0.63601 / 0.33 (17998) SS BOND : bond 0.00436 / 0.36 ( 54) SS BOND : angle 1.92503 / 1.59 ( 108) hydrogen bonds : bond 0.03911 / 2.56 ( 328) hydrogen bonds : angle 6.48814 / 4.52 ( 675) link_ALPHA1-3 : bond 0.00572 / 0.30 ( 1) link_ALPHA1-3 : angle 1.15843 / 0.63 ( 3) link_BETA1-4 : bond 0.00290 / 0.14 ( 4) link_BETA1-4 : angle 0.97207 / 0.54 ( 12) link_NAG-ASN : bond 0.00340 / 0.22 ( 8) link_NAG-ASN : angle 1.39805 / 0.94 ( 24) *********************** 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 118 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8385 (mmm) cc_final: 0.7171 (mmp) REVERT: H 184 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7124 (tp30) REVERT: H 208 TYR cc_start: 0.8213 (m-80) cc_final: 0.7864 (m-80) REVERT: B 45 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7951 (ttm) REVERT: B 211 ASP cc_start: 0.7866 (m-30) cc_final: 0.7413 (m-30) REVERT: C 30 ASN cc_start: 0.8914 (m-40) cc_final: 0.8650 (m-40) REVERT: C 36 TYR cc_start: 0.6246 (m-80) cc_final: 0.5712 (m-80) REVERT: C 143 GLU cc_start: 0.6996 (tt0) cc_final: 0.6780 (tm-30) REVERT: D 84 ASN cc_start: 0.9153 (m-40) cc_final: 0.8860 (p0) REVERT: D 107 MET cc_start: 0.7717 (mtm) cc_final: 0.6572 (mtm) outliers start: 17 outliers final: 9 residues processed: 116 average time/residue: 0.0957 time to fit residues: 16.3353 Evaluate side-chains 91 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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 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 53 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 chunk 77 optimal weight: 0.0670 chunk 103 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 126 optimal weight: 30.0000 chunk 39 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 HIS A 486 HIS B 48 HIS B 158 ASN B 320 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.162888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.111411 restraints weight = 25547.517| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 3.90 r_work: 0.3707 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13316 Z= 0.115 Angle : 0.572 7.928 18145 Z= 0.298 Chirality : 0.045 0.169 2009 Planarity : 0.004 0.054 2353 Dihedral : 4.891 19.666 1786 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.32 % Allowed : 8.58 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.21), residues: 1641 helix: -1.58 (0.50), residues: 97 sheet: 0.37 (0.27), residues: 348 loop : 0.26 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 98 TYR 0.010 0.001 TYR B 163 PHE 0.028 0.002 PHE C 139 TRP 0.012 0.001 TRP D 110 HIS 0.009 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (13249) covalent geometry : angle 0.56260 / 0.29 (17998) SS BOND : bond 0.00256 / 0.21 ( 54) SS BOND : angle 1.31123 / 0.92 ( 108) hydrogen bonds : bond 0.03429 / 2.20 ( 328) hydrogen bonds : angle 6.09688 / 4.25 ( 675) link_ALPHA1-3 : bond 0.00581 / 0.31 ( 1) link_ALPHA1-3 : angle 1.37620 / 0.74 ( 3) link_BETA1-4 : bond 0.00420 / 0.20 ( 4) link_BETA1-4 : angle 0.92900 / 0.50 ( 12) link_NAG-ASN : bond 0.00315 / 0.17 ( 8) link_NAG-ASN : angle 1.16585 / 0.78 ( 24) *********************** 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 115 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9116 (tt) cc_final: 0.8910 (tt) REVERT: A 310 MET cc_start: 0.8209 (pmm) cc_final: 0.7824 (pmm) REVERT: A 485 LYS cc_start: 0.7778 (pttm) cc_final: 0.7267 (mttp) REVERT: A 559 MET cc_start: 0.4764 (mmt) cc_final: 0.4514 (mmt) REVERT: B 45 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7944 (ttm) REVERT: B 211 ASP cc_start: 0.7935 (m-30) cc_final: 0.7432 (m-30) REVERT: C 30 ASN cc_start: 0.9007 (m-40) cc_final: 0.8742 (t0) REVERT: C 36 TYR cc_start: 0.6213 (m-80) cc_final: 0.5775 (m-10) REVERT: D 3 GLN cc_start: 0.8257 (pp30) cc_final: 0.8000 (pp30) REVERT: D 68 PHE cc_start: 0.8349 (m-10) cc_final: 0.7713 (m-10) REVERT: D 84 ASN cc_start: 0.9198 (m-40) cc_final: 0.8989 (p0) REVERT: D 107 MET cc_start: 0.7693 (mtm) cc_final: 0.7414 (mmt) outliers start: 19 outliers final: 11 residues processed: 111 average time/residue: 0.1019 time to fit residues: 16.3770 Evaluate side-chains 92 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 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 320 GLN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain D residue 32 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 126 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN C 79 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.159259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.112653 restraints weight = 24891.181| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 4.70 r_work: 0.3705 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13316 Z= 0.132 Angle : 0.562 9.335 18145 Z= 0.290 Chirality : 0.045 0.160 2009 Planarity : 0.004 0.044 2353 Dihedral : 4.844 22.289 1786 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.67 % Allowed : 8.86 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1641 helix: -1.45 (0.51), residues: 96 sheet: 0.38 (0.28), residues: 348 loop : 0.26 (0.19), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 61 TYR 0.010 0.001 TYR B 590 PHE 0.031 0.002 PHE C 139 TRP 0.009 0.001 TRP D 110 HIS 0.003 0.001 HIS B 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (13249) covalent geometry : angle 0.55448 / 0.29 (17998) SS BOND : bond 0.00388 / 0.30 ( 54) SS BOND : angle 1.13160 / 0.82 ( 108) hydrogen bonds : bond 0.03327 / 2.17 ( 328) hydrogen bonds : angle 5.86011 / 4.07 ( 675) link_ALPHA1-3 : bond 0.00531 / 0.28 ( 1) link_ALPHA1-3 : angle 1.19572 / 0.64 ( 3) link_BETA1-4 : bond 0.00388 / 0.19 ( 4) link_BETA1-4 : angle 0.91174 / 0.50 ( 12) link_NAG-ASN : bond 0.00333 / 0.24 ( 8) link_NAG-ASN : angle 1.29553 / 0.91 ( 24) *********************** 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 109 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.8121 (pmm) cc_final: 0.7825 (pmm) REVERT: A 559 MET cc_start: 0.4724 (mmt) cc_final: 0.4466 (mmt) REVERT: B 45 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8144 (ttm) REVERT: B 211 ASP cc_start: 0.8123 (m-30) cc_final: 0.7540 (m-30) REVERT: B 320 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: C 30 ASN cc_start: 0.9043 (m-40) cc_final: 0.8731 (t0) REVERT: C 36 TYR cc_start: 0.6287 (m-80) cc_final: 0.5895 (m-10) REVERT: C 195 GLU cc_start: 0.8159 (tt0) cc_final: 0.7853 (tp30) REVERT: D 13 GLN cc_start: 0.9232 (pm20) cc_final: 0.8711 (tp40) REVERT: D 84 ASN cc_start: 0.9272 (m-40) cc_final: 0.8994 (p0) REVERT: D 107 MET cc_start: 0.7733 (mtm) cc_final: 0.7377 (mmt) outliers start: 24 outliers final: 15 residues processed: 105 average time/residue: 0.0880 time to fit residues: 14.1437 Evaluate side-chains 95 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 549 CYS 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 320 GLN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 104 PHE 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 77 optimal weight: 0.3980 chunk 57 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN D 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.157818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.111653 restraints weight = 24724.028| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 4.98 r_work: 0.3645 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13316 Z= 0.159 Angle : 0.588 12.044 18145 Z= 0.300 Chirality : 0.046 0.160 2009 Planarity : 0.004 0.043 2353 Dihedral : 4.909 20.014 1786 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.95 % Allowed : 9.07 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.21), residues: 1641 helix: -1.00 (0.54), residues: 88 sheet: 0.38 (0.28), residues: 343 loop : 0.25 (0.19), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 203 TYR 0.014 0.001 TYR B 112 PHE 0.026 0.002 PHE C 139 TRP 0.017 0.001 TRP C 148 HIS 0.004 0.001 HIS B 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (13249) covalent geometry : angle 0.58235 / 0.30 (17998) SS BOND : bond 0.00348 / 0.28 ( 54) SS BOND : angle 1.04346 / 0.72 ( 108) hydrogen bonds : bond 0.03215 / 2.11 ( 328) hydrogen bonds : angle 5.78214 / 4.02 ( 675) link_ALPHA1-3 : bond 0.00767 / 0.40 ( 1) link_ALPHA1-3 : angle 1.28223 / 0.68 ( 3) link_BETA1-4 : bond 0.00359 / 0.17 ( 4) link_BETA1-4 : angle 0.88431 / 0.49 ( 12) link_NAG-ASN : bond 0.00269 / 0.19 ( 8) link_NAG-ASN : angle 1.39153 / 0.95 ( 24) *********************** 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 110 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.8056 (pmm) cc_final: 0.7819 (pmm) REVERT: B 45 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.8017 (ttm) REVERT: B 211 ASP cc_start: 0.7919 (m-30) cc_final: 0.7456 (m-30) REVERT: B 301 TYR cc_start: 0.7252 (t80) cc_final: 0.6993 (t80) REVERT: C 30 ASN cc_start: 0.9066 (m-40) cc_final: 0.8750 (t0) REVERT: C 36 TYR cc_start: 0.6255 (m-80) cc_final: 0.5839 (m-10) REVERT: D 83 MET cc_start: 0.9172 (mpp) cc_final: 0.8845 (mpp) REVERT: D 107 MET cc_start: 0.7701 (mtm) cc_final: 0.6655 (mtm) outliers start: 28 outliers final: 18 residues processed: 105 average time/residue: 0.1103 time to fit residues: 17.3753 Evaluate side-chains 90 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 549 CYS Chi-restraints excluded: chain H residue 185 LYS 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 320 GLN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 61 optimal weight: 2.9990 chunk 161 optimal weight: 40.0000 chunk 142 optimal weight: 30.0000 chunk 82 optimal weight: 0.0170 chunk 9 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN ** D 3 GLN ** 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 = 0.4541 r_free = 0.4541 target = 0.157037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.103169 restraints weight = 25405.534| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 3.91 r_work: 0.3576 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13316 Z= 0.256 Angle : 0.663 8.137 18145 Z= 0.338 Chirality : 0.049 0.179 2009 Planarity : 0.005 0.041 2353 Dihedral : 5.223 22.943 1786 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.67 % Allowed : 9.48 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.21), residues: 1641 helix: -1.69 (0.49), residues: 100 sheet: 0.18 (0.28), residues: 348 loop : 0.21 (0.19), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 61 TYR 0.022 0.002 TYR B 112 PHE 0.024 0.002 PHE D 173 TRP 0.022 0.002 TRP C 148 HIS 0.007 0.001 HIS B 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.26 (13249) covalent geometry : angle 0.65397 / 0.33 (17998) SS BOND : bond 0.00563 / 0.43 ( 54) SS BOND : angle 1.38013 / 0.94 ( 108) hydrogen bonds : bond 0.03372 / 2.23 ( 328) hydrogen bonds : angle 5.83113 / 4.05 ( 675) link_ALPHA1-3 : bond 0.00795 / 0.42 ( 1) link_ALPHA1-3 : angle 1.17371 / 0.62 ( 3) link_BETA1-4 : bond 0.00383 / 0.19 ( 4) link_BETA1-4 : angle 0.96984 / 0.54 ( 12) link_NAG-ASN : bond 0.00430 / 0.29 ( 8) link_NAG-ASN : angle 1.70082 / 1.11 ( 24) *********************** 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 102 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.8100 (pmm) cc_final: 0.7870 (pmm) REVERT: B 527 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7052 (mm-40) REVERT: C 30 ASN cc_start: 0.9047 (m-40) cc_final: 0.8777 (m-40) REVERT: C 70 ASP cc_start: 0.8254 (m-30) cc_final: 0.7671 (t0) outliers start: 24 outliers final: 20 residues processed: 98 average time/residue: 0.0952 time to fit residues: 14.0621 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 : 0.487 ------------------------------------------------------------------------------- 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 342 THR Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 584 HIS Chi-restraints excluded: chain H residue 185 LYS 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 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 527 GLN Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 54 THR 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 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 154 optimal weight: 0.4980 chunk 107 optimal weight: 0.3980 chunk 91 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** 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 = 0.4423 r_free = 0.4423 target = 0.149278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.097371 restraints weight = 25270.948| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.59 r_work: 0.3381 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13316 Z= 0.110 Angle : 0.565 7.282 18145 Z= 0.289 Chirality : 0.045 0.163 2009 Planarity : 0.004 0.041 2353 Dihedral : 4.848 19.668 1786 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.67 % Allowed : 9.83 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.22), residues: 1641 helix: -1.39 (0.53), residues: 93 sheet: 0.24 (0.28), residues: 345 loop : 0.28 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 61 TYR 0.011 0.001 TYR B 441 PHE 0.024 0.002 PHE C 118 TRP 0.015 0.001 TRP C 148 HIS 0.003 0.001 HIS B 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (13249) covalent geometry : angle 0.56034 / 0.29 (17998) SS BOND : bond 0.00259 / 0.20 ( 54) SS BOND : angle 0.88183 / 0.62 ( 108) hydrogen bonds : bond 0.02981 / 1.93 ( 328) hydrogen bonds : angle 5.58104 / 3.87 ( 675) link_ALPHA1-3 : bond 0.00520 / 0.27 ( 1) link_ALPHA1-3 : angle 1.38614 / 0.71 ( 3) link_BETA1-4 : bond 0.00326 / 0.16 ( 4) link_BETA1-4 : angle 0.83577 / 0.46 ( 12) link_NAG-ASN : bond 0.00338 / 0.24 ( 8) link_NAG-ASN : angle 1.27806 / 0.80 ( 24) *********************** 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 108 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.8082 (pmm) cc_final: 0.7866 (pmm) REVERT: A 401 SER cc_start: 0.8205 (t) cc_final: 0.7959 (p) REVERT: A 484 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8563 (mm) REVERT: B 211 ASP cc_start: 0.7940 (m-30) cc_final: 0.7340 (m-30) REVERT: B 282 MET cc_start: 0.8695 (mtm) cc_final: 0.8209 (ptt) REVERT: C 30 ASN cc_start: 0.9032 (m-40) cc_final: 0.8696 (t0) REVERT: C 36 TYR cc_start: 0.6242 (m-80) cc_final: 0.4537 (m-10) REVERT: C 70 ASP cc_start: 0.8319 (m-30) cc_final: 0.7771 (t0) REVERT: D 3 GLN cc_start: 0.8258 (pp30) cc_final: 0.8056 (tm-30) outliers start: 24 outliers final: 17 residues processed: 104 average time/residue: 0.1050 time to fit residues: 16.7143 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 : 0.557 ------------------------------------------------------------------------------- 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 241 THR 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 181 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 54 THR 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 109 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 161 optimal weight: 40.0000 chunk 130 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** 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 = 0.4357 r_free = 0.4357 target = 0.141634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.085891 restraints weight = 25150.660| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.54 r_work: 0.3290 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 13316 Z= 0.275 Angle : 0.693 9.551 18145 Z= 0.353 Chirality : 0.049 0.159 2009 Planarity : 0.005 0.039 2353 Dihedral : 5.301 24.117 1786 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.88 % Allowed : 10.11 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.21), residues: 1641 helix: -1.92 (0.48), residues: 99 sheet: 0.12 (0.28), residues: 353 loop : 0.09 (0.19), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 98 TYR 0.034 0.002 TYR C 36 PHE 0.025 0.002 PHE B 381 TRP 0.016 0.002 TRP B 452 HIS 0.007 0.001 HIS B 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.28 (13249) covalent geometry : angle 0.68355 / 0.35 (17998) SS BOND : bond 0.00584 / 0.46 ( 54) SS BOND : angle 1.34390 / 0.94 ( 108) hydrogen bonds : bond 0.03418 / 2.27 ( 328) hydrogen bonds : angle 5.92659 / 4.10 ( 675) link_ALPHA1-3 : bond 0.00718 / 0.38 ( 1) link_ALPHA1-3 : angle 1.13393 / 0.59 ( 3) link_BETA1-4 : bond 0.00442 / 0.22 ( 4) link_BETA1-4 : angle 1.03273 / 0.59 ( 12) link_NAG-ASN : bond 0.00571 / 0.32 ( 8) link_NAG-ASN : angle 1.98797 / 1.39 ( 24) *********************** 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 109 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.8084 (pmm) cc_final: 0.7882 (pmm) REVERT: C 70 ASP cc_start: 0.8291 (m-30) cc_final: 0.7682 (t0) REVERT: D 83 MET cc_start: 0.9168 (mpp) cc_final: 0.8929 (mpp) outliers start: 27 outliers final: 19 residues processed: 104 average time/residue: 0.0956 time to fit residues: 15.4937 Evaluate side-chains 94 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 241 THR Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 509 CYS 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 266 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 54 THR 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 21 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 64 optimal weight: 0.0470 chunk 158 optimal weight: 40.0000 chunk 59 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 ASN A 347 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.144786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.089460 restraints weight = 25104.631| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.92 r_work: 0.3304 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13316 Z= 0.141 Angle : 0.608 10.812 18145 Z= 0.306 Chirality : 0.046 0.173 2009 Planarity : 0.004 0.055 2353 Dihedral : 5.046 20.434 1786 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.53 % Allowed : 10.74 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.22), residues: 1641 helix: -1.61 (0.52), residues: 93 sheet: 0.16 (0.28), residues: 353 loop : 0.13 (0.19), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 220 TYR 0.018 0.001 TYR C 92 PHE 0.021 0.002 PHE C 118 TRP 0.011 0.001 TRP C 148 HIS 0.003 0.001 HIS B 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (13249) covalent geometry : angle 0.60080 / 0.30 (17998) SS BOND : bond 0.00325 / 0.25 ( 54) SS BOND : angle 1.12319 / 0.90 ( 108) hydrogen bonds : bond 0.03110 / 2.00 ( 328) hydrogen bonds : angle 5.73000 / 3.98 ( 675) link_ALPHA1-3 : bond 0.00578 / 0.30 ( 1) link_ALPHA1-3 : angle 1.39973 / 0.72 ( 3) link_BETA1-4 : bond 0.00278 / 0.13 ( 4) link_BETA1-4 : angle 0.91820 / 0.51 ( 12) link_NAG-ASN : bond 0.00260 / 0.15 ( 8) link_NAG-ASN : angle 1.53400 / 1.02 ( 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 98 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 SER cc_start: 0.8340 (t) cc_final: 0.8005 (p) REVERT: A 484 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8628 (mm) REVERT: H 198 MET cc_start: 0.7358 (mmm) cc_final: 0.6074 (mtp) REVERT: B 211 ASP cc_start: 0.7971 (m-30) cc_final: 0.7336 (m-30) REVERT: B 282 MET cc_start: 0.8774 (mtm) cc_final: 0.8188 (ptt) REVERT: C 70 ASP cc_start: 0.8285 (m-30) cc_final: 0.7710 (t0) outliers start: 22 outliers final: 19 residues processed: 95 average time/residue: 0.0965 time to fit residues: 14.3524 Evaluate side-chains 93 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 241 THR Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 509 CYS 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 181 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 54 THR 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 67 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 110 optimal weight: 0.1980 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 82 GLN ** 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 = 0.4393 r_free = 0.4393 target = 0.145163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.090357 restraints weight = 24946.908| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 4.00 r_work: 0.3339 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13316 Z= 0.133 Angle : 0.597 9.394 18145 Z= 0.300 Chirality : 0.046 0.168 2009 Planarity : 0.004 0.070 2353 Dihedral : 4.952 21.905 1786 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.46 % Allowed : 11.02 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.22), residues: 1641 helix: -1.54 (0.52), residues: 93 sheet: 0.15 (0.28), residues: 348 loop : 0.17 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.014 0.001 TYR C 92 PHE 0.019 0.002 PHE C 118 TRP 0.017 0.001 TRP C 148 HIS 0.004 0.001 HIS B 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (13249) covalent geometry : angle 0.59089 / 0.30 (17998) SS BOND : bond 0.00303 / 0.23 ( 54) SS BOND : angle 1.00640 / 0.78 ( 108) hydrogen bonds : bond 0.03008 / 1.95 ( 328) hydrogen bonds : angle 5.67391 / 3.94 ( 675) link_ALPHA1-3 : bond 0.00703 / 0.37 ( 1) link_ALPHA1-3 : angle 1.41076 / 0.73 ( 3) link_BETA1-4 : bond 0.00376 / 0.18 ( 4) link_BETA1-4 : angle 0.92800 / 0.52 ( 12) link_NAG-ASN : bond 0.00235 / 0.13 ( 8) link_NAG-ASN : angle 1.54006 / 1.05 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3226.74 seconds wall clock time: 55 minutes 56.69 seconds (3356.69 seconds total)