Starting phenix.real_space_refine on Thu Jul 31 05:46:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mn8_23918/07_2025/7mn8_23918.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mn8_23918/07_2025/7mn8_23918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mn8_23918/07_2025/7mn8_23918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mn8_23918/07_2025/7mn8_23918.map" model { file = "/net/cci-nas-00/data/ceres_data/7mn8_23918/07_2025/7mn8_23918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mn8_23918/07_2025/7mn8_23918.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 8055 2.51 5 N 2268 2.21 5 O 2494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12947 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4614 Classifications: {'peptide': 599} Link IDs: {'PTRANS': 39, 'TRANS': 559} Chain breaks: 1 Chain: "H" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain breaks: 1 Chain: "B" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4476 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 540} Chain breaks: 3 Chain: "C" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1649 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "D" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1649 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.40, per 1000 atoms: 0.73 Number of scatterers: 12947 At special positions: 0 Unit cell: (106.752, 126.768, 133.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 2494 8.00 N 2268 7.00 C 8055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 56 " distance=2.03 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 218 " distance=2.02 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 235 " distance=2.04 Simple disulfide: pdb=" SG CYS A 231 " - pdb=" SG CYS A 243 " distance=2.02 Simple disulfide: pdb=" SG CYS A 246 " - pdb=" SG CYS A 255 " distance=2.10 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 286 " distance=2.02 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 354 " distance=2.04 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 493 " distance=2.02 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 509 " distance=2.02 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 517 " distance=2.02 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 533 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 573 " distance=2.01 Simple disulfide: pdb=" SG CYS A 576 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 610 " distance=2.04 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 621 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 629 " distance=2.06 Simple disulfide: pdb=" SG CYS H 182 " - pdb=" SG CYS H 196 " distance=2.07 Simple disulfide: pdb=" SG CYS H 190 " - pdb=" SG CYS H 210 " distance=2.02 Simple disulfide: pdb=" SG CYS H 212 " - pdb=" SG CYS H 221 " distance=2.02 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.05 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.05 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.04 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 295 " distance=2.27 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=2.05 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 331 " distance=2.06 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 338 " distance=2.06 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 367 " distance=2.02 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 504 " distance=2.04 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 520 " distance=2.02 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 544 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.02 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.05 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 623 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.11 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A1101 " - " ASN A 408 " " NAG A1102 " - " ASN A 353 " " NAG A1103 " - " ASN A 414 " " NAG B1501 " - " ASN B 530 " " NAG B1502 " - " ASN B 187 " " NAG E 1 " - " ASN A 469 " " NAG F 1 " - " ASN A 250 " " NAG G 1 " - " ASN B 259 " Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.7 seconds 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 37 sheets defined 14.3% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.076A pdb=" N TRP A 79 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 222 through 226 removed outlier: 4.148A pdb=" N CYS A 226 " --> pdb=" O PRO A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 380 through 390 removed outlier: 3.981A pdb=" N THR A 389 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 423 through 426 Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'H' and resid 185 through 190 removed outlier: 3.507A pdb=" N CYS H 190 " --> pdb=" O LYS H 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 51 removed outlier: 4.652A pdb=" N LEU B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASP B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 77 removed outlier: 4.227A pdb=" N ASP B 76 " --> pdb=" O PHE B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.604A pdb=" N ILE B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 396 through 403 removed outlier: 4.322A pdb=" N THR B 402 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 481 through 485 Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 183 through 188 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 208 through 211 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 7.206A pdb=" N CYS A 29 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 7.184A pdb=" N VAL A 38 " --> pdb=" O CYS H 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.372A pdb=" N LEU A 63 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA A 90 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 65 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 87 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N MET A 120 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 89 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE A 115 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR A 148 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE A 117 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLU A 150 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 119 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL A 147 " --> pdb=" O VAL A 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 235 removed outlier: 3.562A pdb=" N ALA A 245 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLY A 234 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N CYS A 243 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 249 through 251 Processing sheet with id=AA6, first strand: chain 'A' and resid 263 through 266 removed outlier: 3.530A pdb=" N GLN A 271 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 280 through 282 Processing sheet with id=AA8, first strand: chain 'A' and resid 300 through 302 removed outlier: 3.610A pdb=" N VAL A 295 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 363 removed outlier: 4.600A pdb=" N PHE A 428 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TYR A 455 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A 430 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N SER A 457 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE A 432 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 523 through 525 Processing sheet with id=AB3, first strand: chain 'A' and resid 542 through 545 Processing sheet with id=AB4, first strand: chain 'A' and resid 579 through 581 Processing sheet with id=AB5, first strand: chain 'A' and resid 591 through 595 removed outlier: 5.486A pdb=" N HIS A 591 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LYS A 602 " --> pdb=" O HIS A 591 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'B' and resid 25 through 27 removed outlier: 6.823A pdb=" N CYS B 26 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.804A pdb=" N TYR B 112 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU B 154 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 114 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N GLN B 156 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 116 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 153 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 259 through 260 Processing sheet with id=AC1, first strand: chain 'B' and resid 272 through 275 Processing sheet with id=AC2, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AC3, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AC4, first strand: chain 'B' and resid 342 through 343 removed outlier: 6.656A pdb=" N CYS B 342 " --> pdb=" O PHE B 371 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 374 through 376 removed outlier: 5.606A pdb=" N LEU B 465 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N THR B 496 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE B 468 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 553 through 556 Processing sheet with id=AC7, first strand: chain 'B' and resid 590 through 592 Processing sheet with id=AC8, first strand: chain 'B' and resid 615 through 617 Processing sheet with id=AC9, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.527A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.527A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 114 through 118 removed outlier: 3.560A pdb=" N ASN C 138 " --> pdb=" O TYR C 173 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 153 through 154 removed outlier: 4.093A pdb=" N ALA C 193 " --> pdb=" O LYS C 149 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.273A pdb=" N GLY D 10 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR D 33 " --> pdb=" O TRP D 99 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.273A pdb=" N GLY D 10 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 127 through 131 Processing sheet with id=AD9, first strand: chain 'D' and resid 127 through 131 removed outlier: 5.120A pdb=" N ALA D 144 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL D 191 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY D 146 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL D 189 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU D 148 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER D 187 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS D 150 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU D 185 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER D 184 " --> pdb=" O ALA D 175 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA D 175 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 186 " --> pdb=" O PHE D 173 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 158 through 161 340 hydrogen bonds defined for protein. 675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.83 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4016 1.33 - 1.46: 3408 1.46 - 1.60: 5675 1.60 - 1.73: 1 1.73 - 1.87: 149 Bond restraints: 13249 Sorted by residual: bond pdb=" N PRO A 540 " pdb=" CD PRO A 540 " ideal model delta sigma weight residual 1.473 1.583 -0.110 1.40e-02 5.10e+03 6.19e+01 bond pdb=" N PRO H 205 " pdb=" CD PRO H 205 " ideal model delta sigma weight residual 1.473 1.549 -0.076 1.40e-02 5.10e+03 2.93e+01 bond pdb=" N PRO D 209 " pdb=" CD PRO D 209 " ideal model delta sigma weight residual 1.473 1.544 -0.071 1.40e-02 5.10e+03 2.55e+01 bond pdb=" N PRO B 378 " pdb=" CD PRO B 378 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO C 8 " pdb=" CD PRO C 8 " ideal model delta sigma weight residual 1.474 1.419 0.055 1.40e-02 5.10e+03 1.54e+01 ... (remaining 13244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 15741 1.81 - 3.63: 1876 3.63 - 5.44: 256 5.44 - 7.26: 73 7.26 - 9.07: 52 Bond angle restraints: 17998 Sorted by residual: angle pdb=" C PRO A 403 " pdb=" N PRO A 404 " pdb=" CA PRO A 404 " ideal model delta sigma weight residual 119.56 128.53 -8.97 1.02e+00 9.61e-01 7.73e+01 angle pdb=" C ASP A 501 " pdb=" N PRO A 502 " pdb=" CA PRO A 502 " ideal model delta sigma weight residual 119.82 128.32 -8.50 9.80e-01 1.04e+00 7.52e+01 angle pdb=" C GLY B 522 " pdb=" N PRO B 523 " pdb=" CA PRO B 523 " ideal model delta sigma weight residual 119.56 127.98 -8.42 1.01e+00 9.80e-01 6.95e+01 angle pdb=" C LEU A 99 " pdb=" N PRO A 100 " pdb=" CA PRO A 100 " ideal model delta sigma weight residual 119.56 127.97 -8.41 1.01e+00 9.80e-01 6.93e+01 angle pdb=" C GLY A 511 " pdb=" N PRO A 512 " pdb=" CA PRO A 512 " ideal model delta sigma weight residual 119.56 127.84 -8.28 1.01e+00 9.80e-01 6.72e+01 ... (remaining 17993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 7940 21.72 - 43.44: 232 43.44 - 65.17: 56 65.17 - 86.89: 22 86.89 - 108.61: 6 Dihedral angle restraints: 8256 sinusoidal: 3499 harmonic: 4757 Sorted by residual: dihedral pdb=" CB CYS A 290 " pdb=" SG CYS A 290 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 168.21 -75.21 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS B 475 " pdb=" SG CYS B 475 " pdb=" SG CYS B 504 " pdb=" CB CYS B 504 " ideal model delta sinusoidal sigma weight residual 93.00 150.22 -57.22 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 36.01 56.99 1 1.00e+01 1.00e-02 4.37e+01 ... (remaining 8253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1518 0.074 - 0.148: 394 0.148 - 0.221: 70 0.221 - 0.295: 18 0.295 - 0.369: 9 Chirality restraints: 2009 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.72e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.38e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 9.67e+00 ... (remaining 2006 not shown) Planarity restraints: 2361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 280 " 0.096 2.00e-02 2.50e+03 5.00e-02 5.01e+01 pdb=" CG TYR A 280 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR A 280 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR A 280 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 280 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 280 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 280 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 280 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1103 " 0.063 2.00e-02 2.50e+03 5.04e-02 3.18e+01 pdb=" C7 NAG A1103 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG A1103 " 0.049 2.00e-02 2.50e+03 pdb=" N2 NAG A1103 " -0.076 2.00e-02 2.50e+03 pdb=" O7 NAG A1103 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 274 " -0.061 2.00e-02 2.50e+03 3.72e-02 2.77e+01 pdb=" CG TYR B 274 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR B 274 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 274 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR B 274 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR B 274 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 274 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 274 " -0.060 2.00e-02 2.50e+03 ... (remaining 2358 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4342 2.85 - 3.36: 11859 3.36 - 3.88: 22799 3.88 - 4.39: 26715 4.39 - 4.90: 43470 Nonbonded interactions: 109185 Sorted by model distance: nonbonded pdb=" O TYR C 186 " pdb=" OH TYR C 192 " model vdw 2.340 3.040 nonbonded pdb=" OG1 THR D 32 " pdb=" O TRP D 99 " model vdw 2.387 3.040 nonbonded pdb=" NH1 ARG B 552 " pdb=" OG1 THR B 575 " model vdw 2.408 3.120 nonbonded pdb=" OD1 ASP B 30 " pdb=" NZ LYS B 32 " model vdw 2.409 3.120 nonbonded pdb=" OD1 ASP A 581 " pdb=" NZ LYS A 602 " model vdw 2.410 3.120 ... (remaining 109180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.060 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 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 : 11.569 108.610 5044 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.83 % Favored : 98.05 % Rotamer: Outliers : 0.14 % Allowed : 0.77 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1641 helix: -2.52 (0.43), residues: 89 sheet: -0.11 (0.25), residues: 388 loop : 0.33 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP D 110 HIS 0.007 0.001 HIS B 249 PHE 0.050 0.003 PHE A 351 TYR 0.096 0.003 TYR A 280 ARG 0.006 0.001 ARG A 303 Details of bonding type rmsd link_NAG-ASN : bond 0.06677 ( 8) link_NAG-ASN : angle 2.34680 ( 24) link_BETA1-4 : bond 0.04818 ( 4) link_BETA1-4 : angle 1.53193 ( 12) link_ALPHA1-3 : bond 0.05404 ( 1) link_ALPHA1-3 : angle 1.21469 ( 3) hydrogen bonds : bond 0.18234 ( 328) hydrogen bonds : angle 8.73276 ( 675) SS BOND : bond 0.03771 ( 54) SS BOND : angle 4.28640 ( 108) covalent geometry : bond 0.01238 (13249) covalent geometry : angle 1.32449 (17998) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 239 time to evaluate : 1.434 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: 0.3058 time to fit residues: 100.1471 Evaluate side-chains 100 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 77 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.162082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.110570 restraints weight = 25273.417| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.87 r_work: 0.3667 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13316 Z= 0.162 Angle : 0.684 13.086 18145 Z= 0.359 Chirality : 0.047 0.259 2009 Planarity : 0.005 0.052 2353 Dihedral : 6.663 65.907 2057 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.39 % Allowed : 6.56 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.20), residues: 1641 helix: -1.87 (0.48), residues: 97 sheet: 0.43 (0.27), residues: 366 loop : 0.30 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 148 HIS 0.007 0.001 HIS A 465 PHE 0.030 0.002 PHE C 118 TYR 0.018 0.002 TYR B 590 ARG 0.006 0.001 ARG C 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 8) link_NAG-ASN : angle 1.53345 ( 24) link_BETA1-4 : bond 0.00358 ( 4) link_BETA1-4 : angle 1.56301 ( 12) link_ALPHA1-3 : bond 0.00990 ( 1) link_ALPHA1-3 : angle 2.37974 ( 3) hydrogen bonds : bond 0.04468 ( 328) hydrogen bonds : angle 6.85436 ( 675) SS BOND : bond 0.00485 ( 54) SS BOND : angle 2.51870 ( 108) covalent geometry : bond 0.00374 (13249) covalent geometry : angle 0.65442 (17998) *********************** 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 135 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.5121 (mmt) cc_final: 0.4809 (mmt) REVERT: B 211 ASP cc_start: 0.7787 (m-30) cc_final: 0.7271 (m-30) REVERT: B 538 GLN cc_start: 0.7932 (pm20) cc_final: 0.7667 (pm20) REVERT: C 30 ASN cc_start: 0.8891 (m-40) cc_final: 0.8646 (m-40) REVERT: D 27 PHE cc_start: 0.6850 (t80) cc_final: 0.6321 (t80) REVERT: D 83 MET cc_start: 0.8395 (mtm) cc_final: 0.7710 (mtm) REVERT: D 84 ASN cc_start: 0.9140 (m-40) cc_final: 0.8581 (p0) REVERT: D 98 ARG cc_start: 0.7714 (mtm180) cc_final: 0.7494 (ttm170) outliers start: 20 outliers final: 9 residues processed: 126 average time/residue: 0.2861 time to fit residues: 52.9479 Evaluate side-chains 88 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 320 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 104 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 105 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS B 88 HIS B 260 HIS B 470 HIS C 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.150311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.104263 restraints weight = 24961.804| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 3.86 r_work: 0.3501 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 13316 Z= 0.306 Angle : 0.748 8.729 18145 Z= 0.386 Chirality : 0.051 0.189 2009 Planarity : 0.005 0.057 2353 Dihedral : 6.199 44.924 2055 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.02 % Allowed : 7.53 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1641 helix: -2.07 (0.45), residues: 103 sheet: 0.31 (0.28), residues: 348 loop : 0.12 (0.19), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 452 HIS 0.015 0.002 HIS A 157 PHE 0.027 0.002 PHE D 68 TYR 0.021 0.002 TYR B 112 ARG 0.005 0.001 ARG B 330 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 8) link_NAG-ASN : angle 1.66223 ( 24) link_BETA1-4 : bond 0.00417 ( 4) link_BETA1-4 : angle 1.07676 ( 12) link_ALPHA1-3 : bond 0.00853 ( 1) link_ALPHA1-3 : angle 2.00740 ( 3) hydrogen bonds : bond 0.04186 ( 328) hydrogen bonds : angle 6.57626 ( 675) SS BOND : bond 0.00612 ( 54) SS BOND : angle 2.10083 ( 108) covalent geometry : bond 0.00725 (13249) covalent geometry : angle 0.72951 (17998) *********************** 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 128 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 208 TYR cc_start: 0.8603 (m-80) cc_final: 0.7979 (m-80) REVERT: B 45 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8170 (ttt) REVERT: B 211 ASP cc_start: 0.8111 (m-30) cc_final: 0.7563 (m-30) REVERT: C 30 ASN cc_start: 0.8950 (m-40) cc_final: 0.8670 (m-40) REVERT: C 143 GLU cc_start: 0.7070 (tt0) cc_final: 0.6814 (tm-30) REVERT: D 27 PHE cc_start: 0.6824 (t80) cc_final: 0.5899 (t80) REVERT: D 84 ASN cc_start: 0.9189 (m-40) cc_final: 0.8904 (p0) outliers start: 29 outliers final: 14 residues processed: 125 average time/residue: 0.2634 time to fit residues: 48.3188 Evaluate side-chains 96 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 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 249 HIS Chi-restraints excluded: chain B residue 260 HIS 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 Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 54 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 153 optimal weight: 40.0000 chunk 72 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 HIS A 616 ASN B 320 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.158153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.105631 restraints weight = 24714.989| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 3.56 r_work: 0.3654 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3778 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= 0.136 Angle : 0.590 10.086 18145 Z= 0.304 Chirality : 0.046 0.200 2009 Planarity : 0.004 0.047 2353 Dihedral : 5.519 33.268 2055 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.84 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1641 helix: -2.06 (0.46), residues: 108 sheet: 0.26 (0.27), residues: 346 loop : 0.17 (0.19), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 110 HIS 0.003 0.001 HIS B 260 PHE 0.024 0.002 PHE C 139 TYR 0.017 0.001 TYR C 49 ARG 0.004 0.000 ARG C 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 8) link_NAG-ASN : angle 1.30367 ( 24) link_BETA1-4 : bond 0.00379 ( 4) link_BETA1-4 : angle 1.02640 ( 12) link_ALPHA1-3 : bond 0.01025 ( 1) link_ALPHA1-3 : angle 2.30388 ( 3) hydrogen bonds : bond 0.03473 ( 328) hydrogen bonds : angle 6.11875 ( 675) SS BOND : bond 0.00325 ( 54) SS BOND : angle 1.38337 ( 108) covalent geometry : bond 0.00318 (13249) covalent geometry : angle 0.57919 (17998) *********************** 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 117 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 208 TYR cc_start: 0.8558 (m-80) cc_final: 0.8218 (m-80) REVERT: B 45 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8038 (ttt) REVERT: B 211 ASP cc_start: 0.8082 (m-30) cc_final: 0.7542 (m-30) REVERT: C 30 ASN cc_start: 0.9025 (m-40) cc_final: 0.8722 (t0) REVERT: C 143 GLU cc_start: 0.7068 (tt0) cc_final: 0.6807 (tm-30) REVERT: D 27 PHE cc_start: 0.6747 (t80) cc_final: 0.6404 (t80) REVERT: D 28 ASN cc_start: 0.7894 (t0) cc_final: 0.7592 (t0) REVERT: D 84 ASN cc_start: 0.9210 (m-40) cc_final: 0.8971 (p0) REVERT: D 87 ARG cc_start: 0.8885 (ptp-170) cc_final: 0.8458 (ptp-110) outliers start: 24 outliers final: 15 residues processed: 114 average time/residue: 0.2905 time to fit residues: 49.0644 Evaluate side-chains 93 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 1.713 ------------------------------------------------------------------------------- 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 183 CYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain 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 71 PHE Chi-restraints excluded: chain D residue 54 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 36 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 271 GLN A 405 HIS A 486 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.157520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.102018 restraints weight = 25596.449| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.87 r_work: 0.3545 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 13316 Z= 0.302 Angle : 0.737 10.539 18145 Z= 0.376 Chirality : 0.051 0.166 2009 Planarity : 0.005 0.045 2353 Dihedral : 5.855 38.958 2055 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.30 % Allowed : 9.14 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1641 helix: -2.02 (0.47), residues: 100 sheet: 0.14 (0.28), residues: 348 loop : 0.03 (0.19), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 452 HIS 0.008 0.001 HIS B 469 PHE 0.028 0.002 PHE B 381 TYR 0.021 0.002 TYR B 112 ARG 0.006 0.001 ARG C 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 8) link_NAG-ASN : angle 1.83065 ( 24) link_BETA1-4 : bond 0.00635 ( 4) link_BETA1-4 : angle 1.12481 ( 12) link_ALPHA1-3 : bond 0.01468 ( 1) link_ALPHA1-3 : angle 2.19726 ( 3) hydrogen bonds : bond 0.03764 ( 328) hydrogen bonds : angle 6.13358 ( 675) SS BOND : bond 0.00637 ( 54) SS BOND : angle 2.04395 ( 108) covalent geometry : bond 0.00713 (13249) covalent geometry : angle 0.71854 (17998) *********************** 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 114 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.4881 (mmt) cc_final: 0.4656 (mmt) REVERT: B 45 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8152 (ttm) REVERT: B 320 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7941 (mp10) REVERT: C 30 ASN cc_start: 0.9060 (m-40) cc_final: 0.8726 (m-40) REVERT: D 28 ASN cc_start: 0.7796 (t0) cc_final: 0.7593 (t0) REVERT: D 83 MET cc_start: 0.9206 (mpp) cc_final: 0.9003 (mmp) REVERT: D 87 ARG cc_start: 0.8900 (ptp-170) cc_final: 0.8448 (ptp-110) outliers start: 33 outliers final: 23 residues processed: 109 average time/residue: 0.3634 time to fit residues: 61.3424 Evaluate side-chains 95 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 231 CYS 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 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 268 CYS 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 33 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 96 CYS 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 57 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 160 optimal weight: 0.0770 chunk 108 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** 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 = 0.4566 r_free = 0.4566 target = 0.159028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.105274 restraints weight = 25393.757| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 4.13 r_work: 0.3612 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13316 Z= 0.122 Angle : 0.591 10.448 18145 Z= 0.302 Chirality : 0.046 0.167 2009 Planarity : 0.004 0.044 2353 Dihedral : 5.269 35.082 2055 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.88 % Allowed : 9.69 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1641 helix: -1.77 (0.49), residues: 100 sheet: 0.23 (0.28), residues: 345 loop : 0.15 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 148 HIS 0.003 0.001 HIS B 589 PHE 0.023 0.002 PHE C 139 TYR 0.013 0.001 TYR C 49 ARG 0.004 0.000 ARG C 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 8) link_NAG-ASN : angle 1.34909 ( 24) link_BETA1-4 : bond 0.00403 ( 4) link_BETA1-4 : angle 0.98810 ( 12) link_ALPHA1-3 : bond 0.01176 ( 1) link_ALPHA1-3 : angle 2.24233 ( 3) hydrogen bonds : bond 0.03053 ( 328) hydrogen bonds : angle 5.79304 ( 675) SS BOND : bond 0.00297 ( 54) SS BOND : angle 1.58608 ( 108) covalent geometry : bond 0.00285 (13249) covalent geometry : angle 0.57713 (17998) *********************** 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 112 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.4878 (mmt) cc_final: 0.4671 (mmt) REVERT: B 45 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7949 (ttm) REVERT: B 211 ASP cc_start: 0.7851 (m-30) cc_final: 0.7345 (m-30) REVERT: C 30 ASN cc_start: 0.9040 (m-40) cc_final: 0.8690 (t0) REVERT: D 13 GLN cc_start: 0.9359 (pm20) cc_final: 0.8778 (tp40) REVERT: D 87 ARG cc_start: 0.8897 (ptp-170) cc_final: 0.8427 (ptp-110) outliers start: 27 outliers final: 20 residues processed: 108 average time/residue: 0.2353 time to fit residues: 38.7876 Evaluate side-chains 92 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 231 CYS Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 584 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 308 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 104 PHE Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 158 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 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 = 0.4380 r_free = 0.4380 target = 0.143593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.087659 restraints weight = 24889.763| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.75 r_work: 0.3298 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13316 Z= 0.206 Angle : 0.643 9.439 18145 Z= 0.327 Chirality : 0.047 0.170 2009 Planarity : 0.004 0.041 2353 Dihedral : 5.378 35.134 2055 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.23 % Allowed : 10.32 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1641 helix: -1.55 (0.51), residues: 94 sheet: 0.22 (0.29), residues: 343 loop : 0.10 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 148 HIS 0.005 0.001 HIS B 469 PHE 0.030 0.002 PHE C 118 TYR 0.014 0.002 TYR B 112 ARG 0.003 0.000 ARG B 536 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 8) link_NAG-ASN : angle 1.70888 ( 24) link_BETA1-4 : bond 0.00380 ( 4) link_BETA1-4 : angle 1.00776 ( 12) link_ALPHA1-3 : bond 0.01175 ( 1) link_ALPHA1-3 : angle 1.78644 ( 3) hydrogen bonds : bond 0.03307 ( 328) hydrogen bonds : angle 5.79017 ( 675) SS BOND : bond 0.00452 ( 54) SS BOND : angle 1.64084 ( 108) covalent geometry : bond 0.00489 (13249) covalent geometry : angle 0.62898 (17998) *********************** 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 106 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8327 (ttm) REVERT: C 30 ASN cc_start: 0.9022 (m-40) cc_final: 0.8747 (m-40) REVERT: C 55 TYR cc_start: 0.8193 (t80) cc_final: 0.7961 (t80) REVERT: C 70 ASP cc_start: 0.8216 (m-30) cc_final: 0.7595 (t0) REVERT: D 13 GLN cc_start: 0.9401 (pm20) cc_final: 0.8854 (tp40) REVERT: D 87 ARG cc_start: 0.8918 (ptp-170) cc_final: 0.8459 (ptp-110) outliers start: 32 outliers final: 28 residues processed: 100 average time/residue: 0.2635 time to fit residues: 39.8666 Evaluate side-chains 100 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 468 LEU 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 45 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 VAL 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 33 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 104 PHE Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 153 optimal weight: 50.0000 chunk 47 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN B 471 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 = 0.4382 r_free = 0.4382 target = 0.145850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.091346 restraints weight = 25191.479| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.72 r_work: 0.3308 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13316 Z= 0.169 Angle : 0.613 10.908 18145 Z= 0.312 Chirality : 0.046 0.170 2009 Planarity : 0.004 0.041 2353 Dihedral : 5.273 34.127 2055 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.30 % Allowed : 10.67 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1641 helix: -1.52 (0.52), residues: 94 sheet: 0.26 (0.29), residues: 341 loop : 0.11 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 452 HIS 0.003 0.001 HIS A 405 PHE 0.027 0.002 PHE C 118 TYR 0.012 0.001 TYR B 112 ARG 0.002 0.000 ARG H 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 8) link_NAG-ASN : angle 1.65985 ( 24) link_BETA1-4 : bond 0.00330 ( 4) link_BETA1-4 : angle 0.97286 ( 12) link_ALPHA1-3 : bond 0.01104 ( 1) link_ALPHA1-3 : angle 1.85937 ( 3) hydrogen bonds : bond 0.03169 ( 328) hydrogen bonds : angle 5.72799 ( 675) SS BOND : bond 0.00400 ( 54) SS BOND : angle 1.51523 ( 108) covalent geometry : bond 0.00402 (13249) covalent geometry : angle 0.60045 (17998) *********************** 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 107 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8249 (ttm) REVERT: C 30 ASN cc_start: 0.8985 (m-40) cc_final: 0.8642 (t0) REVERT: C 70 ASP cc_start: 0.8204 (m-30) cc_final: 0.7604 (t0) REVERT: D 13 GLN cc_start: 0.9410 (pm20) cc_final: 0.8866 (tp40) REVERT: D 87 ARG cc_start: 0.8922 (ptp-170) cc_final: 0.8462 (ptp-110) outliers start: 33 outliers final: 28 residues processed: 101 average time/residue: 0.2356 time to fit residues: 35.8355 Evaluate side-chains 101 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 231 CYS Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 468 LEU 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 45 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 320 GLN Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 104 PHE Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 79 optimal weight: 0.9980 chunk 153 optimal weight: 30.0000 chunk 95 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 161 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN B 471 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 = 0.4380 r_free = 0.4380 target = 0.143362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.092923 restraints weight = 24827.064| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 4.06 r_work: 0.3327 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4830 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= 0.137 Angle : 0.599 11.302 18145 Z= 0.304 Chirality : 0.046 0.171 2009 Planarity : 0.004 0.040 2353 Dihedral : 5.162 33.073 2055 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.23 % Allowed : 10.81 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1641 helix: -1.46 (0.52), residues: 94 sheet: 0.26 (0.29), residues: 341 loop : 0.12 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 148 HIS 0.003 0.001 HIS B 589 PHE 0.023 0.002 PHE C 118 TYR 0.012 0.001 TYR C 49 ARG 0.004 0.000 ARG C 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 8) link_NAG-ASN : angle 1.60947 ( 24) link_BETA1-4 : bond 0.00371 ( 4) link_BETA1-4 : angle 1.01124 ( 12) link_ALPHA1-3 : bond 0.00994 ( 1) link_ALPHA1-3 : angle 1.72930 ( 3) hydrogen bonds : bond 0.03032 ( 328) hydrogen bonds : angle 5.67500 ( 675) SS BOND : bond 0.00335 ( 54) SS BOND : angle 1.51167 ( 108) covalent geometry : bond 0.00325 (13249) covalent geometry : angle 0.58564 (17998) *********************** 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 106 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 SER cc_start: 0.8308 (t) cc_final: 0.7997 (p) REVERT: B 45 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8302 (ttm) REVERT: B 320 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: C 24 ARG cc_start: 0.7709 (tmt170) cc_final: 0.7406 (ttp80) REVERT: C 30 ASN cc_start: 0.9001 (m-40) cc_final: 0.8750 (m-40) REVERT: C 70 ASP cc_start: 0.8192 (m-30) cc_final: 0.7667 (t0) REVERT: D 13 GLN cc_start: 0.9414 (pm20) cc_final: 0.8873 (tp40) REVERT: D 87 ARG cc_start: 0.8919 (ptp-170) cc_final: 0.8463 (ptp-110) outliers start: 32 outliers final: 29 residues processed: 100 average time/residue: 0.2511 time to fit residues: 37.8178 Evaluate side-chains 102 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 71 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 468 LEU 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 45 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 320 GLN Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 104 PHE Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 118 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 chunk 154 optimal weight: 0.0370 chunk 159 optimal weight: 7.9990 chunk 141 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 96 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN B 471 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 = 0.4386 r_free = 0.4386 target = 0.143136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.098386 restraints weight = 24342.475| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.69 r_work: 0.3448 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13316 Z= 0.108 Angle : 0.596 11.895 18145 Z= 0.300 Chirality : 0.045 0.171 2009 Planarity : 0.004 0.040 2353 Dihedral : 5.013 31.879 2055 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.81 % Allowed : 11.44 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.22), residues: 1641 helix: -1.65 (0.51), residues: 94 sheet: 0.29 (0.29), residues: 343 loop : 0.16 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 148 HIS 0.004 0.001 HIS B 470 PHE 0.021 0.001 PHE D 173 TYR 0.017 0.001 TYR C 92 ARG 0.002 0.000 ARG C 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 8) link_NAG-ASN : angle 1.51747 ( 24) link_BETA1-4 : bond 0.00331 ( 4) link_BETA1-4 : angle 1.01205 ( 12) link_ALPHA1-3 : bond 0.00907 ( 1) link_ALPHA1-3 : angle 1.64906 ( 3) hydrogen bonds : bond 0.03003 ( 328) hydrogen bonds : angle 5.66399 ( 675) SS BOND : bond 0.00249 ( 54) SS BOND : angle 1.34883 ( 108) covalent geometry : bond 0.00253 (13249) covalent geometry : angle 0.58537 (17998) ********************** 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 100 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8228 (ttm) REVERT: B 211 ASP cc_start: 0.7971 (m-30) cc_final: 0.7377 (m-30) REVERT: B 282 MET cc_start: 0.8813 (mtm) cc_final: 0.8257 (ptt) REVERT: B 320 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: B 536 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7028 (tmt-80) REVERT: C 24 ARG cc_start: 0.7791 (tmt170) cc_final: 0.7498 (ttp80) REVERT: C 30 ASN cc_start: 0.9022 (m-40) cc_final: 0.8769 (t0) REVERT: C 70 ASP cc_start: 0.8195 (m-30) cc_final: 0.7665 (t0) REVERT: C 103 LYS cc_start: 0.8860 (mttt) cc_final: 0.8640 (tppt) REVERT: D 13 GLN cc_start: 0.9416 (pm20) cc_final: 0.8863 (tp40) REVERT: D 87 ARG cc_start: 0.8916 (ptp-170) cc_final: 0.8440 (ptp-110) outliers start: 26 outliers final: 23 residues processed: 95 average time/residue: 0.2419 time to fit residues: 34.6143 Evaluate side-chains 95 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 584 HIS Chi-restraints excluded: chain H residue 197 PHE Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 320 GLN Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 104 PHE Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 114 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 159 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN B 471 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 = 0.4387 r_free = 0.4387 target = 0.143983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.087996 restraints weight = 24720.221| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.65 r_work: 0.3327 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13316 Z= 0.163 Angle : 0.618 12.091 18145 Z= 0.311 Chirality : 0.046 0.173 2009 Planarity : 0.004 0.044 2353 Dihedral : 5.080 32.265 2055 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.95 % Allowed : 11.58 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1641 helix: -1.66 (0.51), residues: 94 sheet: 0.25 (0.29), residues: 343 loop : 0.16 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 452 HIS 0.003 0.001 HIS B 589 PHE 0.019 0.002 PHE C 118 TYR 0.018 0.001 TYR H 208 ARG 0.002 0.000 ARG C 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 8) link_NAG-ASN : angle 1.66807 ( 24) link_BETA1-4 : bond 0.00288 ( 4) link_BETA1-4 : angle 0.95603 ( 12) link_ALPHA1-3 : bond 0.01015 ( 1) link_ALPHA1-3 : angle 1.64786 ( 3) hydrogen bonds : bond 0.03056 ( 328) hydrogen bonds : angle 5.72608 ( 675) SS BOND : bond 0.00362 ( 54) SS BOND : angle 1.42707 ( 108) covalent geometry : bond 0.00390 (13249) covalent geometry : angle 0.60690 (17998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8090.15 seconds wall clock time: 145 minutes 55.62 seconds (8755.62 seconds total)