Starting phenix.real_space_refine on Sun Aug 24 03:43:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vjc_43280/08_2025/8vjc_43280_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vjc_43280/08_2025/8vjc_43280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vjc_43280/08_2025/8vjc_43280_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vjc_43280/08_2025/8vjc_43280_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vjc_43280/08_2025/8vjc_43280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vjc_43280/08_2025/8vjc_43280.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3397 atoms to isotropic. 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 111 5.16 5 C 8843 2.51 5 N 2402 2.21 5 O 2571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13927 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6386 Classifications: {'peptide': 787} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 745} Chain breaks: 8 Chain: "B" Number of atoms: 6495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6495 Classifications: {'peptide': 802} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 758} Chain breaks: 5 Chain: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain breaks: 1 Chain: "D" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 420 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Chain: "E" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 1 Time building chain proxies: 3.68, per 1000 atoms: 0.26 Number of scatterers: 13927 At special positions: 0 Unit cell: (117.72, 132.84, 185.76, 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 111 16.00 O 2571 8.00 N 2402 7.00 C 8843 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 860 " distance=2.03 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 860 " distance=2.03 Simple disulfide: pdb=" SG CYS B 786 " - pdb=" SG CYS B 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 47 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 51 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 47 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 60 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 47 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 51 " distance=2.03 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 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 715.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 29 sheets defined 15.2% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 18 through 26 removed outlier: 4.147A pdb=" N ASN A 25 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 26 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 323 through 329 removed outlier: 4.246A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 435 through 447 removed outlier: 4.056A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 644 removed outlier: 3.574A pdb=" N LEU A 641 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 644 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 714 removed outlier: 3.760A pdb=" N LEU A 696 " --> pdb=" O ILE A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 870 Processing helix chain 'B' and resid 16 through 24 removed outlier: 3.888A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.613A pdb=" N PHE B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.547A pdb=" N ASP B 142 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.002A pdb=" N ASN B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.739A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 4.021A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 Processing helix chain 'B' and resid 702 through 715 removed outlier: 4.013A pdb=" N GLU B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP B 707 " --> pdb=" O LYS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 869 Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.619A pdb=" N CYS C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.722A pdb=" N CYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 17 removed outlier: 4.136A pdb=" N ASP D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 52 through 58 removed outlier: 3.742A pdb=" N LEU D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 22 removed outlier: 3.964A pdb=" N ASP E 15 " --> pdb=" O GLY E 11 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY E 22 " --> pdb=" O GLN E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 removed outlier: 3.971A pdb=" N THR E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 5.967A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN A 34 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 36 " --> pdb=" O ILE A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 13 removed outlier: 5.967A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN A 34 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 36 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET A 98 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG A 65 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ARG A 118 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL A 94 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N GLU A 120 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE A 96 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASN A 122 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N MET A 98 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR A 144 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.827A pdb=" N ILE A 364 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 320 through 321 removed outlier: 7.689A pdb=" N PHE A 427 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR A 401 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N HIS A 429 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 403 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 475 through 480 removed outlier: 3.558A pdb=" N TYR A 477 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A 488 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 479 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 530 through 534 removed outlier: 4.193A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 599 through 605 removed outlier: 6.825A pdb=" N LYS A 614 " --> pdb=" O PRO A 601 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER A 603 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE A 612 " --> pdb=" O SER A 603 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 759 through 762 Processing sheet with id=AB4, first strand: chain 'A' and resid 819 through 822 Processing sheet with id=AB5, first strand: chain 'A' and resid 856 through 862 removed outlier: 3.661A pdb=" N LEU A 844 " --> pdb=" O THR A 889 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 880 through 882 removed outlier: 3.564A pdb=" N PHE A 903 " --> pdb=" O TYR A 882 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.525A pdb=" N MET B 11 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU B 36 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE B 13 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N MET B 38 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 64 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL B 146 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE B 119 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC1, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AC2, first strand: chain 'B' and resid 278 through 279 Processing sheet with id=AC3, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 321 removed outlier: 3.965A pdb=" N LEU B 314 " --> pdb=" O ASN B 337 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER B 339 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N GLU B 316 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 10.555A pdb=" N ILE B 341 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N GLU B 318 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 336 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLY B 366 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY B 338 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 11.039A pdb=" N GLU B 363 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 10.161A pdb=" N GLU B 391 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N SER B 365 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 321 removed outlier: 3.965A pdb=" N LEU B 314 " --> pdb=" O ASN B 337 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER B 339 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N GLU B 316 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 10.555A pdb=" N ILE B 341 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N GLU B 318 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N LYS B 369 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 340 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ARG B 371 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 342 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N PHE B 427 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR B 401 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS B 429 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B 403 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 475 through 479 Processing sheet with id=AC7, first strand: chain 'B' and resid 530 through 533 removed outlier: 3.503A pdb=" N GLY B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 599 through 604 removed outlier: 6.809A pdb=" N LYS B 614 " --> pdb=" O PRO B 601 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER B 603 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 612 " --> pdb=" O SER B 603 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.603A pdb=" N GLU B 760 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 630 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 819 through 822 Processing sheet with id=AD2, first strand: chain 'B' and resid 856 through 862 323 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4562 1.35 - 1.46: 3384 1.46 - 1.58: 6177 1.58 - 1.70: 0 1.70 - 1.82: 133 Bond restraints: 14256 Sorted by residual: bond pdb=" N ALA B 592 " pdb=" CA ALA B 592 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.50e+00 bond pdb=" N ASP B 591 " pdb=" CA ASP B 591 " ideal model delta sigma weight residual 1.453 1.496 -0.043 1.41e-02 5.03e+03 9.37e+00 bond pdb=" N THR B 593 " pdb=" CA THR B 593 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.19e-02 7.06e+03 7.82e+00 bond pdb=" N ASN B 594 " pdb=" CA ASN B 594 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.39e-02 5.18e+03 5.83e+00 bond pdb=" N LEU A 315 " pdb=" CA LEU A 315 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.50e+00 ... (remaining 14251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 19124 2.78 - 5.56: 164 5.56 - 8.33: 16 8.33 - 11.11: 2 11.11 - 13.89: 2 Bond angle restraints: 19308 Sorted by residual: angle pdb=" C PHE B 714 " pdb=" N VAL B 715 " pdb=" CA VAL B 715 " ideal model delta sigma weight residual 122.13 129.84 -7.71 1.85e+00 2.92e-01 1.74e+01 angle pdb=" CA LEU A 37 " pdb=" CB LEU A 37 " pdb=" CG LEU A 37 " ideal model delta sigma weight residual 116.30 130.19 -13.89 3.50e+00 8.16e-02 1.57e+01 angle pdb=" N THR B 593 " pdb=" CA THR B 593 " pdb=" C THR B 593 " ideal model delta sigma weight residual 107.88 113.33 -5.45 1.41e+00 5.03e-01 1.49e+01 angle pdb=" CB MET A 11 " pdb=" CG MET A 11 " pdb=" SD MET A 11 " ideal model delta sigma weight residual 112.70 123.71 -11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N SER B 481 " pdb=" CA SER B 481 " pdb=" C SER B 481 " ideal model delta sigma weight residual 108.23 113.07 -4.84 1.38e+00 5.25e-01 1.23e+01 ... (remaining 19303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 7529 18.04 - 36.08: 856 36.08 - 54.13: 213 54.13 - 72.17: 37 72.17 - 90.21: 15 Dihedral angle restraints: 8650 sinusoidal: 3620 harmonic: 5030 Sorted by residual: dihedral pdb=" CB CYS B 241 " pdb=" SG CYS B 241 " pdb=" SG CYS B 253 " pdb=" CB CYS B 253 " ideal model delta sinusoidal sigma weight residual 93.00 -176.79 -90.21 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 -178.30 -88.70 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 155 " pdb=" CB CYS B 155 " ideal model delta sinusoidal sigma weight residual -86.00 2.43 -88.43 1 1.00e+01 1.00e-02 9.34e+01 ... (remaining 8647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1503 0.042 - 0.084: 409 0.084 - 0.126: 166 0.126 - 0.168: 20 0.168 - 0.210: 3 Chirality restraints: 2101 Sorted by residual: chirality pdb=" CB VAL E 43 " pdb=" CA VAL E 43 " pdb=" CG1 VAL E 43 " pdb=" CG2 VAL E 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CG LEU B 411 " pdb=" CB LEU B 411 " pdb=" CD1 LEU B 411 " pdb=" CD2 LEU B 411 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA ILE B 781 " pdb=" N ILE B 781 " pdb=" C ILE B 781 " pdb=" CB ILE B 781 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.92e-01 ... (remaining 2098 not shown) Planarity restraints: 2491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 590 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C THR B 590 " -0.050 2.00e-02 2.50e+03 pdb=" O THR B 590 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP B 591 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 834 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO B 835 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 835 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 835 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 302 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO A 303 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 303 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 303 " 0.020 5.00e-02 4.00e+02 ... (remaining 2488 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 529 2.71 - 3.25: 14129 3.25 - 3.80: 23114 3.80 - 4.35: 28910 4.35 - 4.90: 46873 Nonbonded interactions: 113555 Sorted by model distance: nonbonded pdb=" NE ARG D 40 " pdb=" OE2 GLU D 45 " model vdw 2.157 3.120 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.179 3.040 nonbonded pdb=" O SER B 878 " pdb=" OH TYR B 882 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 127 " pdb=" O ILE B 158 " model vdw 2.220 3.040 nonbonded pdb=" O PHE B 714 " pdb=" NH1 ARG B 717 " model vdw 2.237 3.120 ... (remaining 113550 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 'A' and (resid 3 through 518 or resid 528 through 539 or resid 546 throug \ h 656 or resid 701 through 905)) selection = (chain 'B' and (resid 3 through 152 or resid 179 through 270 or resid 274 throug \ h 346 or resid 351 through 573 or resid 577 through 905)) } ncs_group { reference = (chain 'C' and (resid 8 through 25 or resid 43 through 62)) selection = (chain 'E' and (resid 8 through 41 or resid 43 through 62)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.710 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 0.003 0.043 14297 Z= 0.147 Angle : 0.650 13.889 19390 Z= 0.340 Chirality : 0.045 0.210 2101 Planarity : 0.004 0.038 2491 Dihedral : 15.458 86.205 5277 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.19 % Favored : 91.63 % Rotamer: Outliers : 0.51 % Allowed : 18.48 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.21), residues: 1684 helix: -0.90 (0.38), residues: 195 sheet: -0.37 (0.29), residues: 348 loop : -1.22 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 38 TYR 0.011 0.001 TYR A 292 PHE 0.019 0.001 PHE D 48 TRP 0.024 0.001 TRP B 412 HIS 0.008 0.001 HIS B 710 Details of bonding type rmsd covalent geometry : bond 0.00288 (14256) covalent geometry : angle 0.64829 (19308) SS BOND : bond 0.00199 ( 41) SS BOND : angle 1.04744 ( 82) hydrogen bonds : bond 0.17239 ( 319) hydrogen bonds : angle 8.54197 ( 813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8300 (pp20) REVERT: A 831 MET cc_start: 0.8281 (tpt) cc_final: 0.8004 (tpt) outliers start: 8 outliers final: 2 residues processed: 71 average time/residue: 0.0999 time to fit residues: 11.2440 Evaluate side-chains 62 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.0270 overall best weight: 3.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 148 ASN A 276 GLN A 337 ASN A 691 GLN A 764 ASN B 90 ASN B 328 GLN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN B 594 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.096014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.064756 restraints weight = 55194.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.063738 restraints weight = 35355.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.063655 restraints weight = 29287.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.063970 restraints weight = 27851.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.064072 restraints weight = 24995.015| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14297 Z= 0.250 Angle : 0.660 10.905 19390 Z= 0.339 Chirality : 0.046 0.205 2101 Planarity : 0.004 0.043 2491 Dihedral : 5.425 78.419 1896 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.97 % Favored : 90.91 % Rotamer: Outliers : 3.64 % Allowed : 16.62 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.21), residues: 1684 helix: -0.74 (0.38), residues: 194 sheet: -0.65 (0.28), residues: 361 loop : -1.28 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 38 TYR 0.019 0.001 TYR A 512 PHE 0.032 0.002 PHE C 19 TRP 0.021 0.002 TRP B 632 HIS 0.006 0.001 HIS B 710 Details of bonding type rmsd covalent geometry : bond 0.00571 (14256) covalent geometry : angle 0.65701 (19308) SS BOND : bond 0.00252 ( 41) SS BOND : angle 1.14643 ( 82) hydrogen bonds : bond 0.04490 ( 319) hydrogen bonds : angle 6.92498 ( 813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 57 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.4746 (OUTLIER) cc_final: 0.4496 (tp) REVERT: A 831 MET cc_start: 0.7870 (tpt) cc_final: 0.6750 (tpt) REVERT: B 111 ASN cc_start: 0.7129 (OUTLIER) cc_final: 0.6925 (t0) REVERT: B 314 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8939 (mp) REVERT: B 404 ASP cc_start: 0.8248 (t0) cc_final: 0.7956 (t0) REVERT: B 897 TRP cc_start: 0.9414 (m100) cc_final: 0.9061 (m100) REVERT: C 8 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5895 (pp) REVERT: C 57 GLU cc_start: 0.8850 (tp30) cc_final: 0.8645 (tp30) outliers start: 57 outliers final: 21 residues processed: 109 average time/residue: 0.0969 time to fit residues: 16.7054 Evaluate side-chains 77 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 128 optimal weight: 1.9990 chunk 72 optimal weight: 40.0000 chunk 155 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 66 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS A 337 ASN A 610 GLN A 691 GLN ** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.095515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.064105 restraints weight = 55389.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.063188 restraints weight = 34759.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.062946 restraints weight = 29951.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.063334 restraints weight = 30238.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.063454 restraints weight = 25096.828| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14297 Z= 0.261 Angle : 0.669 8.727 19390 Z= 0.342 Chirality : 0.047 0.302 2101 Planarity : 0.004 0.042 2491 Dihedral : 5.092 55.059 1893 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.67 % Favored : 91.21 % Rotamer: Outliers : 4.22 % Allowed : 17.39 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.20), residues: 1684 helix: -0.96 (0.37), residues: 194 sheet: -0.72 (0.28), residues: 359 loop : -1.38 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 40 TYR 0.021 0.001 TYR A 512 PHE 0.022 0.002 PHE C 19 TRP 0.020 0.002 TRP B 632 HIS 0.008 0.001 HIS B 710 Details of bonding type rmsd covalent geometry : bond 0.00598 (14256) covalent geometry : angle 0.66606 (19308) SS BOND : bond 0.00401 ( 41) SS BOND : angle 1.13324 ( 82) hydrogen bonds : bond 0.04287 ( 319) hydrogen bonds : angle 6.79827 ( 813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 53 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8588 (mmm) cc_final: 0.7481 (mpp) REVERT: A 314 LEU cc_start: 0.5086 (OUTLIER) cc_final: 0.4663 (tp) REVERT: A 318 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7355 (mm-30) REVERT: B 111 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.7196 (t0) REVERT: B 314 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8964 (mp) REVERT: B 340 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8932 (mp) REVERT: B 404 ASP cc_start: 0.7837 (t0) cc_final: 0.7455 (t0) REVERT: C 8 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5714 (pp) outliers start: 66 outliers final: 38 residues processed: 115 average time/residue: 0.0975 time to fit residues: 17.9832 Evaluate side-chains 94 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 50 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 73 optimal weight: 30.0000 chunk 95 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 135 optimal weight: 0.7980 chunk 43 optimal weight: 0.0570 chunk 80 optimal weight: 0.9990 chunk 21 optimal weight: 40.0000 chunk 93 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 247 HIS A 691 GLN A 764 ASN A 865 HIS ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.097359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.064636 restraints weight = 55522.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.064324 restraints weight = 37051.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.065108 restraints weight = 27767.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.065548 restraints weight = 22445.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.065528 restraints weight = 20820.557| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14297 Z= 0.108 Angle : 0.591 10.277 19390 Z= 0.302 Chirality : 0.045 0.276 2101 Planarity : 0.004 0.042 2491 Dihedral : 4.727 50.517 1893 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.48 % Favored : 92.40 % Rotamer: Outliers : 2.75 % Allowed : 18.99 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.20), residues: 1684 helix: -0.69 (0.38), residues: 188 sheet: -0.42 (0.28), residues: 356 loop : -1.35 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 49 TYR 0.010 0.001 TYR A 507 PHE 0.019 0.001 PHE A 705 TRP 0.016 0.001 TRP B 412 HIS 0.006 0.001 HIS B 710 Details of bonding type rmsd covalent geometry : bond 0.00240 (14256) covalent geometry : angle 0.58898 (19308) SS BOND : bond 0.00220 ( 41) SS BOND : angle 1.00709 ( 82) hydrogen bonds : bond 0.03488 ( 319) hydrogen bonds : angle 6.43862 ( 813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 65 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8663 (mmm) cc_final: 0.7722 (mpp) REVERT: A 110 MET cc_start: 0.7474 (mmm) cc_final: 0.7190 (mmm) REVERT: A 318 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7225 (mm-30) REVERT: B 59 ASP cc_start: 0.8629 (m-30) cc_final: 0.8254 (m-30) REVERT: B 314 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8869 (mp) REVERT: B 404 ASP cc_start: 0.8075 (t0) cc_final: 0.7642 (t0) REVERT: B 806 MET cc_start: 0.6550 (mmm) cc_final: 0.6329 (mmp) REVERT: B 831 MET cc_start: 0.7164 (mmm) cc_final: 0.6827 (tpt) REVERT: C 8 LEU cc_start: 0.6000 (OUTLIER) cc_final: 0.5661 (pp) outliers start: 43 outliers final: 23 residues processed: 104 average time/residue: 0.1019 time to fit residues: 17.2371 Evaluate side-chains 85 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 764 ASN Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 126 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 3 optimal weight: 50.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 GLN A 764 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 431 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.097329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.066736 restraints weight = 54996.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.064932 restraints weight = 34848.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.065406 restraints weight = 28837.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.065718 restraints weight = 25113.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.065765 restraints weight = 22064.623| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14297 Z= 0.112 Angle : 0.583 11.299 19390 Z= 0.294 Chirality : 0.044 0.247 2101 Planarity : 0.004 0.043 2491 Dihedral : 4.517 47.981 1890 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.90 % Favored : 91.98 % Rotamer: Outliers : 3.07 % Allowed : 18.99 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.21), residues: 1684 helix: -0.69 (0.39), residues: 189 sheet: -0.39 (0.28), residues: 358 loop : -1.31 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 40 TYR 0.020 0.001 TYR B 708 PHE 0.016 0.001 PHE A 705 TRP 0.020 0.001 TRP B 412 HIS 0.005 0.000 HIS B 710 Details of bonding type rmsd covalent geometry : bond 0.00253 (14256) covalent geometry : angle 0.58147 (19308) SS BOND : bond 0.00174 ( 41) SS BOND : angle 0.93595 ( 82) hydrogen bonds : bond 0.03351 ( 319) hydrogen bonds : angle 6.31707 ( 813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 66 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8662 (mmm) cc_final: 0.7764 (mpp) REVERT: A 314 LEU cc_start: 0.4438 (OUTLIER) cc_final: 0.4052 (tp) REVERT: A 318 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7296 (mm-30) REVERT: B 59 ASP cc_start: 0.8653 (m-30) cc_final: 0.8236 (m-30) REVERT: B 314 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8898 (mp) REVERT: B 831 MET cc_start: 0.7040 (mmm) cc_final: 0.6626 (tpt) REVERT: C 8 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5647 (pp) outliers start: 48 outliers final: 29 residues processed: 111 average time/residue: 0.0846 time to fit residues: 15.2459 Evaluate side-chains 93 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 163 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 10 optimal weight: 30.0000 chunk 164 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.096597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.064052 restraints weight = 55360.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.063460 restraints weight = 37372.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.064138 restraints weight = 28620.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.064481 restraints weight = 23995.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.064476 restraints weight = 21450.875| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14297 Z= 0.160 Angle : 0.602 11.409 19390 Z= 0.306 Chirality : 0.045 0.226 2101 Planarity : 0.004 0.042 2491 Dihedral : 4.547 45.871 1890 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.08 % Favored : 91.75 % Rotamer: Outliers : 3.26 % Allowed : 19.63 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.21), residues: 1684 helix: -0.66 (0.39), residues: 189 sheet: -0.38 (0.28), residues: 358 loop : -1.30 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 40 TYR 0.014 0.001 TYR B 628 PHE 0.020 0.001 PHE C 19 TRP 0.019 0.001 TRP B 412 HIS 0.005 0.001 HIS B 710 Details of bonding type rmsd covalent geometry : bond 0.00368 (14256) covalent geometry : angle 0.59930 (19308) SS BOND : bond 0.00206 ( 41) SS BOND : angle 1.07116 ( 82) hydrogen bonds : bond 0.03425 ( 319) hydrogen bonds : angle 6.25786 ( 813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 61 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7568 (mm) REVERT: A 38 MET cc_start: 0.8594 (mmm) cc_final: 0.7785 (mpp) REVERT: A 314 LEU cc_start: 0.4570 (OUTLIER) cc_final: 0.4216 (tp) REVERT: A 318 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7310 (mm-30) REVERT: B 59 ASP cc_start: 0.8679 (m-30) cc_final: 0.8264 (m-30) REVERT: B 314 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8955 (mp) REVERT: B 404 ASP cc_start: 0.8001 (t0) cc_final: 0.7686 (t0) REVERT: B 831 MET cc_start: 0.6937 (mmm) cc_final: 0.6492 (tpt) outliers start: 51 outliers final: 33 residues processed: 110 average time/residue: 0.0936 time to fit residues: 16.9114 Evaluate side-chains 94 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 57 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 138 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 157 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 145 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 chunk 11 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.096986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.065082 restraints weight = 55103.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.064282 restraints weight = 33381.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.064481 restraints weight = 28836.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.064787 restraints weight = 24640.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.064885 restraints weight = 21994.674| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14297 Z= 0.126 Angle : 0.601 11.459 19390 Z= 0.301 Chirality : 0.045 0.338 2101 Planarity : 0.003 0.043 2491 Dihedral : 4.337 20.325 1888 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.48 % Favored : 92.40 % Rotamer: Outliers : 3.39 % Allowed : 19.69 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.21), residues: 1684 helix: -0.68 (0.39), residues: 190 sheet: -0.34 (0.29), residues: 358 loop : -1.28 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 40 TYR 0.011 0.001 TYR B 628 PHE 0.015 0.001 PHE C 19 TRP 0.019 0.001 TRP B 412 HIS 0.006 0.001 HIS B 710 Details of bonding type rmsd covalent geometry : bond 0.00287 (14256) covalent geometry : angle 0.59873 (19308) SS BOND : bond 0.00183 ( 41) SS BOND : angle 0.93045 ( 82) hydrogen bonds : bond 0.03249 ( 319) hydrogen bonds : angle 6.11985 ( 813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 60 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.8000 (mm) REVERT: A 318 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: A 477 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.8036 (p90) REVERT: A 831 MET cc_start: 0.7967 (tpt) cc_final: 0.7122 (tpt) REVERT: B 59 ASP cc_start: 0.8613 (m-30) cc_final: 0.8200 (m-30) REVERT: B 314 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8900 (mp) REVERT: B 404 ASP cc_start: 0.7833 (t0) cc_final: 0.7474 (t0) REVERT: B 831 MET cc_start: 0.7037 (mmm) cc_final: 0.6362 (tpt) outliers start: 53 outliers final: 34 residues processed: 111 average time/residue: 0.0985 time to fit residues: 17.4305 Evaluate side-chains 97 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 59 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 39 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 152 optimal weight: 20.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** B 264 HIS ** 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 = 0.4080 r_free = 0.4080 target = 0.095543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.063996 restraints weight = 55117.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.062360 restraints weight = 36621.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.062665 restraints weight = 30475.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062994 restraints weight = 26472.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.063035 restraints weight = 23386.292| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14297 Z= 0.240 Angle : 0.669 12.776 19390 Z= 0.335 Chirality : 0.047 0.287 2101 Planarity : 0.004 0.042 2491 Dihedral : 4.571 20.549 1888 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.61 % Favored : 91.27 % Rotamer: Outliers : 3.52 % Allowed : 19.82 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.21), residues: 1684 helix: -0.96 (0.38), residues: 196 sheet: -0.58 (0.28), residues: 368 loop : -1.32 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 40 TYR 0.019 0.001 TYR A 512 PHE 0.022 0.002 PHE C 19 TRP 0.019 0.002 TRP B 632 HIS 0.007 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00550 (14256) covalent geometry : angle 0.66615 (19308) SS BOND : bond 0.00240 ( 41) SS BOND : angle 1.10838 ( 82) hydrogen bonds : bond 0.03696 ( 319) hydrogen bonds : angle 6.25527 ( 813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 55 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8181 (mm) REVERT: A 314 LEU cc_start: 0.4936 (OUTLIER) cc_final: 0.4428 (tp) REVERT: A 318 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7327 (mm-30) REVERT: A 477 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8119 (p90) REVERT: A 831 MET cc_start: 0.8087 (tpt) cc_final: 0.7527 (tpt) REVERT: B 314 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9026 (mp) REVERT: B 404 ASP cc_start: 0.8002 (t0) cc_final: 0.7639 (t0) REVERT: B 831 MET cc_start: 0.7037 (mmm) cc_final: 0.6492 (tpt) REVERT: E 12 GLU cc_start: 0.8693 (pm20) cc_final: 0.8281 (pm20) outliers start: 55 outliers final: 36 residues processed: 109 average time/residue: 0.1002 time to fit residues: 17.4385 Evaluate side-chains 93 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 52 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 104 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 137 optimal weight: 0.0010 chunk 45 optimal weight: 0.6980 chunk 150 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.096628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.063553 restraints weight = 55367.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.063342 restraints weight = 37514.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.064547 restraints weight = 28212.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.064826 restraints weight = 22122.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.064656 restraints weight = 19050.519| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14297 Z= 0.130 Angle : 0.624 12.044 19390 Z= 0.312 Chirality : 0.045 0.283 2101 Planarity : 0.003 0.044 2491 Dihedral : 4.437 20.915 1888 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.19 % Favored : 92.64 % Rotamer: Outliers : 2.75 % Allowed : 20.52 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.21), residues: 1684 helix: -0.89 (0.37), residues: 201 sheet: -0.47 (0.28), residues: 361 loop : -1.31 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 757 TYR 0.011 0.001 TYR B 628 PHE 0.015 0.001 PHE A 705 TRP 0.033 0.001 TRP B 412 HIS 0.004 0.001 HIS B 710 Details of bonding type rmsd covalent geometry : bond 0.00296 (14256) covalent geometry : angle 0.62216 (19308) SS BOND : bond 0.00187 ( 41) SS BOND : angle 0.95926 ( 82) hydrogen bonds : bond 0.03307 ( 319) hydrogen bonds : angle 6.11997 ( 813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 57 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8195 (mm) REVERT: A 318 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7109 (mm-30) REVERT: A 477 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.8173 (p90) REVERT: A 831 MET cc_start: 0.8047 (tpt) cc_final: 0.7252 (tpt) REVERT: B 59 ASP cc_start: 0.8644 (m-30) cc_final: 0.8210 (m-30) REVERT: B 314 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8915 (mp) REVERT: B 404 ASP cc_start: 0.7976 (t0) cc_final: 0.7601 (t0) REVERT: B 831 MET cc_start: 0.7025 (mmm) cc_final: 0.6477 (tpt) REVERT: E 12 GLU cc_start: 0.8605 (pm20) cc_final: 0.8167 (pm20) outliers start: 43 outliers final: 35 residues processed: 100 average time/residue: 0.1001 time to fit residues: 15.9886 Evaluate side-chains 96 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 57 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 757 ARG Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 60 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 10 optimal weight: 50.0000 chunk 61 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 107 optimal weight: 0.3980 chunk 24 optimal weight: 10.0000 chunk 52 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.097099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.064273 restraints weight = 55215.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.064619 restraints weight = 37050.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.064764 restraints weight = 26163.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.064868 restraints weight = 25795.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.065076 restraints weight = 22649.207| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14297 Z= 0.114 Angle : 0.614 11.856 19390 Z= 0.305 Chirality : 0.045 0.286 2101 Planarity : 0.003 0.043 2491 Dihedral : 4.347 24.829 1888 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.48 % Favored : 92.34 % Rotamer: Outliers : 2.37 % Allowed : 20.84 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.21), residues: 1684 helix: -0.88 (0.37), residues: 203 sheet: -0.40 (0.28), residues: 361 loop : -1.30 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 757 TYR 0.011 0.001 TYR B 708 PHE 0.016 0.001 PHE A 705 TRP 0.030 0.001 TRP B 412 HIS 0.004 0.000 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00260 (14256) covalent geometry : angle 0.61245 (19308) SS BOND : bond 0.00158 ( 41) SS BOND : angle 0.90782 ( 82) hydrogen bonds : bond 0.03154 ( 319) hydrogen bonds : angle 5.99293 ( 813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 57 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8133 (mm) REVERT: A 318 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7277 (mm-30) REVERT: A 477 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8083 (p90) REVERT: A 806 MET cc_start: 0.8507 (ptp) cc_final: 0.8280 (pmm) REVERT: A 831 MET cc_start: 0.8299 (tpt) cc_final: 0.7494 (tpt) REVERT: B 59 ASP cc_start: 0.8630 (m-30) cc_final: 0.8243 (m-30) REVERT: B 314 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8896 (mp) REVERT: B 404 ASP cc_start: 0.8022 (t0) cc_final: 0.7619 (t0) REVERT: B 831 MET cc_start: 0.7009 (mmm) cc_final: 0.6432 (tpt) REVERT: E 12 GLU cc_start: 0.8681 (pm20) cc_final: 0.8216 (pm20) outliers start: 37 outliers final: 32 residues processed: 94 average time/residue: 0.0951 time to fit residues: 14.5137 Evaluate side-chains 92 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 56 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 87 optimal weight: 0.7980 chunk 153 optimal weight: 30.0000 chunk 42 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 14 optimal weight: 50.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.096280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.064299 restraints weight = 54857.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063585 restraints weight = 37804.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.063839 restraints weight = 27527.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.064093 restraints weight = 26274.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.064102 restraints weight = 22253.867| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14297 Z= 0.160 Angle : 0.632 11.978 19390 Z= 0.315 Chirality : 0.046 0.290 2101 Planarity : 0.004 0.043 2491 Dihedral : 4.443 27.058 1888 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.14 % Favored : 91.69 % Rotamer: Outliers : 2.69 % Allowed : 20.72 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.21), residues: 1684 helix: -1.00 (0.36), residues: 208 sheet: -0.48 (0.28), residues: 366 loop : -1.29 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 757 TYR 0.013 0.001 TYR B 628 PHE 0.017 0.001 PHE C 19 TRP 0.026 0.001 TRP B 412 HIS 0.004 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00370 (14256) covalent geometry : angle 0.63024 (19308) SS BOND : bond 0.00177 ( 41) SS BOND : angle 0.97685 ( 82) hydrogen bonds : bond 0.03288 ( 319) hydrogen bonds : angle 5.98756 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2362.84 seconds wall clock time: 41 minutes 34.57 seconds (2494.57 seconds total)