Starting phenix.real_space_refine on Sun Jun 15 00:30:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vjc_43280/06_2025/8vjc_43280_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vjc_43280/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vjc_43280/06_2025/8vjc_43280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vjc_43280/06_2025/8vjc_43280.map" model { file = "/net/cci-nas-00/data/ceres_data/8vjc_43280/06_2025/8vjc_43280_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vjc_43280/06_2025/8vjc_43280_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.13, per 1000 atoms: 0.58 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: 3.74 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.65 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: 4.89 Time building geometry restraints manager: 4.11 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.050 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.210 ------------------------------------------------------------------------------- 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 : 15.56 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (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 TRP 0.024 0.001 TRP B 412 HIS 0.008 0.001 HIS B 710 PHE 0.019 0.001 PHE D 48 TYR 0.011 0.001 TYR A 292 ARG 0.005 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.17239 ( 319) hydrogen bonds : angle 8.54197 ( 813) SS BOND : bond 0.00199 ( 41) SS BOND : angle 1.04744 ( 82) covalent geometry : bond 0.00288 (14256) covalent geometry : angle 0.64829 (19308) *********************** 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 : 1.680 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: 0.2487 time to fit residues: 28.3235 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 : 1.706 ------------------------------------------------------------------------------- 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 144 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 155 optimal weight: 30.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 865 HIS 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.096228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.064371 restraints weight = 55053.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.063722 restraints weight = 34873.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063827 restraints weight = 26961.867| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14297 Z= 0.234 Angle : 0.647 10.909 19390 Z= 0.333 Chirality : 0.046 0.203 2101 Planarity : 0.004 0.042 2491 Dihedral : 5.393 79.113 1896 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.85 % Favored : 90.97 % Rotamer: Outliers : 3.32 % Allowed : 16.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.21), residues: 1684 helix: -0.71 (0.38), residues: 194 sheet: -0.63 (0.28), residues: 361 loop : -1.27 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 632 HIS 0.005 0.001 HIS B 710 PHE 0.030 0.002 PHE C 19 TYR 0.019 0.001 TYR A 512 ARG 0.008 0.000 ARG D 40 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 319) hydrogen bonds : angle 6.89330 ( 813) SS BOND : bond 0.00244 ( 41) SS BOND : angle 1.11953 ( 82) covalent geometry : bond 0.00534 (14256) covalent geometry : angle 0.64463 (19308) *********************** 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 109 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 57 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.4703 (OUTLIER) cc_final: 0.4453 (tp) REVERT: A 318 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: A 329 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8460 (pp20) REVERT: A 831 MET cc_start: 0.7809 (tpt) cc_final: 0.6666 (tpt) REVERT: B 314 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8937 (mp) REVERT: B 404 ASP cc_start: 0.8041 (t0) cc_final: 0.7731 (t0) REVERT: B 897 TRP cc_start: 0.9363 (m100) cc_final: 0.9024 (m100) REVERT: C 8 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5879 (pp) REVERT: C 57 GLU cc_start: 0.8810 (tp30) cc_final: 0.8596 (tp30) outliers start: 52 outliers final: 18 residues processed: 105 average time/residue: 0.2540 time to fit residues: 41.8147 Evaluate side-chains 76 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 318 GLU 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 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 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 45 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 141 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 HIS A 691 GLN A 764 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 405 ASN B 431 ASN E 18 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.097604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.066078 restraints weight = 54999.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.065238 restraints weight = 39326.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.065281 restraints weight = 31461.919| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14297 Z= 0.115 Angle : 0.593 9.849 19390 Z= 0.302 Chirality : 0.045 0.304 2101 Planarity : 0.004 0.040 2491 Dihedral : 5.179 75.702 1896 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.54 % Favored : 92.34 % Rotamer: Outliers : 2.81 % Allowed : 17.77 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.21), residues: 1684 helix: -0.65 (0.39), residues: 188 sheet: -0.49 (0.28), residues: 363 loop : -1.29 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 632 HIS 0.005 0.001 HIS B 710 PHE 0.017 0.001 PHE A 705 TYR 0.020 0.001 TYR B 708 ARG 0.005 0.000 ARG D 40 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 319) hydrogen bonds : angle 6.53729 ( 813) SS BOND : bond 0.00185 ( 41) SS BOND : angle 0.90977 ( 82) covalent geometry : bond 0.00259 (14256) covalent geometry : angle 0.59141 (19308) *********************** 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 111 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 67 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8679 (mmm) cc_final: 0.7643 (mpp) REVERT: A 329 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8459 (pp20) REVERT: A 831 MET cc_start: 0.7894 (tpt) cc_final: 0.6811 (tpt) REVERT: B 314 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8845 (mp) REVERT: B 404 ASP cc_start: 0.8083 (t0) cc_final: 0.7658 (t0) REVERT: C 8 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5721 (pp) REVERT: D 40 ARG cc_start: 0.8232 (mmm-85) cc_final: 0.7945 (mmm-85) outliers start: 44 outliers final: 19 residues processed: 106 average time/residue: 0.3087 time to fit residues: 53.0665 Evaluate side-chains 81 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 2.508 ------------------------------------------------------------------------------- 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 315 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 431 ASN 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 111 ASN 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 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 D residue 20 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 131 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 152 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 154 optimal weight: 30.0000 chunk 99 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 610 GLN A 691 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.098230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.061535 restraints weight = 56352.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.063245 restraints weight = 31926.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.064270 restraints weight = 22851.058| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1253 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= 0.141 Angle : 0.594 10.102 19390 Z= 0.303 Chirality : 0.045 0.278 2101 Planarity : 0.004 0.041 2491 Dihedral : 4.685 51.596 1893 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.25 % Favored : 91.63 % Rotamer: Outliers : 3.20 % Allowed : 18.09 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.21), residues: 1684 helix: -0.70 (0.38), residues: 191 sheet: -0.47 (0.28), residues: 363 loop : -1.29 (0.19), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 632 HIS 0.006 0.001 HIS B 710 PHE 0.018 0.001 PHE C 19 TYR 0.012 0.001 TYR B 708 ARG 0.006 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 319) hydrogen bonds : angle 6.42347 ( 813) SS BOND : bond 0.00187 ( 41) SS BOND : angle 1.02344 ( 82) covalent geometry : bond 0.00322 (14256) covalent geometry : angle 0.59149 (19308) *********************** 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 113 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 63 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8850 (mmm) cc_final: 0.8055 (mpp) REVERT: A 110 MET cc_start: 0.7294 (mmm) cc_final: 0.6870 (mmm) REVERT: A 314 LEU cc_start: 0.4505 (OUTLIER) cc_final: 0.4194 (tp) REVERT: A 318 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7128 (mm-30) REVERT: A 329 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8372 (pp20) REVERT: B 314 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8917 (mp) REVERT: B 404 ASP cc_start: 0.7839 (t0) cc_final: 0.7473 (t0) REVERT: B 576 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7932 (mtm180) REVERT: B 831 MET cc_start: 0.7011 (mmm) cc_final: 0.6782 (tpt) REVERT: C 8 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5664 (pp) outliers start: 50 outliers final: 26 residues processed: 110 average time/residue: 0.2259 time to fit residues: 40.3383 Evaluate side-chains 91 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 1.588 ------------------------------------------------------------------------------- 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 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 431 ASN 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 715 VAL 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 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 518 PHE Chi-restraints excluded: chain B residue 576 ARG 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 62 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 146 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 5 optimal weight: 50.0000 chunk 8 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 50.0000 chunk 19 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 chunk 103 optimal weight: 10.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN B 90 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 177 GLN ** B 264 HIS ** 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 = 0.4081 r_free = 0.4081 target = 0.095548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.062852 restraints weight = 55305.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.062352 restraints weight = 39670.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.062302 restraints weight = 28124.602| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1636 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= 0.259 Angle : 0.674 10.337 19390 Z= 0.342 Chirality : 0.047 0.251 2101 Planarity : 0.004 0.042 2491 Dihedral : 4.959 48.502 1893 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.79 % Favored : 91.09 % Rotamer: Outliers : 3.77 % Allowed : 18.93 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.20), residues: 1684 helix: -0.92 (0.37), residues: 196 sheet: -0.58 (0.28), residues: 363 loop : -1.38 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 632 HIS 0.007 0.001 HIS B 710 PHE 0.023 0.002 PHE C 19 TYR 0.023 0.001 TYR B 708 ARG 0.005 0.000 ARG D 40 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 319) hydrogen bonds : angle 6.55936 ( 813) SS BOND : bond 0.00261 ( 41) SS BOND : angle 1.14539 ( 82) covalent geometry : bond 0.00593 (14256) covalent geometry : angle 0.67140 (19308) *********************** 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 115 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 56 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7555 (mm) REVERT: A 38 MET cc_start: 0.8655 (mmm) cc_final: 0.7764 (mpp) REVERT: A 314 LEU cc_start: 0.4835 (OUTLIER) cc_final: 0.4411 (tp) REVERT: B 111 ASN cc_start: 0.7400 (OUTLIER) cc_final: 0.7101 (t0) REVERT: B 314 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9053 (mp) REVERT: B 404 ASP cc_start: 0.7959 (t0) cc_final: 0.7550 (t0) REVERT: B 831 MET cc_start: 0.6905 (mmm) cc_final: 0.6471 (tpt) REVERT: C 8 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5636 (pp) REVERT: E 12 GLU cc_start: 0.8624 (pm20) cc_final: 0.8193 (pm20) outliers start: 59 outliers final: 39 residues processed: 111 average time/residue: 0.2173 time to fit residues: 39.7848 Evaluate side-chains 96 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 52 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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 315 LEU 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 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 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 260 GLN 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 769 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 135 optimal weight: 0.9990 chunk 96 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 8 optimal weight: 40.0000 chunk 157 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS A 337 ASN A 691 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.095454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.061134 restraints weight = 55551.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.062010 restraints weight = 36199.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.063874 restraints weight = 24727.447| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14297 Z= 0.239 Angle : 0.659 11.072 19390 Z= 0.333 Chirality : 0.046 0.223 2101 Planarity : 0.004 0.042 2491 Dihedral : 4.963 46.508 1893 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.43 % Favored : 91.39 % Rotamer: Outliers : 4.09 % Allowed : 18.61 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.20), residues: 1684 helix: -1.04 (0.37), residues: 198 sheet: -0.61 (0.28), residues: 363 loop : -1.41 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 412 HIS 0.006 0.001 HIS B 710 PHE 0.022 0.001 PHE C 19 TYR 0.020 0.001 TYR A 512 ARG 0.004 0.000 ARG D 40 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 319) hydrogen bonds : angle 6.52863 ( 813) SS BOND : bond 0.00275 ( 41) SS BOND : angle 1.24262 ( 82) covalent geometry : bond 0.00550 (14256) covalent geometry : angle 0.65571 (19308) *********************** 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 115 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 51 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8217 (mm) REVERT: A 314 LEU cc_start: 0.4447 (OUTLIER) cc_final: 0.4144 (tp) REVERT: A 477 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8195 (p90) REVERT: B 56 MET cc_start: 0.7890 (ttt) cc_final: 0.7662 (ttt) REVERT: B 314 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8977 (mp) REVERT: B 404 ASP cc_start: 0.8404 (t0) cc_final: 0.7946 (t0) REVERT: B 831 MET cc_start: 0.7129 (mmm) cc_final: 0.6734 (tpt) REVERT: C 8 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6128 (pp) outliers start: 64 outliers final: 44 residues processed: 114 average time/residue: 0.2258 time to fit residues: 42.9886 Evaluate side-chains 100 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 51 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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 315 LEU 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 435 CYS 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 566 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 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 159 CYS 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 566 VAL Chi-restraints excluded: chain B residue 769 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 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 51 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 60 optimal weight: 0.4980 chunk 136 optimal weight: 10.0000 chunk 162 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 97 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.096944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.064110 restraints weight = 55188.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.063771 restraints weight = 37216.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.064244 restraints weight = 28015.573| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14297 Z= 0.111 Angle : 0.617 11.743 19390 Z= 0.311 Chirality : 0.046 0.349 2101 Planarity : 0.004 0.043 2491 Dihedral : 4.766 43.615 1893 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.54 % Favored : 92.28 % Rotamer: Outliers : 3.20 % Allowed : 19.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.21), residues: 1684 helix: -0.77 (0.38), residues: 191 sheet: -0.46 (0.28), residues: 358 loop : -1.35 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 412 HIS 0.005 0.001 HIS B 710 PHE 0.020 0.001 PHE A 705 TYR 0.010 0.001 TYR B 628 ARG 0.002 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 319) hydrogen bonds : angle 6.34008 ( 813) SS BOND : bond 0.00188 ( 41) SS BOND : angle 0.96502 ( 82) covalent geometry : bond 0.00249 (14256) covalent geometry : angle 0.61506 (19308) *********************** 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 108 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 58 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8100 (mm) REVERT: A 314 LEU cc_start: 0.4619 (OUTLIER) cc_final: 0.4218 (tp) REVERT: A 318 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7224 (mm-30) REVERT: A 477 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.8105 (p90) REVERT: A 831 MET cc_start: 0.8262 (tpt) cc_final: 0.7441 (tpt) REVERT: B 59 ASP cc_start: 0.8592 (m-30) cc_final: 0.8202 (m-30) REVERT: B 314 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8941 (mp) REVERT: B 404 ASP cc_start: 0.8276 (t0) cc_final: 0.8033 (t0) REVERT: B 831 MET cc_start: 0.7039 (mmm) cc_final: 0.6451 (tpt) REVERT: C 8 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.6012 (pp) outliers start: 50 outliers final: 33 residues processed: 108 average time/residue: 0.2107 time to fit residues: 37.0377 Evaluate side-chains 93 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 54 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 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 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 47 CYS 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 163 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 69 optimal weight: 40.0000 chunk 31 optimal weight: 8.9990 chunk 116 optimal weight: 0.0670 chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 82 optimal weight: 0.0770 chunk 50 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.097099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.062705 restraints weight = 54946.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.064558 restraints weight = 33299.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.064797 restraints weight = 22942.986| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1836 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= 0.112 Angle : 0.619 13.198 19390 Z= 0.308 Chirality : 0.045 0.293 2101 Planarity : 0.003 0.043 2491 Dihedral : 4.515 40.940 1891 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.66 % Favored : 92.16 % Rotamer: Outliers : 2.88 % Allowed : 20.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.21), residues: 1684 helix: -0.86 (0.38), residues: 197 sheet: -0.36 (0.29), residues: 356 loop : -1.34 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 412 HIS 0.011 0.001 HIS B 829 PHE 0.018 0.001 PHE A 705 TYR 0.009 0.001 TYR B 628 ARG 0.004 0.000 ARG A 757 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 319) hydrogen bonds : angle 6.19141 ( 813) SS BOND : bond 0.00198 ( 41) SS BOND : angle 0.89721 ( 82) covalent geometry : bond 0.00250 (14256) covalent geometry : angle 0.61746 (19308) *********************** 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 105 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 60 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8211 (mm) REVERT: A 318 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7096 (mm-30) REVERT: A 831 MET cc_start: 0.8265 (tpt) cc_final: 0.7444 (tpt) REVERT: B 56 MET cc_start: 0.7727 (ttt) cc_final: 0.7414 (ttt) REVERT: B 59 ASP cc_start: 0.8678 (m-30) cc_final: 0.8279 (m-30) REVERT: B 314 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8874 (mp) REVERT: B 831 MET cc_start: 0.6959 (mmm) cc_final: 0.6495 (tpt) REVERT: C 8 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.6050 (pp) REVERT: E 12 GLU cc_start: 0.8617 (pm20) cc_final: 0.8154 (pm20) outliers start: 45 outliers final: 32 residues processed: 105 average time/residue: 0.2239 time to fit residues: 39.2846 Evaluate side-chains 93 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 57 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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 90 ASN 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 486 LEU Chi-restraints excluded: chain A residue 532 VAL 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 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 47 CYS Chi-restraints excluded: chain D residue 42 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 81 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.096816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.064173 restraints weight = 54603.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.063742 restraints weight = 36340.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.064585 restraints weight = 26863.140| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14297 Z= 0.130 Angle : 0.625 12.307 19390 Z= 0.311 Chirality : 0.045 0.311 2101 Planarity : 0.003 0.043 2491 Dihedral : 4.537 40.958 1891 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.14 % Favored : 91.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.21), residues: 1684 helix: -0.99 (0.37), residues: 204 sheet: -0.39 (0.28), residues: 361 loop : -1.31 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 412 HIS 0.005 0.001 HIS B 440 PHE 0.017 0.001 PHE C 19 TYR 0.011 0.001 TYR B 628 ARG 0.004 0.000 ARG A 757 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 319) hydrogen bonds : angle 6.13242 ( 813) SS BOND : bond 0.00167 ( 41) SS BOND : angle 0.92045 ( 82) covalent geometry : bond 0.00298 (14256) covalent geometry : angle 0.62321 (19308) *********************** 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 101 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 58 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7989 (mm) REVERT: A 314 LEU cc_start: 0.4649 (OUTLIER) cc_final: 0.4197 (tp) REVERT: A 318 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7253 (mm-30) REVERT: A 477 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8113 (p90) REVERT: A 806 MET cc_start: 0.8331 (ptp) cc_final: 0.8063 (pmm) REVERT: A 831 MET cc_start: 0.8190 (tpt) cc_final: 0.7328 (tpt) REVERT: B 59 ASP cc_start: 0.8685 (m-30) cc_final: 0.8283 (m-30) REVERT: B 314 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8923 (mp) REVERT: B 404 ASP cc_start: 0.8399 (t0) cc_final: 0.8144 (t0) REVERT: B 831 MET cc_start: 0.7013 (mmm) cc_final: 0.6616 (tpt) REVERT: C 8 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.6001 (pp) REVERT: E 12 GLU cc_start: 0.8620 (pm20) cc_final: 0.8173 (pm20) outliers start: 43 outliers final: 34 residues processed: 100 average time/residue: 0.2473 time to fit residues: 39.6087 Evaluate side-chains 98 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 58 time to evaluate : 1.773 ------------------------------------------------------------------------------- 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 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 8 LEU Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 44 optimal weight: 0.7980 chunk 144 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 chunk 151 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.096103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.062032 restraints weight = 55146.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063214 restraints weight = 36088.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.063436 restraints weight = 24315.107| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14297 Z= 0.171 Angle : 0.645 12.199 19390 Z= 0.321 Chirality : 0.046 0.290 2101 Planarity : 0.004 0.043 2491 Dihedral : 4.640 41.549 1891 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.43 % Favored : 91.39 % Rotamer: Outliers : 2.62 % Allowed : 20.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.21), residues: 1684 helix: -1.03 (0.36), residues: 205 sheet: -0.48 (0.29), residues: 356 loop : -1.30 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 632 HIS 0.004 0.001 HIS B 440 PHE 0.019 0.001 PHE C 19 TYR 0.014 0.001 TYR B 628 ARG 0.004 0.000 ARG A 757 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 319) hydrogen bonds : angle 6.15050 ( 813) SS BOND : bond 0.00185 ( 41) SS BOND : angle 1.01686 ( 82) covalent geometry : bond 0.00395 (14256) covalent geometry : angle 0.64311 (19308) ********************** 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 98 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 57 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8197 (mm) REVERT: A 477 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8104 (p90) REVERT: A 806 MET cc_start: 0.8542 (ptp) cc_final: 0.8188 (pmm) REVERT: A 831 MET cc_start: 0.8374 (tpt) cc_final: 0.7600 (tpt) REVERT: B 59 ASP cc_start: 0.8662 (m-30) cc_final: 0.8251 (m-30) REVERT: B 314 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8961 (mp) REVERT: B 404 ASP cc_start: 0.8170 (t0) cc_final: 0.7914 (t0) REVERT: B 442 MET cc_start: 0.9228 (mmm) cc_final: 0.8983 (tpp) REVERT: B 831 MET cc_start: 0.7066 (mmm) cc_final: 0.6704 (tpt) REVERT: E 12 GLU cc_start: 0.8651 (pm20) cc_final: 0.8185 (pm20) outliers start: 41 outliers final: 34 residues processed: 98 average time/residue: 0.2664 time to fit residues: 44.2560 Evaluate side-chains 92 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 55 time to evaluate : 2.110 ------------------------------------------------------------------------------- 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 90 ASN Chi-restraints excluded: chain A residue 304 CYS 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 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 47 CYS Chi-restraints excluded: chain D residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 GLN ** 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 = 0.4061 r_free = 0.4061 target = 0.094726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.061111 restraints weight = 55330.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.060752 restraints weight = 37933.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.061254 restraints weight = 29295.905| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 14297 Z= 0.288 Angle : 0.726 11.438 19390 Z= 0.362 Chirality : 0.048 0.284 2101 Planarity : 0.004 0.043 2491 Dihedral : 4.997 43.786 1891 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.32 % Favored : 90.50 % Rotamer: Outliers : 2.56 % Allowed : 20.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.20), residues: 1684 helix: -1.32 (0.35), residues: 211 sheet: -0.71 (0.28), residues: 355 loop : -1.39 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 632 HIS 0.006 0.001 HIS B 548 PHE 0.024 0.002 PHE C 19 TYR 0.023 0.001 TYR A 512 ARG 0.005 0.001 ARG A 757 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 319) hydrogen bonds : angle 6.38282 ( 813) SS BOND : bond 0.00264 ( 41) SS BOND : angle 1.24635 ( 82) covalent geometry : bond 0.00659 (14256) covalent geometry : angle 0.72290 (19308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5185.23 seconds wall clock time: 94 minutes 27.91 seconds (5667.91 seconds total)