Starting phenix.real_space_refine on Tue Apr 9 19:51:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjc_43280/04_2024/8vjc_43280_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjc_43280/04_2024/8vjc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjc_43280/04_2024/8vjc_43280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjc_43280/04_2024/8vjc_43280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjc_43280/04_2024/8vjc_43280_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjc_43280/04_2024/8vjc_43280_neut.pdb" } 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 Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 697": "OE1" <-> "OE2" Residue "A TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "D ASP 23": "OD1" <-> "OD2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "E ASP 52": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 7.18, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 5.23 Conformation dependent library (CDL) restraints added in 2.4 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: 1.55 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: 5.06 Time building geometry restraints manager: 5.71 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: 98.33 - 105.48: 291 105.48 - 112.63: 7317 112.63 - 119.78: 4723 119.78 - 126.93: 6772 126.93 - 134.07: 205 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 2.520 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.179 2.440 nonbonded pdb=" O SER B 878 " pdb=" OH TYR B 882 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR B 127 " pdb=" O ILE B 158 " model vdw 2.220 2.440 nonbonded pdb=" O PHE B 714 " pdb=" NH1 ARG B 717 " model vdw 2.237 2.520 ... (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 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: 1.230 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: 4.870 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 38.260 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.960 ------------------------------------------------------------------------------- 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 14256 Z= 0.190 Angle : 0.648 13.889 19308 Z= 0.339 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 *********************** 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 fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 1.682 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: 0.2541 time to fit residues: 28.6804 Evaluate side-chains 62 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 1.721 ------------------------------------------------------------------------------- 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: 5.9990 chunk 129 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 51 optimal weight: 0.0670 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 155 optimal weight: 50.0000 overall best weight: 1.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN A 541 ASN A 691 GLN B 328 GLN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.0573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14256 Z= 0.223 Angle : 0.578 10.898 19308 Z= 0.295 Chirality : 0.044 0.195 2101 Planarity : 0.004 0.040 2491 Dihedral : 5.155 73.635 1896 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.25 % Favored : 91.57 % Rotamer: Outliers : 2.49 % Allowed : 17.52 % Favored : 79.99 % 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: -0.60 (0.38), residues: 199 sheet: -0.49 (0.28), residues: 363 loop : -1.25 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 632 HIS 0.007 0.001 HIS B 710 PHE 0.019 0.001 PHE C 19 TYR 0.013 0.001 TYR B 628 ARG 0.006 0.000 ARG D 40 *********************** 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 100 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 61 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8765 (mmp) cc_final: 0.7542 (mpp) REVERT: A 831 MET cc_start: 0.8015 (tpt) cc_final: 0.6903 (tpt) REVERT: A 841 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9191 (tp) REVERT: B 404 ASP cc_start: 0.8142 (t0) cc_final: 0.7825 (t0) REVERT: C 8 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5747 (pp) REVERT: C 57 GLU cc_start: 0.8715 (tp30) cc_final: 0.8480 (tp30) outliers start: 39 outliers final: 12 residues processed: 95 average time/residue: 0.2437 time to fit residues: 37.5470 Evaluate side-chains 71 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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 420 THR Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 787 ASN 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 86 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 129 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN E 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14256 Z= 0.344 Angle : 0.625 9.006 19308 Z= 0.317 Chirality : 0.045 0.194 2101 Planarity : 0.004 0.040 2491 Dihedral : 4.770 55.711 1890 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 4.03 % Allowed : 17.26 % 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: -1.56 (0.20), residues: 1684 helix: -0.59 (0.38), residues: 195 sheet: -0.56 (0.28), residues: 356 loop : -1.33 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 632 HIS 0.010 0.001 HIS B 710 PHE 0.023 0.001 PHE C 19 TYR 0.020 0.001 TYR B 708 ARG 0.007 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 56 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8628 (mmp) cc_final: 0.7571 (mpp) REVERT: A 329 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8432 (pp20) REVERT: B 314 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8982 (mp) REVERT: B 404 ASP cc_start: 0.8222 (t0) cc_final: 0.7865 (t0) REVERT: B 897 TRP cc_start: 0.9401 (m100) cc_final: 0.8764 (m100) REVERT: C 8 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5642 (pp) REVERT: C 57 GLU cc_start: 0.8810 (tp30) cc_final: 0.8587 (tp30) outliers start: 63 outliers final: 31 residues processed: 114 average time/residue: 0.2213 time to fit residues: 41.1338 Evaluate side-chains 85 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 51 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 354 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 541 ASN 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 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 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 518 PHE Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain D residue 42 ILE 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 153 optimal weight: 40.0000 chunk 116 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 50.0000 chunk 74 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN B 90 ASN B 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14256 Z= 0.291 Angle : 0.599 9.502 19308 Z= 0.305 Chirality : 0.045 0.254 2101 Planarity : 0.004 0.039 2491 Dihedral : 4.715 54.299 1890 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 3.77 % Allowed : 18.80 % Favored : 77.43 % 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: -1.68 (0.20), residues: 1684 helix: -0.83 (0.37), residues: 206 sheet: -0.61 (0.28), residues: 363 loop : -1.40 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 412 HIS 0.009 0.001 HIS B 710 PHE 0.020 0.001 PHE C 19 TYR 0.017 0.001 TYR A 512 ARG 0.004 0.000 ARG D 40 *********************** 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 117 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 58 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8567 (mmp) cc_final: 0.7611 (mpp) REVERT: A 329 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8450 (pp20) REVERT: B 314 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8954 (mp) REVERT: B 404 ASP cc_start: 0.8140 (t0) cc_final: 0.7738 (t0) REVERT: B 897 TRP cc_start: 0.9416 (m100) cc_final: 0.8781 (m100) REVERT: C 8 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5645 (pp) outliers start: 59 outliers final: 37 residues processed: 113 average time/residue: 0.2121 time to fit residues: 39.4088 Evaluate side-chains 95 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 55 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 202 THR Chi-restraints excluded: chain A residue 304 CYS 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 405 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 541 ASN 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 801 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 45 ASP 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 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 412 TRP Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 15 ASP 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 137 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 141 optimal weight: 30.0000 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 462 ASN E 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14256 Z= 0.260 Angle : 0.591 10.645 19308 Z= 0.298 Chirality : 0.044 0.237 2101 Planarity : 0.004 0.040 2491 Dihedral : 4.682 52.005 1890 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.67 % Favored : 91.15 % Rotamer: Outliers : 3.84 % Allowed : 19.44 % 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: -1.67 (0.20), residues: 1684 helix: -0.85 (0.37), residues: 207 sheet: -0.62 (0.28), residues: 363 loop : -1.38 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 412 HIS 0.008 0.001 HIS B 710 PHE 0.018 0.001 PHE C 19 TYR 0.021 0.001 TYR B 708 ARG 0.003 0.000 ARG D 38 *********************** 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 117 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 57 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8538 (mmp) cc_final: 0.7617 (mpp) REVERT: A 329 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8430 (pp20) REVERT: A 831 MET cc_start: 0.8289 (tpt) cc_final: 0.7416 (tpt) REVERT: B 314 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9033 (mp) REVERT: B 404 ASP cc_start: 0.8151 (t0) cc_final: 0.7724 (t0) REVERT: B 897 TRP cc_start: 0.9416 (m100) cc_final: 0.8781 (m100) REVERT: C 8 LEU cc_start: 0.6096 (OUTLIER) cc_final: 0.5697 (pp) outliers start: 60 outliers final: 48 residues processed: 114 average time/residue: 0.2346 time to fit residues: 42.3983 Evaluate side-chains 105 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 54 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 72 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 304 CYS 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 405 ASN 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 479 ARG Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 541 ASN 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 16 ASN Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 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 518 PHE Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 15 ASP 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 55 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 76 optimal weight: 50.0000 chunk 13 optimal weight: 50.0000 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14256 Z= 0.208 Angle : 0.577 11.132 19308 Z= 0.292 Chirality : 0.044 0.214 2101 Planarity : 0.003 0.040 2491 Dihedral : 4.609 49.243 1890 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.55 % Favored : 91.27 % Rotamer: Outliers : 3.52 % Allowed : 19.76 % 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: -1.62 (0.21), residues: 1684 helix: -0.80 (0.37), residues: 206 sheet: -0.55 (0.28), residues: 363 loop : -1.36 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 412 HIS 0.009 0.001 HIS B 710 PHE 0.016 0.001 PHE C 19 TYR 0.020 0.001 TYR B 708 ARG 0.004 0.000 ARG B 780 *********************** 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 111 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 56 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7460 (mm) REVERT: A 38 MET cc_start: 0.8516 (mmp) cc_final: 0.7592 (mpp) REVERT: A 329 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8418 (pp20) REVERT: A 831 MET cc_start: 0.8276 (tpt) cc_final: 0.7394 (tpt) REVERT: B 314 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9006 (mp) REVERT: B 404 ASP cc_start: 0.8130 (t0) cc_final: 0.7694 (t0) REVERT: B 442 MET cc_start: 0.9292 (mmm) cc_final: 0.8880 (tpp) REVERT: B 897 TRP cc_start: 0.9412 (m100) cc_final: 0.8774 (m100) outliers start: 55 outliers final: 41 residues processed: 108 average time/residue: 0.2074 time to fit residues: 37.0388 Evaluate side-chains 98 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 54 time to evaluate : 1.704 ------------------------------------------------------------------------------- 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 202 THR 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 354 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 405 ASN 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 541 ASN 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 16 ASN Chi-restraints excluded: chain B residue 45 ASP 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 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 0.9980 chunk 18 optimal weight: 50.0000 chunk 94 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 164 optimal weight: 0.0980 chunk 103 optimal weight: 10.0000 chunk 100 optimal weight: 0.3980 chunk 76 optimal weight: 50.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS A 337 ASN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 462 ASN E 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14256 Z= 0.174 Angle : 0.575 12.450 19308 Z= 0.289 Chirality : 0.044 0.201 2101 Planarity : 0.003 0.040 2491 Dihedral : 4.498 47.142 1890 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.08 % Favored : 91.75 % Rotamer: Outliers : 3.64 % Allowed : 19.76 % 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: -1.53 (0.21), residues: 1684 helix: -0.70 (0.38), residues: 201 sheet: -0.41 (0.28), residues: 358 loop : -1.34 (0.19), residues: 1125 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 0.015 0.001 PHE A 705 TYR 0.010 0.001 TYR A 507 ARG 0.004 0.000 ARG B 780 *********************** 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 117 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 60 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8520 (mmp) cc_final: 0.8309 (mmm) REVERT: A 329 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8423 (pp20) REVERT: A 806 MET cc_start: 0.8564 (ptp) cc_final: 0.8341 (pmm) REVERT: A 831 MET cc_start: 0.8255 (tpt) cc_final: 0.7388 (tpt) REVERT: B 314 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8979 (mp) REVERT: B 404 ASP cc_start: 0.8120 (t0) cc_final: 0.7653 (t0) REVERT: B 897 TRP cc_start: 0.9407 (m100) cc_final: 0.8768 (m100) outliers start: 57 outliers final: 41 residues processed: 114 average time/residue: 0.2460 time to fit residues: 44.0709 Evaluate side-chains 100 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 57 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 72 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 304 CYS 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 405 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 541 ASN 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 16 ASN Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain E residue 15 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN B 108 ASN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14256 Z= 0.457 Angle : 0.698 11.400 19308 Z= 0.350 Chirality : 0.046 0.189 2101 Planarity : 0.004 0.041 2491 Dihedral : 4.759 22.807 1888 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.38 % Favored : 90.44 % Rotamer: Outliers : 4.22 % Allowed : 19.44 % Favored : 76.34 % 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: -1.84 (0.20), residues: 1684 helix: -1.10 (0.35), residues: 207 sheet: -0.69 (0.28), residues: 362 loop : -1.49 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 412 HIS 0.009 0.001 HIS B 710 PHE 0.025 0.002 PHE C 19 TYR 0.024 0.002 TYR A 512 ARG 0.008 0.001 ARG D 49 *********************** 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 117 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 51 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8521 (mmp) cc_final: 0.8311 (mmm) REVERT: A 329 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8440 (pp20) REVERT: A 477 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.8169 (p90) REVERT: B 314 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9059 (mp) REVERT: B 404 ASP cc_start: 0.8222 (t0) cc_final: 0.7758 (t0) REVERT: B 897 TRP cc_start: 0.9448 (m100) cc_final: 0.8811 (m100) REVERT: D 44 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7180 (pm20) outliers start: 66 outliers final: 44 residues processed: 114 average time/residue: 0.2481 time to fit residues: 45.1155 Evaluate side-chains 98 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 50 time to evaluate : 1.859 ------------------------------------------------------------------------------- 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 72 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 304 CYS 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 405 ASN 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 479 ARG Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 593 THR 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 45 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 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 479 ARG Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain E residue 15 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14256 Z= 0.204 Angle : 0.619 12.173 19308 Z= 0.309 Chirality : 0.045 0.321 2101 Planarity : 0.003 0.040 2491 Dihedral : 4.574 22.162 1888 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.48 % Favored : 92.34 % Rotamer: Outliers : 3.01 % Allowed : 20.46 % Favored : 76.53 % 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: -1.70 (0.20), residues: 1684 helix: -0.89 (0.37), residues: 200 sheet: -0.65 (0.27), residues: 369 loop : -1.39 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 412 HIS 0.008 0.001 HIS B 710 PHE 0.016 0.001 PHE A 705 TYR 0.011 0.001 TYR B 628 ARG 0.006 0.000 ARG D 49 *********************** 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 102 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 55 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8495 (mmp) cc_final: 0.8294 (mmm) REVERT: A 329 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8391 (pp20) REVERT: A 831 MET cc_start: 0.8282 (tpt) cc_final: 0.7425 (tpt) REVERT: B 314 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8996 (mp) REVERT: B 404 ASP cc_start: 0.8199 (t0) cc_final: 0.7703 (t0) REVERT: B 442 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.9022 (tpp) REVERT: B 897 TRP cc_start: 0.9432 (m100) cc_final: 0.8795 (m100) REVERT: D 44 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7234 (pm20) outliers start: 47 outliers final: 40 residues processed: 99 average time/residue: 0.2247 time to fit residues: 36.6760 Evaluate side-chains 98 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 54 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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 72 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 304 CYS 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 405 ASN 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 541 ASN Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 566 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 45 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain E residue 15 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14256 Z= 0.191 Angle : 0.599 11.875 19308 Z= 0.298 Chirality : 0.045 0.265 2101 Planarity : 0.003 0.040 2491 Dihedral : 4.455 25.782 1888 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.19 % Favored : 91.63 % Rotamer: Outliers : 2.88 % Allowed : 20.72 % Favored : 76.41 % 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: -1.60 (0.21), residues: 1684 helix: -0.74 (0.38), residues: 198 sheet: -0.62 (0.28), residues: 362 loop : -1.32 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 412 HIS 0.008 0.001 HIS B 710 PHE 0.014 0.001 PHE A 705 TYR 0.010 0.001 TYR B 628 ARG 0.006 0.000 ARG D 49 ********************** 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 100 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 55 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8536 (mmp) cc_final: 0.8315 (mmm) REVERT: A 329 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8386 (pp20) REVERT: A 831 MET cc_start: 0.8242 (tpt) cc_final: 0.7374 (tpt) REVERT: B 314 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8969 (mp) REVERT: B 404 ASP cc_start: 0.8125 (t0) cc_final: 0.7650 (t0) REVERT: B 442 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.9011 (tpp) REVERT: B 897 TRP cc_start: 0.9437 (m100) cc_final: 0.8801 (m100) REVERT: D 44 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7164 (pm20) outliers start: 45 outliers final: 38 residues processed: 98 average time/residue: 0.2341 time to fit residues: 37.5777 Evaluate side-chains 97 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 55 time to evaluate : 1.717 ------------------------------------------------------------------------------- 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 72 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 304 CYS 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 405 ASN 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 541 ASN Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain E residue 15 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 37 optimal weight: 6.9990 chunk 135 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 17 optimal weight: 50.0000 chunk 25 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.095249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.062706 restraints weight = 54860.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.061438 restraints weight = 40198.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.061728 restraints weight = 34131.757| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14256 Z= 0.399 Angle : 0.680 12.004 19308 Z= 0.341 Chirality : 0.047 0.257 2101 Planarity : 0.004 0.041 2491 Dihedral : 4.781 25.669 1888 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.50 % Favored : 90.32 % Rotamer: Outliers : 2.75 % Allowed : 20.78 % Favored : 76.47 % 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: -1.84 (0.20), residues: 1684 helix: -1.11 (0.36), residues: 207 sheet: -0.76 (0.28), residues: 367 loop : -1.46 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 412 HIS 0.007 0.001 HIS B 710 PHE 0.019 0.002 PHE E 19 TYR 0.021 0.001 TYR A 512 ARG 0.006 0.001 ARG D 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2337.15 seconds wall clock time: 44 minutes 3.88 seconds (2643.88 seconds total)