Starting phenix.real_space_refine on Tue Aug 6 14:46:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjc_43280/08_2024/8vjc_43280_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjc_43280/08_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_43280/08_2024/8vjc_43280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjc_43280/08_2024/8vjc_43280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjc_43280/08_2024/8vjc_43280_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjc_43280/08_2024/8vjc_43280_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3397 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 8843 2.51 5 N 2402 2.21 5 O 2571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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-5409/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: 7.69, per 1000 atoms: 0.55 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: 5.13 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: 1.64 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: 5.05 Time building geometry restraints manager: 5.73 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 3.120 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.179 3.040 nonbonded pdb=" O SER B 878 " pdb=" OH TYR B 882 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 127 " pdb=" O ILE B 158 " model vdw 2.220 3.040 nonbonded pdb=" O PHE B 714 " pdb=" NH1 ARG B 717 " model vdw 2.237 3.120 ... (remaining 113550 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 518 or resid 528 through 539 or resid 546 throug \ h 656 or resid 701 through 905)) selection = (chain 'B' and (resid 3 through 152 or resid 179 through 270 or resid 274 throug \ h 346 or resid 351 through 573 or resid 577 through 905)) } ncs_group { reference = (chain 'C' and (resid 8 through 25 or resid 43 through 62)) selection = (chain 'E' and (resid 8 through 41 or resid 43 through 62)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.800 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.430 ------------------------------------------------------------------------------- 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 : 1.673 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: 0.2516 time to fit residues: 28.3263 Evaluate side-chains 62 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 155 optimal weight: 30.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 148 ASN A 276 GLN A 337 ASN A 691 GLN A 865 HIS B 328 GLN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN B 594 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14256 Z= 0.351 Angle : 0.645 10.909 19308 Z= 0.331 Chirality : 0.046 0.203 2101 Planarity : 0.004 0.042 2491 Dihedral : 5.393 79.115 1896 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.85 % Favored : 90.97 % Rotamer: Outliers : 3.32 % Allowed : 16.94 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.21), residues: 1684 helix: -0.71 (0.38), residues: 194 sheet: -0.63 (0.28), residues: 361 loop : -1.27 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 632 HIS 0.005 0.001 HIS B 710 PHE 0.030 0.002 PHE C 19 TYR 0.019 0.001 TYR A 512 ARG 0.008 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 57 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8444 (pp20) REVERT: A 831 MET cc_start: 0.7877 (tpt) cc_final: 0.6760 (tpt) REVERT: B 314 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8932 (mp) REVERT: B 404 ASP cc_start: 0.8126 (t0) cc_final: 0.7808 (t0) REVERT: B 897 TRP cc_start: 0.9424 (m100) cc_final: 0.9076 (m100) REVERT: C 8 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5862 (pp) REVERT: C 57 GLU cc_start: 0.8831 (tp30) cc_final: 0.8613 (tp30) outliers start: 52 outliers final: 18 residues processed: 105 average time/residue: 0.2380 time to fit residues: 39.4358 Evaluate side-chains 74 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 53 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 431 ASN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 42 optimal weight: 0.3980 chunk 155 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 154 optimal weight: 40.0000 chunk 53 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 HIS A 691 GLN A 764 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14256 Z= 0.194 Angle : 0.595 9.342 19308 Z= 0.304 Chirality : 0.045 0.287 2101 Planarity : 0.004 0.040 2491 Dihedral : 4.787 55.404 1893 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.66 % Favored : 92.22 % Rotamer: Outliers : 2.75 % Allowed : 17.97 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.21), residues: 1684 helix: -0.75 (0.38), residues: 195 sheet: -0.51 (0.28), residues: 363 loop : -1.31 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 632 HIS 0.006 0.001 HIS B 710 PHE 0.016 0.001 PHE A 705 TYR 0.018 0.001 TYR B 708 ARG 0.005 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 106 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 63 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8654 (mmm) cc_final: 0.7606 (mpp) REVERT: A 329 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8438 (pp20) REVERT: A 831 MET cc_start: 0.7865 (tpt) cc_final: 0.6761 (tpt) REVERT: B 314 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8880 (mp) REVERT: B 404 ASP cc_start: 0.8098 (t0) cc_final: 0.7645 (t0) REVERT: C 8 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5746 (pp) REVERT: D 40 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.7989 (mmm-85) outliers start: 43 outliers final: 19 residues processed: 102 average time/residue: 0.2209 time to fit residues: 36.0685 Evaluate side-chains 79 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 50.0000 chunk 116 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 50.0000 chunk 74 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 610 GLN A 691 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1314 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= 0.279 Angle : 0.607 9.727 19308 Z= 0.310 Chirality : 0.045 0.284 2101 Planarity : 0.004 0.041 2491 Dihedral : 4.798 53.474 1893 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.73 % Favored : 91.15 % Rotamer: Outliers : 3.26 % Allowed : 18.16 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.21), residues: 1684 helix: -0.72 (0.38), residues: 194 sheet: -0.53 (0.28), residues: 363 loop : -1.32 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 632 HIS 0.006 0.001 HIS B 710 PHE 0.020 0.001 PHE C 19 TYR 0.014 0.001 TYR B 628 ARG 0.007 0.000 ARG D 49 *********************** 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 110 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 59 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8652 (mmm) cc_final: 0.7688 (mpp) REVERT: A 110 MET cc_start: 0.7595 (mmm) cc_final: 0.7342 (mmm) REVERT: B 314 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8974 (mp) REVERT: B 404 ASP cc_start: 0.8134 (t0) cc_final: 0.7704 (t0) REVERT: B 831 MET cc_start: 0.6635 (mmm) cc_final: 0.6291 (tpt) REVERT: C 8 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5522 (pp) outliers start: 51 outliers final: 32 residues processed: 108 average time/residue: 0.2134 time to fit residues: 37.2368 Evaluate side-chains 91 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 57 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 41 optimal weight: 0.0670 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 431 ASN E 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1425 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= 0.173 Angle : 0.585 11.116 19308 Z= 0.297 Chirality : 0.044 0.249 2101 Planarity : 0.004 0.043 2491 Dihedral : 4.650 50.066 1893 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.48 % Favored : 92.40 % Rotamer: Outliers : 3.26 % Allowed : 18.80 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.47 (0.21), residues: 1684 helix: -0.60 (0.39), residues: 189 sheet: -0.36 (0.28), residues: 358 loop : -1.30 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 412 HIS 0.006 0.000 HIS B 710 PHE 0.015 0.001 PHE A 705 TYR 0.020 0.001 TYR B 708 ARG 0.004 0.000 ARG D 40 *********************** 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 119 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 68 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7466 (mm) REVERT: A 38 MET cc_start: 0.8641 (mmm) cc_final: 0.7732 (mpp) REVERT: A 329 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8459 (pp20) REVERT: B 59 ASP cc_start: 0.8653 (m-30) cc_final: 0.8253 (m-30) REVERT: B 314 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8919 (mp) REVERT: B 831 MET cc_start: 0.6995 (mmm) cc_final: 0.6614 (tpt) REVERT: C 8 LEU cc_start: 0.5911 (OUTLIER) cc_final: 0.5579 (pp) REVERT: E 12 GLU cc_start: 0.8556 (pm20) cc_final: 0.8118 (pm20) outliers start: 51 outliers final: 29 residues processed: 114 average time/residue: 0.2187 time to fit residues: 40.0604 Evaluate side-chains 93 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 60 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 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 461 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 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: 9.9990 chunk 148 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 165 optimal weight: 0.4980 chunk 137 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 313 HIS A 337 ASN A 691 GLN B 90 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 177 GLN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 14256 Z= 0.395 Angle : 0.669 10.818 19308 Z= 0.339 Chirality : 0.046 0.229 2101 Planarity : 0.004 0.042 2491 Dihedral : 4.917 48.092 1893 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.14 % Favored : 90.68 % Rotamer: Outliers : 3.77 % Allowed : 18.61 % Favored : 77.62 % 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: -1.64 (0.20), residues: 1684 helix: -0.93 (0.38), residues: 196 sheet: -0.53 (0.28), residues: 363 loop : -1.36 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 632 HIS 0.006 0.001 HIS B 710 PHE 0.023 0.002 PHE C 19 TYR 0.021 0.001 TYR A 512 ARG 0.007 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 56 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7951 (mm) REVERT: B 314 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9060 (mp) REVERT: B 404 ASP cc_start: 0.8296 (t0) cc_final: 0.8040 (t0) REVERT: B 831 MET cc_start: 0.7012 (mmm) cc_final: 0.6589 (tpt) REVERT: C 8 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5680 (pp) REVERT: E 12 GLU cc_start: 0.8674 (pm20) cc_final: 0.8183 (pm20) outliers start: 59 outliers final: 43 residues processed: 113 average time/residue: 0.2098 time to fit residues: 39.3737 Evaluate side-chains 100 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 54 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 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 479 ARG Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 781 ILE Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 44 GLU 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: 9.9990 chunk 18 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 100 optimal weight: 0.3980 chunk 76 optimal weight: 5.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 691 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14256 Z= 0.236 Angle : 0.618 11.938 19308 Z= 0.312 Chirality : 0.045 0.220 2101 Planarity : 0.004 0.043 2491 Dihedral : 4.817 45.826 1893 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.72 % Favored : 92.10 % Rotamer: Outliers : 3.71 % Allowed : 19.05 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.21), residues: 1684 helix: -0.76 (0.39), residues: 189 sheet: -0.54 (0.28), residues: 363 loop : -1.33 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 412 HIS 0.005 0.001 HIS B 710 PHE 0.017 0.001 PHE C 19 TYR 0.022 0.001 TYR B 708 ARG 0.005 0.000 ARG C 49 *********************** 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 115 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 57 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7955 (mm) REVERT: A 477 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8131 (p90) REVERT: A 831 MET cc_start: 0.8201 (tpt) cc_final: 0.7638 (tpt) REVERT: B 59 ASP cc_start: 0.8686 (m-30) cc_final: 0.8283 (m-30) REVERT: B 314 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9010 (mp) REVERT: B 404 ASP cc_start: 0.8151 (t0) cc_final: 0.7783 (t0) REVERT: B 831 MET cc_start: 0.7080 (mmm) cc_final: 0.6642 (tpt) REVERT: C 8 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.6033 (pp) REVERT: E 12 GLU cc_start: 0.8649 (pm20) cc_final: 0.8164 (pm20) outliers start: 58 outliers final: 39 residues processed: 113 average time/residue: 0.2052 time to fit residues: 38.0471 Evaluate side-chains 97 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 54 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 15 optimal weight: 50.0000 chunk 129 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 691 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1863 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= 0.283 Angle : 0.637 11.782 19308 Z= 0.321 Chirality : 0.046 0.355 2101 Planarity : 0.004 0.043 2491 Dihedral : 4.706 42.595 1891 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 3.39 % Allowed : 20.14 % 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: -1.63 (0.20), residues: 1684 helix: -0.85 (0.38), residues: 195 sheet: -0.58 (0.28), residues: 363 loop : -1.35 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 412 HIS 0.006 0.001 HIS B 710 PHE 0.019 0.001 PHE C 19 TYR 0.019 0.001 TYR B 708 ARG 0.005 0.000 ARG A 757 *********************** 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 107 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 54 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7996 (mm) REVERT: A 477 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8067 (p90) REVERT: B 59 ASP cc_start: 0.8703 (m-30) cc_final: 0.8294 (m-30) REVERT: B 314 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9026 (mp) REVERT: B 404 ASP cc_start: 0.8161 (t0) cc_final: 0.7782 (t0) REVERT: B 831 MET cc_start: 0.7024 (mmm) cc_final: 0.6415 (tpt) REVERT: C 8 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.6021 (pp) REVERT: E 12 GLU cc_start: 0.8676 (pm20) cc_final: 0.8204 (pm20) outliers start: 53 outliers final: 38 residues processed: 107 average time/residue: 0.2117 time to fit residues: 37.6042 Evaluate side-chains 96 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 54 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 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 769 VAL Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 8.9990 chunk 157 optimal weight: 30.0000 chunk 144 optimal weight: 9.9990 chunk 153 optimal weight: 50.0000 chunk 92 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 145 optimal weight: 0.0870 chunk 100 optimal weight: 0.8980 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1915 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= 0.217 Angle : 0.631 11.663 19308 Z= 0.317 Chirality : 0.046 0.304 2101 Planarity : 0.004 0.043 2491 Dihedral : 4.682 42.161 1891 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.08 % Favored : 91.75 % Rotamer: Outliers : 3.13 % Allowed : 20.33 % 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: -1.59 (0.21), residues: 1684 helix: -0.83 (0.38), residues: 195 sheet: -0.48 (0.29), residues: 358 loop : -1.35 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 412 HIS 0.005 0.001 HIS B 710 PHE 0.016 0.001 PHE C 19 TYR 0.012 0.001 TYR B 628 ARG 0.005 0.000 ARG A 757 *********************** 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 104 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 55 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8029 (mm) REVERT: A 477 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.8123 (p90) REVERT: A 831 MET cc_start: 0.8189 (tpt) cc_final: 0.7575 (tpt) REVERT: B 59 ASP cc_start: 0.8671 (m-30) cc_final: 0.8263 (m-30) REVERT: B 314 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8976 (mp) REVERT: B 404 ASP cc_start: 0.8143 (t0) cc_final: 0.7756 (t0) REVERT: B 831 MET cc_start: 0.6979 (mmm) cc_final: 0.6496 (tpt) REVERT: C 8 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5904 (pp) REVERT: E 12 GLU cc_start: 0.8645 (pm20) cc_final: 0.8159 (pm20) outliers start: 49 outliers final: 35 residues processed: 104 average time/residue: 0.2102 time to fit residues: 36.6008 Evaluate side-chains 93 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 54 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 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 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 112 optimal weight: 0.7980 chunk 170 optimal weight: 7.9990 chunk 156 optimal weight: 40.0000 chunk 135 optimal weight: 0.9990 chunk 14 optimal weight: 50.0000 chunk 104 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 107 optimal weight: 0.0170 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14256 Z= 0.164 Angle : 0.623 11.669 19308 Z= 0.311 Chirality : 0.045 0.325 2101 Planarity : 0.003 0.043 2491 Dihedral : 4.571 41.341 1891 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.30 % Favored : 92.52 % Rotamer: Outliers : 2.43 % Allowed : 21.10 % 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: -1.53 (0.21), residues: 1684 helix: -0.84 (0.38), residues: 201 sheet: -0.39 (0.29), residues: 356 loop : -1.31 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 412 HIS 0.005 0.000 HIS B 710 PHE 0.018 0.001 PHE A 705 TYR 0.009 0.001 TYR A 507 ARG 0.004 0.000 ARG A 757 ********************** 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 96 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 58 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8036 (mm) REVERT: A 329 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8471 (pp20) REVERT: A 477 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8064 (p90) REVERT: B 59 ASP cc_start: 0.8580 (m-30) cc_final: 0.8186 (m-30) REVERT: B 314 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8927 (mp) REVERT: B 404 ASP cc_start: 0.8133 (t0) cc_final: 0.7727 (t0) REVERT: B 831 MET cc_start: 0.6989 (mmm) cc_final: 0.6610 (tpt) REVERT: C 8 LEU cc_start: 0.6116 (OUTLIER) cc_final: 0.5893 (pp) REVERT: E 12 GLU cc_start: 0.8624 (pm20) cc_final: 0.8111 (pm20) outliers start: 38 outliers final: 31 residues processed: 96 average time/residue: 0.2150 time to fit residues: 33.6262 Evaluate side-chains 91 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 55 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 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 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 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain D residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 20 optimal weight: 40.0000 chunk 37 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.096019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.062902 restraints weight = 54588.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.062531 restraints weight = 37206.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.062949 restraints weight = 28685.638| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14256 Z= 0.294 Angle : 0.648 13.340 19308 Z= 0.324 Chirality : 0.046 0.309 2101 Planarity : 0.004 0.043 2491 Dihedral : 4.664 42.228 1891 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.55 % Favored : 91.27 % Rotamer: Outliers : 2.62 % Allowed : 20.78 % 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: -1.59 (0.21), residues: 1684 helix: -0.89 (0.37), residues: 202 sheet: -0.55 (0.28), residues: 368 loop : -1.30 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 632 HIS 0.005 0.001 HIS B 710 PHE 0.019 0.001 PHE C 19 TYR 0.015 0.001 TYR A 512 ARG 0.006 0.000 ARG D 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2317.77 seconds wall clock time: 42 minutes 36.52 seconds (2556.52 seconds total)