Starting phenix.real_space_refine on Sun Jul 5 12:32:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9puw_71878/07_2026/9puw_71878.cif Found real_map, /net/cci-nas-00/data/ceres_data/9puw_71878/07_2026/9puw_71878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9puw_71878/07_2026/9puw_71878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9puw_71878/07_2026/9puw_71878.map" model { file = "/net/cci-nas-00/data/ceres_data/9puw_71878/07_2026/9puw_71878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9puw_71878/07_2026/9puw_71878.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 102 5.16 5 C 8695 2.51 5 N 2338 2.21 5 O 2545 1.98 5 H 13249 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26929 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 11964 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 39, 'TRANS': 709} Chain breaks: 4 Chain: "B" Number of atoms: 12474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 12474 Classifications: {'peptide': 782} Link IDs: {'PTRANS': 42, 'TRANS': 739} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 671 Classifications: {'peptide': 47} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "M" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 186 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "N" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 186 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "P" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 354 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "Q" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 671 Classifications: {'peptide': 47} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "R" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 423 Classifications: {'peptide': 27} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 26} Time building chain proxies: 4.18, per 1000 atoms: 0.16 Number of scatterers: 26929 At special positions: 0 Unit cell: (159, 134.62, 146.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 102 16.00 O 2545 8.00 N 2338 7.00 C 8695 6.00 H 13249 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " 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=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.04 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=2.04 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 304 " - pdb=" SG CYS B 308 " distance=2.04 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 6 " - pdb=" SG CYS C 11 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS P 19 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 6 " - pdb=" SG CYS Q 11 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 7 " - pdb=" SG CYS R 7 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 20 " - pdb=" SG CYS R 19 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 887.9 milliseconds 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 32 sheets defined 16.6% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.795A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.852A pdb=" N PHE A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.749A pdb=" N CYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 267 " --> pdb=" O HIS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.929A pdb=" N GLY A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 4.337A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 359 Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.862A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N HIS A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.671A pdb=" N PHE A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 638 through 643' Processing helix chain 'A' and resid 863 through 870 Processing helix chain 'B' and resid 17 through 24 removed outlier: 3.955A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.680A pdb=" N PHE B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 47' Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.732A pdb=" N ILE B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 255 through 267 removed outlier: 4.332A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 323 through 329 removed outlier: 4.202A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 359 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.631A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 644 Processing helix chain 'B' and resid 808 through 812 removed outlier: 3.587A pdb=" N ASP B 812 " --> pdb=" O ALA B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 870 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 12 through 19 removed outlier: 3.996A pdb=" N TYR C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 28 Processing helix chain 'C' and resid 32 through 45 Processing helix chain 'M' and resid 706 through 714 Processing helix chain 'N' and resid 706 through 714 removed outlier: 3.719A pdb=" N PHE N 714 " --> pdb=" O HIS N 710 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 19 Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 12 through 18 Processing helix chain 'Q' and resid 32 through 43 Processing helix chain 'R' and resid 8 through 19 removed outlier: 3.828A pdb=" N VAL R 12 " --> pdb=" O GLY R 8 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.577A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 212 through 216 removed outlier: 5.450A pdb=" N LEU A 213 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N CYS A 228 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN A 215 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.545A pdb=" N PHE A 231 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 294 removed outlier: 3.851A pdb=" N THR A 302 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 368 through 369 removed outlier: 6.995A pdb=" N LEU A 368 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N LEU A 403 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N HIS A 429 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.238A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 532 through 534 removed outlier: 3.598A 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 604 removed outlier: 5.867A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 604 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 759 through 762 removed outlier: 3.535A pdb=" N GLU A 760 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A 627 " --> pdb=" O CYS A 786 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN A 788 " --> pdb=" O ARG A 794 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 759 through 762 removed outlier: 3.535A pdb=" N GLU A 760 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A 627 " --> pdb=" O CYS A 786 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 818 through 821 Processing sheet with id=AB6, first strand: chain 'A' and resid 857 through 862 removed outlier: 7.041A pdb=" N THR A 889 " --> pdb=" O VAL A 843 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR A 845 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG A 887 " --> pdb=" O TYR A 845 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL A 847 " --> pdb=" O ARG A 885 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG A 885 " --> pdb=" O VAL A 847 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR A 849 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER A 883 " --> pdb=" O TYR A 849 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG A 851 " --> pdb=" O ASN A 881 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ASN A 881 " --> pdb=" O ARG A 851 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 7 through 9 removed outlier: 6.284A pdb=" N CYS B 8 " --> pdb=" O GLU B 30 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.317A pdb=" N LEU B 33 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N PHE B 64 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE B 35 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL B 66 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU B 37 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL B 146 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 119 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN B 148 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LYS B 121 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 212 through 216 removed outlier: 7.074A pdb=" N ASN B 215 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N CYS B 225 " --> pdb=" O ASN B 215 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AC2, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AC3, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 312 removed outlier: 3.661A pdb=" N ILE B 336 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 319 through 321 removed outlier: 6.036A pdb=" N LYS B 319 " --> pdb=" O ILE B 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 368 through 369 removed outlier: 7.035A pdb=" N LEU B 368 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N LEU B 403 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N HIS B 429 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 475 through 480 removed outlier: 3.804A pdb=" N TYR B 477 " --> pdb=" O ARG B 488 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET B 553 " --> pdb=" O ILE B 485 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 500 through 502 removed outlier: 6.740A pdb=" N LEU B 569 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 506 through 509 Processing sheet with id=AD1, first strand: chain 'B' and resid 599 through 607 removed outlier: 5.521A pdb=" N ASP B 600 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS B 616 " --> pdb=" O ASP B 600 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLN B 610 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.672A pdb=" N HIS B 627 " --> pdb=" O CYS B 786 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG B 794 " --> pdb=" O ASN B 787 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.672A pdb=" N HIS B 627 " --> pdb=" O CYS B 786 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 783 " --> pdb=" O ALA B 799 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 818 through 822 Processing sheet with id=AD5, first strand: chain 'B' and resid 857 through 862 329 hydrogen bonds defined for protein. 840 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: 6.50 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13237 1.03 - 1.23: 258 1.23 - 1.43: 5787 1.43 - 1.63: 7857 1.63 - 1.82: 124 Bond restraints: 27263 Sorted by residual: bond pdb=" CB PRO B 791 " pdb=" CG PRO B 791 " ideal model delta sigma weight residual 1.492 1.542 -0.050 5.00e-02 4.00e+02 1.02e+00 bond pdb=" N ASP B 59 " pdb=" CA ASP B 59 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.22e-02 6.72e+03 8.08e-01 bond pdb=" CA ARG A 409 " pdb=" CB ARG A 409 " ideal model delta sigma weight residual 1.536 1.523 0.013 1.46e-02 4.69e+03 7.93e-01 bond pdb=" CB ASN A 405 " pdb=" CG ASN A 405 " ideal model delta sigma weight residual 1.516 1.494 0.022 2.50e-02 1.60e+03 7.85e-01 bond pdb=" CB ASN A 431 " pdb=" CG ASN A 431 " ideal model delta sigma weight residual 1.516 1.494 0.022 2.50e-02 1.60e+03 7.70e-01 ... (remaining 27258 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 46592 1.12 - 2.24: 2339 2.24 - 3.35: 162 3.35 - 4.47: 45 4.47 - 5.59: 9 Bond angle restraints: 49147 Sorted by residual: angle pdb=" C SER A 545 " pdb=" N GLN A 546 " pdb=" CA GLN A 546 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.96e+00 angle pdb=" N GLN A 465 " pdb=" CA GLN A 465 " pdb=" C GLN A 465 " ideal model delta sigma weight residual 112.57 109.91 2.66 1.13e+00 7.83e-01 5.54e+00 angle pdb=" C GLN B 249 " pdb=" N ASP B 250 " pdb=" CA ASP B 250 " ideal model delta sigma weight residual 121.54 126.03 -4.49 1.91e+00 2.74e-01 5.53e+00 angle pdb=" N GLY C 45 " pdb=" CA GLY C 45 " pdb=" C GLY C 45 " ideal model delta sigma weight residual 113.18 118.13 -4.95 2.37e+00 1.78e-01 4.36e+00 angle pdb=" CA MET A 56 " pdb=" CB MET A 56 " pdb=" CG MET A 56 " ideal model delta sigma weight residual 114.10 118.25 -4.15 2.00e+00 2.50e-01 4.30e+00 ... (remaining 49142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 11367 16.73 - 33.46: 1149 33.46 - 50.19: 341 50.19 - 66.92: 84 66.92 - 83.65: 32 Dihedral angle restraints: 12973 sinusoidal: 7009 harmonic: 5964 Sorted by residual: dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 163.96 -70.96 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " pdb=" SG CYS B 182 " pdb=" CB CYS B 182 " ideal model delta sinusoidal sigma weight residual -86.00 -154.57 68.57 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS A 304 " pdb=" SG CYS A 304 " pdb=" SG CYS A 308 " pdb=" CB CYS A 308 " ideal model delta sinusoidal sigma weight residual 93.00 37.77 55.23 1 1.00e+01 1.00e-02 4.13e+01 ... (remaining 12970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1245 0.029 - 0.057: 522 0.057 - 0.086: 118 0.086 - 0.114: 115 0.114 - 0.143: 54 Chirality restraints: 2054 Sorted by residual: chirality pdb=" CA ILE B 119 " pdb=" N ILE B 119 " pdb=" C ILE B 119 " pdb=" CB ILE B 119 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CG LEU A 262 " pdb=" CB LEU A 262 " pdb=" CD1 LEU A 262 " pdb=" CD2 LEU A 262 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE B 35 " pdb=" N ILE B 35 " pdb=" C ILE B 35 " pdb=" CB ILE B 35 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 2051 not shown) Planarity restraints: 4051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 490 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO A 491 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 490 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO B 491 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 496 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.73e+00 pdb=" C ASP A 496 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP A 496 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE A 497 " 0.008 2.00e-02 2.50e+03 ... (remaining 4048 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1202 2.15 - 2.77: 51599 2.77 - 3.38: 74279 3.38 - 3.99: 96445 3.99 - 4.60: 148051 Nonbonded interactions: 371576 Sorted by model distance: nonbonded pdb=" OE1 GLU R 21 " pdb=" H GLU R 21 " model vdw 1.543 2.450 nonbonded pdb=" O LEU A 613 " pdb=" HG SER A 767 " model vdw 1.562 2.450 nonbonded pdb=" O THR A 18 " pdb=" HD1 HIS A 21 " model vdw 1.573 2.450 nonbonded pdb=" OE2 GLU B 355 " pdb=" HE ARG B 383 " model vdw 1.573 2.450 nonbonded pdb=" H SER Q 12 " pdb=" OE1 GLN Q 15 " model vdw 1.587 2.450 ... (remaining 371571 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 7 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 127 through 200 or (resid 201 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 202 through 518 or (resid 519 and (name N or name CA or name C or name O or na \ me CB or name H or name HA or name HB2 or name HB3)) or resid 529 through 909)) selection = (chain 'B' and (resid 7 through 147 or resid 196 through 434 or (resid 435 and ( \ name N or name CA or name C or name O or name CB or name SG or name H or name HA \ or name HB2 or name HB3)) or resid 436 through 467 or (resid 468 and (name N or \ name CA or name C or name O or name CB or name SG or name H or name HA or name \ HB2 or name HB3)) or resid 469 through 909)) } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'P' selection = (chain 'R' and resid 5 through 27) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 26.200 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 0.050 14048 Z= 0.137 Angle : 0.540 5.588 19064 Z= 0.286 Chirality : 0.043 0.143 2054 Planarity : 0.003 0.046 2453 Dihedral : 15.158 83.647 5164 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.09 % Favored : 89.73 % Rotamer: Outliers : 0.26 % Allowed : 16.13 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.21), residues: 1665 helix: -0.42 (0.37), residues: 199 sheet: -0.89 (0.29), residues: 360 loop : -1.56 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 229 TYR 0.014 0.001 TYR A 232 PHE 0.017 0.001 PHE A 482 TRP 0.012 0.001 TRP C 44 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (14014) covalent geometry : angle 0.53893 / 0.29 (18996) SS BOND : bond 0.00276 / 0.19 ( 34) SS BOND : angle 0.83212 / 0.55 ( 68) hydrogen bonds : bond 0.23884 / 16.36 ( 308) hydrogen bonds : angle 10.24299 / 6.97 ( 840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 114 average time/residue: 0.2721 time to fit residues: 45.5951 Evaluate side-chains 111 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 546 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0270 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 357 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.191144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.120705 restraints weight = 64909.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.125100 restraints weight = 37833.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.125162 restraints weight = 22458.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.126052 restraints weight = 20238.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.126423 restraints weight = 19290.153| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14048 Z= 0.134 Angle : 0.560 5.164 19064 Z= 0.299 Chirality : 0.044 0.167 2054 Planarity : 0.004 0.050 2453 Dihedral : 5.282 54.525 1864 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.47 % Favored : 91.35 % Rotamer: Outliers : 1.57 % Allowed : 14.70 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.21), residues: 1665 helix: -0.62 (0.35), residues: 199 sheet: -0.95 (0.29), residues: 351 loop : -1.48 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 577 TYR 0.011 0.001 TYR A 374 PHE 0.016 0.001 PHE A 565 TRP 0.016 0.001 TRP C 44 HIS 0.005 0.001 HIS R 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (14014) covalent geometry : angle 0.55906 / 0.30 (18996) SS BOND : bond 0.00500 / 0.24 ( 34) SS BOND : angle 0.75558 / 0.49 ( 68) hydrogen bonds : bond 0.04846 / 3.16 ( 308) hydrogen bonds : angle 7.56665 / 5.11 ( 840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 135 average time/residue: 0.2634 time to fit residues: 52.8092 Evaluate side-chains 125 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain R residue 7 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 31 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 73 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 144 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.186934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.124206 restraints weight = 65138.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.122552 restraints weight = 36748.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.121701 restraints weight = 28303.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.122327 restraints weight = 26866.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.122487 restraints weight = 23768.103| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 14048 Z= 0.305 Angle : 0.637 5.493 19064 Z= 0.344 Chirality : 0.046 0.181 2054 Planarity : 0.005 0.057 2453 Dihedral : 5.652 54.689 1863 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.19 % Favored : 87.63 % Rotamer: Outliers : 2.35 % Allowed : 15.55 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.20), residues: 1665 helix: -0.92 (0.34), residues: 205 sheet: -1.13 (0.28), residues: 346 loop : -1.82 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 46 TYR 0.017 0.002 TYR B 430 PHE 0.026 0.002 PHE A 565 TRP 0.015 0.002 TRP C 44 HIS 0.006 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.31 (14014) covalent geometry : angle 0.63594 / 0.34 (18996) SS BOND : bond 0.00286 / 0.20 ( 34) SS BOND : angle 0.86154 / 0.59 ( 68) hydrogen bonds : bond 0.04878 / 3.18 ( 308) hydrogen bonds : angle 7.28890 / 4.95 ( 840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 31 residues processed: 138 average time/residue: 0.2658 time to fit residues: 54.6637 Evaluate side-chains 139 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 631 PHE Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain R residue 7 CYS Chi-restraints excluded: chain R residue 17 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 55 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 135 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.187914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.120023 restraints weight = 64754.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.120291 restraints weight = 38580.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.120805 restraints weight = 25250.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.121414 restraints weight = 23692.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.121779 restraints weight = 21721.995| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14048 Z= 0.218 Angle : 0.585 5.124 19064 Z= 0.315 Chirality : 0.044 0.151 2054 Planarity : 0.004 0.051 2453 Dihedral : 5.550 51.796 1863 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.81 % Favored : 88.95 % Rotamer: Outliers : 2.35 % Allowed : 16.46 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.20), residues: 1665 helix: -0.74 (0.34), residues: 198 sheet: -1.21 (0.28), residues: 346 loop : -1.73 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 46 TYR 0.013 0.001 TYR A 374 PHE 0.020 0.002 PHE A 565 TRP 0.014 0.001 TRP C 44 HIS 0.005 0.001 HIS A 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (14014) covalent geometry : angle 0.58470 / 0.31 (18996) SS BOND : bond 0.00252 / 0.17 ( 34) SS BOND : angle 0.77320 / 0.52 ( 68) hydrogen bonds : bond 0.04081 / 2.65 ( 308) hydrogen bonds : angle 6.98356 / 4.75 ( 840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 MET cc_start: 0.7374 (ttp) cc_final: 0.6891 (ttp) REVERT: R 10 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.6884 (t70) outliers start: 36 outliers final: 29 residues processed: 133 average time/residue: 0.2263 time to fit residues: 44.7869 Evaluate side-chains 135 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain R residue 10 HIS Chi-restraints excluded: chain R residue 17 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 37 optimal weight: 0.2980 chunk 24 optimal weight: 7.9990 chunk 87 optimal weight: 0.1980 chunk 121 optimal weight: 0.6980 chunk 163 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.190293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.124900 restraints weight = 64627.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.123921 restraints weight = 37366.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.124620 restraints weight = 25756.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.125272 restraints weight = 22765.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.125829 restraints weight = 22229.108| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14048 Z= 0.108 Angle : 0.526 5.119 19064 Z= 0.279 Chirality : 0.043 0.148 2054 Planarity : 0.004 0.046 2453 Dihedral : 5.211 50.025 1863 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.77 % Favored : 90.99 % Rotamer: Outliers : 1.76 % Allowed : 16.72 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.20), residues: 1665 helix: -0.43 (0.35), residues: 193 sheet: -1.09 (0.28), residues: 347 loop : -1.54 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 46 TYR 0.010 0.001 TYR M 708 PHE 0.024 0.001 PHE B 631 TRP 0.014 0.001 TRP C 44 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (14014) covalent geometry : angle 0.52590 / 0.28 (18996) SS BOND : bond 0.00277 / 0.15 ( 34) SS BOND : angle 0.66275 / 0.43 ( 68) hydrogen bonds : bond 0.03618 / 2.36 ( 308) hydrogen bonds : angle 6.70184 / 4.57 ( 840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 404 ASP cc_start: 0.7881 (t0) cc_final: 0.7657 (t0) REVERT: R 10 HIS cc_start: 0.8085 (OUTLIER) cc_final: 0.6920 (t70) outliers start: 27 outliers final: 23 residues processed: 133 average time/residue: 0.2427 time to fit residues: 47.8798 Evaluate side-chains 129 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain R residue 10 HIS Chi-restraints excluded: chain R residue 17 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 115 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.189291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.125135 restraints weight = 64862.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.121029 restraints weight = 37092.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.122104 restraints weight = 33330.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.123660 restraints weight = 24668.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.124258 restraints weight = 21356.052| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14048 Z= 0.153 Angle : 0.538 5.125 19064 Z= 0.284 Chirality : 0.043 0.151 2054 Planarity : 0.004 0.047 2453 Dihedral : 5.292 49.785 1863 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.85 % Favored : 89.97 % Rotamer: Outliers : 1.76 % Allowed : 16.92 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.20), residues: 1665 helix: -0.37 (0.36), residues: 193 sheet: -1.13 (0.28), residues: 347 loop : -1.56 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 46 TYR 0.014 0.001 TYR A 232 PHE 0.017 0.001 PHE A 565 TRP 0.014 0.001 TRP C 44 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (14014) covalent geometry : angle 0.53648 / 0.28 (18996) SS BOND : bond 0.00256 / 0.17 ( 34) SS BOND : angle 0.81120 / 0.51 ( 68) hydrogen bonds : bond 0.03589 / 2.34 ( 308) hydrogen bonds : angle 6.58136 / 4.48 ( 840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 404 ASP cc_start: 0.7960 (t0) cc_final: 0.7756 (t0) REVERT: R 10 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7009 (t70) outliers start: 27 outliers final: 24 residues processed: 127 average time/residue: 0.2745 time to fit residues: 51.4148 Evaluate side-chains 133 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain R residue 10 HIS Chi-restraints excluded: chain R residue 17 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 161 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 0.0270 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 0.0470 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.187530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.117872 restraints weight = 64871.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.119932 restraints weight = 39233.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.120981 restraints weight = 23833.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.121384 restraints weight = 22162.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.121830 restraints weight = 20421.408| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14048 Z= 0.228 Angle : 0.577 5.094 19064 Z= 0.308 Chirality : 0.044 0.159 2054 Planarity : 0.004 0.060 2453 Dihedral : 5.455 48.915 1863 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.89 % Favored : 87.93 % Rotamer: Outliers : 2.42 % Allowed : 16.53 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.20), residues: 1665 helix: -0.56 (0.35), residues: 199 sheet: -1.19 (0.28), residues: 344 loop : -1.67 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 46 TYR 0.013 0.001 TYR B 430 PHE 0.023 0.002 PHE A 565 TRP 0.015 0.001 TRP C 44 HIS 0.005 0.001 HIS A 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (14014) covalent geometry : angle 0.57556 / 0.31 (18996) SS BOND : bond 0.00257 / 0.18 ( 34) SS BOND : angle 0.81160 / 0.54 ( 68) hydrogen bonds : bond 0.03709 / 2.41 ( 308) hydrogen bonds : angle 6.54024 / 4.45 ( 840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 GLU cc_start: 0.7529 (pm20) cc_final: 0.7253 (pp20) REVERT: R 10 HIS cc_start: 0.8173 (OUTLIER) cc_final: 0.7017 (t70) outliers start: 37 outliers final: 26 residues processed: 137 average time/residue: 0.2650 time to fit residues: 53.6148 Evaluate side-chains 133 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain R residue 10 HIS Chi-restraints excluded: chain R residue 17 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 121 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 112 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.189491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.123667 restraints weight = 64388.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.123026 restraints weight = 37564.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.123517 restraints weight = 24863.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.123925 restraints weight = 23888.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.124125 restraints weight = 21845.682| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14048 Z= 0.127 Angle : 0.537 5.302 19064 Z= 0.283 Chirality : 0.043 0.150 2054 Planarity : 0.004 0.054 2453 Dihedral : 5.129 47.618 1860 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.55 % Favored : 90.27 % Rotamer: Outliers : 1.96 % Allowed : 17.11 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.20), residues: 1665 helix: -0.36 (0.36), residues: 193 sheet: -1.11 (0.29), residues: 339 loop : -1.56 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 46 TYR 0.014 0.001 TYR A 232 PHE 0.015 0.001 PHE A 258 TRP 0.015 0.001 TRP A 559 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (14014) covalent geometry : angle 0.53637 / 0.28 (18996) SS BOND : bond 0.00317 / 0.18 ( 34) SS BOND : angle 0.77908 / 0.54 ( 68) hydrogen bonds : bond 0.03437 / 2.22 ( 308) hydrogen bonds : angle 6.44077 / 4.38 ( 840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 404 ASP cc_start: 0.7935 (t0) cc_final: 0.7723 (t0) REVERT: C 34 GLU cc_start: 0.7521 (pm20) cc_final: 0.7204 (pp20) REVERT: R 10 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.6919 (t70) outliers start: 30 outliers final: 28 residues processed: 130 average time/residue: 0.2661 time to fit residues: 51.1772 Evaluate side-chains 134 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain R residue 10 HIS Chi-restraints excluded: chain R residue 17 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 121 optimal weight: 0.0980 chunk 57 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.189427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.124471 restraints weight = 64801.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.124986 restraints weight = 37297.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.125001 restraints weight = 25271.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.125334 restraints weight = 23919.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.125534 restraints weight = 24445.408| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14048 Z= 0.133 Angle : 0.530 5.082 19064 Z= 0.279 Chirality : 0.043 0.148 2054 Planarity : 0.004 0.057 2453 Dihedral : 5.125 47.170 1860 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.09 % Favored : 89.73 % Rotamer: Outliers : 1.89 % Allowed : 17.31 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.21), residues: 1665 helix: -0.27 (0.36), residues: 194 sheet: -1.06 (0.29), residues: 349 loop : -1.53 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 46 TYR 0.013 0.001 TYR A 292 PHE 0.016 0.001 PHE A 258 TRP 0.014 0.001 TRP C 44 HIS 0.005 0.001 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (14014) covalent geometry : angle 0.52882 / 0.28 (18996) SS BOND : bond 0.00250 / 0.16 ( 34) SS BOND : angle 0.74120 / 0.49 ( 68) hydrogen bonds : bond 0.03360 / 2.18 ( 308) hydrogen bonds : angle 6.31146 / 4.29 ( 840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 404 ASP cc_start: 0.7931 (t0) cc_final: 0.7704 (t0) REVERT: C 34 GLU cc_start: 0.7495 (pm20) cc_final: 0.7165 (pp20) REVERT: R 10 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.6962 (t70) outliers start: 29 outliers final: 26 residues processed: 127 average time/residue: 0.2794 time to fit residues: 52.5331 Evaluate side-chains 132 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain R residue 10 HIS Chi-restraints excluded: chain R residue 17 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 17 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 68 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 148 optimal weight: 30.0000 chunk 64 optimal weight: 5.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.187422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.116827 restraints weight = 64589.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.117505 restraints weight = 39885.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.119888 restraints weight = 27365.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.121154 restraints weight = 21218.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.121987 restraints weight = 19496.209| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14048 Z= 0.217 Angle : 0.577 5.117 19064 Z= 0.307 Chirality : 0.044 0.155 2054 Planarity : 0.004 0.061 2453 Dihedral : 5.292 46.798 1860 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.19 % Favored : 87.63 % Rotamer: Outliers : 1.96 % Allowed : 17.31 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.20), residues: 1665 helix: -0.49 (0.36), residues: 200 sheet: -1.14 (0.29), residues: 349 loop : -1.65 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 46 TYR 0.018 0.001 TYR A 232 PHE 0.022 0.002 PHE A 565 TRP 0.014 0.001 TRP C 44 HIS 0.007 0.001 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (14014) covalent geometry : angle 0.57587 / 0.31 (18996) SS BOND : bond 0.00260 / 0.17 ( 34) SS BOND : angle 0.81484 / 0.55 ( 68) hydrogen bonds : bond 0.03532 / 2.30 ( 308) hydrogen bonds : angle 6.33307 / 4.31 ( 840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 MET cc_start: 0.7988 (pmm) cc_final: 0.7756 (pmm) REVERT: C 34 GLU cc_start: 0.7570 (pm20) cc_final: 0.7300 (pp20) REVERT: R 10 HIS cc_start: 0.8132 (OUTLIER) cc_final: 0.6962 (t70) outliers start: 30 outliers final: 25 residues processed: 129 average time/residue: 0.2654 time to fit residues: 50.5992 Evaluate side-chains 133 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain R residue 10 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 156 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 ASN ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.189327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.124004 restraints weight = 64444.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.122543 restraints weight = 34851.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.122332 restraints weight = 26581.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.123558 restraints weight = 25197.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.124199 restraints weight = 21465.594| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14048 Z= 0.132 Angle : 0.530 5.319 19064 Z= 0.280 Chirality : 0.043 0.146 2054 Planarity : 0.004 0.059 2453 Dihedral : 5.123 45.327 1860 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.55 % Favored : 90.27 % Rotamer: Outliers : 1.89 % Allowed : 17.31 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.21), residues: 1665 helix: -0.28 (0.36), residues: 195 sheet: -1.06 (0.29), residues: 349 loop : -1.53 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 46 TYR 0.013 0.001 TYR A 292 PHE 0.017 0.001 PHE B 631 TRP 0.016 0.001 TRP C 44 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (14014) covalent geometry : angle 0.52937 / 0.28 (18996) SS BOND : bond 0.00249 / 0.16 ( 34) SS BOND : angle 0.75227 / 0.51 ( 68) hydrogen bonds : bond 0.03305 / 2.15 ( 308) hydrogen bonds : angle 6.20113 / 4.23 ( 840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4405.91 seconds wall clock time: 75 minutes 58.77 seconds (4558.77 seconds total)