Starting phenix.real_space_refine on Fri May 16 08:58:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xkr_38423/05_2025/8xkr_38423.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xkr_38423/05_2025/8xkr_38423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xkr_38423/05_2025/8xkr_38423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xkr_38423/05_2025/8xkr_38423.map" model { file = "/net/cci-nas-00/data/ceres_data/8xkr_38423/05_2025/8xkr_38423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xkr_38423/05_2025/8xkr_38423.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 8924 2.51 5 N 2427 2.21 5 O 2643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14118 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 311 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 1 Chain: "D" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 254 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain breaks: 1 Chain: "E" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain breaks: 1 Chain: "C" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Chain: "A" Number of atoms: 6544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 813, 6544 Classifications: {'peptide': 813} Link IDs: {'PTRANS': 42, 'TRANS': 770} Chain breaks: 13 Chain: "B" Number of atoms: 6383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6383 Classifications: {'peptide': 795} Link IDs: {'PTRANS': 42, 'TRANS': 752} Chain breaks: 6 Time building chain proxies: 10.60, per 1000 atoms: 0.75 Number of scatterers: 14118 At special positions: 0 Unit cell: (99.66, 155.1, 165, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 2643 8.00 N 2427 7.00 C 8924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 48 " distance=2.03 Simple disulfide: pdb=" SG CYS F 18 " - pdb=" SG CYS F 61 " distance=2.03 Simple disulfide: pdb=" SG CYS F 47 " - pdb=" SG CYS F 52 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 52 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 48 " distance=2.05 Simple disulfide: pdb=" SG CYS E 18 " - pdb=" SG CYS E 61 " distance=2.01 Simple disulfide: pdb=" SG CYS E 47 " - pdb=" SG CYS E 52 " distance=2.04 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 48 " distance=2.03 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 61 " distance=2.02 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 462 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 887 " distance=2.03 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 822 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 209 " distance=2.02 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 215 " distance=2.02 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 228 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 243 " distance=2.03 Simple disulfide: pdb=" SG CYS B 239 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 280 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 674 " - pdb=" SG CYS B 887 " distance=2.03 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 822 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.7 seconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3306 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 30 sheets defined 16.4% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'F' and resid 7 through 18 removed outlier: 3.522A pdb=" N VAL F 11 " --> pdb=" O GLY F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 61 removed outlier: 3.722A pdb=" N GLU F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR F 60 " --> pdb=" O ARG F 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 removed outlier: 3.521A pdb=" N VAL D 11 " --> pdb=" O GLY D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 removed outlier: 3.839A pdb=" N GLU D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET D 59 " --> pdb=" O ARG D 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 19 removed outlier: 4.016A pdb=" N GLY E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 51 Processing helix chain 'E' and resid 53 through 62 removed outlier: 4.655A pdb=" N MET E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 Processing helix chain 'C' and resid 42 through 48 Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.615A pdb=" N MET C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 60 " --> pdb=" O ARG C 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 48 removed outlier: 4.126A pdb=" N HIS A 48 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.233A pdb=" N ILE A 163 " --> pdb=" O ASP A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.530A pdb=" N HIS A 290 " --> pdb=" O CYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 358 removed outlier: 4.615A pdb=" N GLU A 356 " --> pdb=" O SER A 353 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 358 " --> pdb=" O GLN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.227A pdb=" N PHE A 408 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.726A pdb=" N ILE A 466 " --> pdb=" O CYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.635A pdb=" N GLU A 670 " --> pdb=" O SER A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 740 Processing helix chain 'A' and resid 889 through 894 removed outlier: 3.917A pdb=" N PHE A 893 " --> pdb=" O SER A 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 51 removed outlier: 3.716A pdb=" N ARG B 46 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 48 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.642A pdb=" N LYS B 191 " --> pdb=" O PRO B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 283 through 295 removed outlier: 3.767A pdb=" N CYS B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 377 through 386 Processing helix chain 'B' and resid 462 through 472 Processing helix chain 'B' and resid 523 through 527 Processing helix chain 'B' and resid 569 through 573 Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.981A pdb=" N GLU B 670 " --> pdb=" O SER B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 897 removed outlier: 3.841A pdb=" N LEU B 895 " --> pdb=" O LYS B 891 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.263A pdb=" N GLU A 33 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 55 " --> pdb=" O GLU A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 121 removed outlier: 5.731A pdb=" N SER A 143 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 120 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 201 removed outlier: 3.565A pdb=" N THR A 199 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 319 through 321 Processing sheet with id=AA5, first strand: chain 'A' and resid 362 through 363 Processing sheet with id=AA6, first strand: chain 'A' and resid 367 through 369 Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 512 Processing sheet with id=AA8, first strand: chain 'A' and resid 557 through 561 removed outlier: 3.879A pdb=" N GLY A 529 " --> pdb=" O LEU A 596 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 561 removed outlier: 3.684A pdb=" N ILE A 591 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 629 through 634 removed outlier: 6.233A pdb=" N GLN A 637 " --> pdb=" O ASN A 633 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 786 through 789 removed outlier: 3.671A pdb=" N VAL A 789 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 655 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 830 " --> pdb=" O TYR A 806 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 removed outlier: 3.878A pdb=" N VAL A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 883 through 887 removed outlier: 3.753A pdb=" N GLU A 873 " --> pdb=" O ARG A 914 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 914 " --> pdb=" O GLU A 873 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 930 " --> pdb=" O TYR A 909 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 33 through 35 removed outlier: 7.220A pdb=" N GLU B 33 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE B 56 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N CYS B 35 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.259A pdb=" N LEU B 60 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ARG B 145 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 121 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLU B 147 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE B 123 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL B 144 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL B 173 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE B 146 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 198 through 199 Processing sheet with id=AB8, first strand: chain 'B' and resid 239 through 243 removed outlier: 5.906A pdb=" N LEU B 240 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N CYS B 255 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN B 242 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AC1, first strand: chain 'B' and resid 272 through 275 Processing sheet with id=AC2, first strand: chain 'B' and resid 320 through 322 removed outlier: 4.162A pdb=" N LEU B 327 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.419A pdb=" N LYS B 346 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU B 367 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ARG B 398 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE B 369 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE B 427 " --> pdb=" O PHE B 454 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 362 through 363 Processing sheet with id=AC5, first strand: chain 'B' and resid 557 through 561 Processing sheet with id=AC6, first strand: chain 'B' and resid 626 through 631 removed outlier: 4.655A pdb=" N ASP B 627 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 643 " --> pdb=" O ASP B 627 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 657 through 658 Processing sheet with id=AC8, first strand: chain 'B' and resid 805 through 810 removed outlier: 4.154A pdb=" N TYR B 806 " --> pdb=" O ALA B 830 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 830 " --> pdb=" O TYR B 806 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 813 through 815 removed outlier: 3.995A pdb=" N GLN B 815 " --> pdb=" O ARG B 821 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 847 through 850 removed outlier: 3.781A pdb=" N VAL B 854 " --> pdb=" O PHE B 850 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 883 through 889 removed outlier: 6.012A pdb=" N ILE B 913 " --> pdb=" O TRP B 924 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TRP B 924 " --> pdb=" O ILE B 913 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ALA B 915 " --> pdb=" O GLY B 922 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 883 through 889 removed outlier: 3.607A pdb=" N GLY B 907 " --> pdb=" O VAL B 932 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 911 " --> pdb=" O THR B 928 " (cutoff:3.500A) 285 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3388 1.33 - 1.45: 3023 1.45 - 1.57: 7867 1.57 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 14428 Sorted by residual: bond pdb=" C LEU B 50 " pdb=" N GLU B 51 " ideal model delta sigma weight residual 1.335 1.293 0.042 1.34e-02 5.57e+03 9.96e+00 bond pdb=" N SER B 77 " pdb=" CA SER B 77 " ideal model delta sigma weight residual 1.456 1.422 0.035 1.16e-02 7.43e+03 8.87e+00 bond pdb=" CA ASP A 510 " pdb=" C ASP A 510 " ideal model delta sigma weight residual 1.524 1.483 0.041 1.43e-02 4.89e+03 8.21e+00 bond pdb=" CA CYS E 61 " pdb=" CB CYS E 61 " ideal model delta sigma weight residual 1.529 1.486 0.043 1.58e-02 4.01e+03 7.28e+00 bond pdb=" CA CYS E 48 " pdb=" C CYS E 48 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.28e-02 6.10e+03 7.18e+00 ... (remaining 14423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 19179 2.27 - 4.54: 277 4.54 - 6.80: 40 6.80 - 9.07: 12 9.07 - 11.34: 6 Bond angle restraints: 19514 Sorted by residual: angle pdb=" N LEU E 10 " pdb=" CA LEU E 10 " pdb=" C LEU E 10 " ideal model delta sigma weight residual 111.14 101.89 9.25 1.08e+00 8.57e-01 7.33e+01 angle pdb=" N CYS B 209 " pdb=" CA CYS B 209 " pdb=" C CYS B 209 " ideal model delta sigma weight residual 108.46 114.95 -6.49 1.51e+00 4.39e-01 1.84e+01 angle pdb=" C LYS A 511 " pdb=" N ILE A 512 " pdb=" CA ILE A 512 " ideal model delta sigma weight residual 122.93 117.71 5.22 1.26e+00 6.30e-01 1.72e+01 angle pdb=" CB ARG D 55 " pdb=" CG ARG D 55 " pdb=" CD ARG D 55 " ideal model delta sigma weight residual 111.30 120.01 -8.71 2.30e+00 1.89e-01 1.43e+01 angle pdb=" CB MET C 59 " pdb=" CG MET C 59 " pdb=" SD MET C 59 " ideal model delta sigma weight residual 112.70 124.04 -11.34 3.00e+00 1.11e-01 1.43e+01 ... (remaining 19509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 7463 17.68 - 35.36: 955 35.36 - 53.04: 289 53.04 - 70.72: 49 70.72 - 88.40: 22 Dihedral angle restraints: 8778 sinusoidal: 3665 harmonic: 5113 Sorted by residual: dihedral pdb=" CB CYS B 186 " pdb=" SG CYS B 186 " pdb=" SG CYS B 209 " pdb=" CB CYS B 209 " ideal model delta sinusoidal sigma weight residual 93.00 -179.67 -87.33 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS B 286 " pdb=" SG CYS B 286 " pdb=" SG CYS B 311 " pdb=" CB CYS B 311 " ideal model delta sinusoidal sigma weight residual -86.00 -161.82 75.82 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CB CYS A 315 " pdb=" SG CYS A 315 " pdb=" SG CYS A 328 " pdb=" CB CYS A 328 " ideal model delta sinusoidal sigma weight residual 93.00 149.44 -56.44 1 1.00e+01 1.00e-02 4.29e+01 ... (remaining 8775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1803 0.062 - 0.123: 303 0.123 - 0.185: 17 0.185 - 0.246: 1 0.246 - 0.308: 2 Chirality restraints: 2126 Sorted by residual: chirality pdb=" CG LEU B 89 " pdb=" CB LEU B 89 " pdb=" CD1 LEU B 89 " pdb=" CD2 LEU B 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CG LEU E 10 " pdb=" CB LEU E 10 " pdb=" CD1 LEU E 10 " pdb=" CD2 LEU E 10 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CG LEU B 155 " pdb=" CB LEU B 155 " pdb=" CD1 LEU B 155 " pdb=" CD2 LEU B 155 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.61e-01 ... (remaining 2123 not shown) Planarity restraints: 2522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 9 " 0.012 2.00e-02 2.50e+03 2.53e-02 6.41e+00 pdb=" C GLU E 9 " -0.044 2.00e-02 2.50e+03 pdb=" O GLU E 9 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU E 10 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 156 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C ALA B 156 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA B 156 " -0.015 2.00e-02 2.50e+03 pdb=" N THR B 157 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E 47 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C CYS E 47 " -0.035 2.00e-02 2.50e+03 pdb=" O CYS E 47 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS E 48 " 0.012 2.00e-02 2.50e+03 ... (remaining 2519 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1517 2.74 - 3.28: 15231 3.28 - 3.82: 24281 3.82 - 4.36: 28243 4.36 - 4.90: 46366 Nonbonded interactions: 115638 Sorted by model distance: nonbonded pdb=" O TYR A 534 " pdb=" OG1 THR A 557 " model vdw 2.205 3.040 nonbonded pdb=" O LEU A 106 " pdb=" N LEU A 136 " model vdw 2.213 3.120 nonbonded pdb=" O LEU A 640 " pdb=" OG SER A 794 " model vdw 2.222 3.040 nonbonded pdb=" O ILE B 82 " pdb=" OG1 THR B 107 " model vdw 2.225 3.040 nonbonded pdb=" ND2 ASN B 791 " pdb=" O GLN B 811 " model vdw 2.229 3.120 ... (remaining 115633 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 31 through 157 or resid 159 through 519 or resid 521 throu \ gh 651 or resid 653 through 679 or resid 785 through 837 or resid 840 through 93 \ 5)) selection = (chain 'B' and (resid 31 through 40 or resid 42 through 107 or resid 109 through \ 134 or resid 136 through 184 or resid 186 through 273 or resid 275 through 592 \ or resid 594 through 642 or resid 644 through 801 or resid 803 through 837 or re \ sid 840 through 917 or resid 919 through 935)) } ncs_group { reference = (chain 'C' and (resid 4 through 20 or resid 41 through 61)) selection = (chain 'F' and (resid 4 through 20 or resid 41 through 61)) } ncs_group { reference = (chain 'D' and (resid 6 through 17 or resid 42 or resid 44 through 59)) selection = (chain 'E' and (resid 6 through 17 or resid 19 or resid 44 through 59)) } 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: 15.800 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: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 34.750 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 : 0.004 0.046 14470 Z= 0.180 Angle : 0.704 11.339 19598 Z= 0.370 Chirality : 0.045 0.308 2126 Planarity : 0.004 0.049 2522 Dihedral : 17.123 88.396 5346 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.27 % Favored : 89.61 % Rotamer: Outliers : 0.82 % Allowed : 27.81 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.21), residues: 1704 helix: -1.54 (0.37), residues: 202 sheet: -0.47 (0.37), residues: 231 loop : -1.43 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 441 HIS 0.004 0.001 HIS A 737 PHE 0.022 0.001 PHE A 509 TYR 0.009 0.001 TYR B 87 ARG 0.005 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.27386 ( 265) hydrogen bonds : angle 10.41327 ( 735) SS BOND : bond 0.00475 ( 42) SS BOND : angle 0.85693 ( 84) covalent geometry : bond 0.00352 (14428) covalent geometry : angle 0.70297 (19514) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.2960 (OUTLIER) cc_final: 0.2256 (p90) outliers start: 13 outliers final: 5 residues processed: 75 average time/residue: 0.3075 time to fit residues: 34.4869 Evaluate side-chains 62 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 89 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 0.0980 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 ASN A 811 GLN ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.099289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.067699 restraints weight = 83704.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.068744 restraints weight = 43690.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.069532 restraints weight = 29465.315| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14470 Z= 0.173 Angle : 0.657 11.312 19598 Z= 0.336 Chirality : 0.045 0.177 2126 Planarity : 0.005 0.075 2522 Dihedral : 5.754 55.772 1926 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 3.28 % Allowed : 25.91 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1704 helix: -1.42 (0.35), residues: 223 sheet: -0.60 (0.36), residues: 228 loop : -1.41 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 441 HIS 0.005 0.001 HIS A 290 PHE 0.017 0.001 PHE A 732 TYR 0.016 0.001 TYR F 60 ARG 0.006 0.001 ARG A 506 Details of bonding type rmsd hydrogen bonds : bond 0.05077 ( 265) hydrogen bonds : angle 7.63606 ( 735) SS BOND : bond 0.00330 ( 42) SS BOND : angle 1.05355 ( 84) covalent geometry : bond 0.00383 (14428) covalent geometry : angle 0.65442 (19514) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 60 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.3803 (OUTLIER) cc_final: 0.2512 (p90) REVERT: A 83 MET cc_start: 0.0274 (mmm) cc_final: -0.0120 (mmm) REVERT: A 114 LEU cc_start: 0.4006 (OUTLIER) cc_final: 0.3696 (mt) REVERT: A 656 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7436 (tp) REVERT: A 809 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: B 71 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7532 (tm-30) outliers start: 52 outliers final: 24 residues processed: 108 average time/residue: 0.2257 time to fit residues: 39.0117 Evaluate side-chains 86 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 809 GLU Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 117 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 HIS ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.097758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.065090 restraints weight = 83246.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.066445 restraints weight = 43121.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.067209 restraints weight = 29257.978| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14470 Z= 0.218 Angle : 0.675 11.387 19598 Z= 0.343 Chirality : 0.045 0.169 2126 Planarity : 0.005 0.060 2522 Dihedral : 5.821 57.520 1926 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 5.30 % Allowed : 25.03 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.20), residues: 1704 helix: -1.67 (0.32), residues: 237 sheet: -0.78 (0.35), residues: 231 loop : -1.44 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 441 HIS 0.005 0.001 HIS B 340 PHE 0.017 0.002 PHE B 408 TYR 0.012 0.001 TYR F 60 ARG 0.009 0.001 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 265) hydrogen bonds : angle 7.07861 ( 735) SS BOND : bond 0.00361 ( 42) SS BOND : angle 0.89344 ( 84) covalent geometry : bond 0.00486 (14428) covalent geometry : angle 0.67345 (19514) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 55 time to evaluate : 1.542 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: F 16 PHE cc_start: 0.4047 (OUTLIER) cc_final: 0.2905 (p90) REVERT: C 9 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: A 83 MET cc_start: 0.0472 (mmm) cc_final: -0.0005 (mmm) REVERT: A 656 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7746 (tp) REVERT: B 364 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8132 (m110) outliers start: 84 outliers final: 40 residues processed: 136 average time/residue: 0.2419 time to fit residues: 50.9971 Evaluate side-chains 95 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 51 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 809 GLU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 364 ASN Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 824 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 114 optimal weight: 6.9990 chunk 164 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 99 optimal weight: 0.0370 chunk 49 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 163 optimal weight: 30.0000 chunk 70 optimal weight: 6.9990 overall best weight: 3.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.096879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.065590 restraints weight = 83203.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.065475 restraints weight = 43330.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.066188 restraints weight = 30222.597| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14470 Z= 0.265 Angle : 0.706 9.447 19598 Z= 0.360 Chirality : 0.046 0.145 2126 Planarity : 0.005 0.048 2522 Dihedral : 6.040 59.036 1926 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.38 % Favored : 88.56 % Rotamer: Outliers : 5.49 % Allowed : 25.35 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.20), residues: 1704 helix: -1.81 (0.32), residues: 237 sheet: -1.02 (0.34), residues: 240 loop : -1.50 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 578 HIS 0.006 0.001 HIS B 340 PHE 0.027 0.002 PHE A 409 TYR 0.017 0.001 TYR F 60 ARG 0.006 0.000 ARG D 55 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 265) hydrogen bonds : angle 6.96521 ( 735) SS BOND : bond 0.00475 ( 42) SS BOND : angle 1.01654 ( 84) covalent geometry : bond 0.00589 (14428) covalent geometry : angle 0.70400 (19514) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 57 time to evaluate : 1.521 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: F 16 PHE cc_start: 0.4106 (OUTLIER) cc_final: 0.3098 (p90) REVERT: F 59 MET cc_start: 0.8074 (mpp) cc_final: 0.7534 (mmm) REVERT: C 9 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: A 656 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7810 (tp) REVERT: B 71 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7490 (tm-30) REVERT: B 141 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8164 (ttt180) REVERT: B 364 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.8116 (m110) REVERT: B 437 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8071 (tp-100) outliers start: 87 outliers final: 56 residues processed: 140 average time/residue: 0.2232 time to fit residues: 49.1513 Evaluate side-chains 117 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 54 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 809 GLU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 364 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 30.0000 chunk 9 optimal weight: 0.0020 chunk 17 optimal weight: 0.7980 chunk 151 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 22 optimal weight: 0.3980 chunk 148 optimal weight: 0.0270 chunk 82 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.3846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN B 202 ASN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.099699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.067668 restraints weight = 84315.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.069153 restraints weight = 42593.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.070020 restraints weight = 28359.170| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14470 Z= 0.110 Angle : 0.620 8.304 19598 Z= 0.313 Chirality : 0.045 0.191 2126 Planarity : 0.004 0.054 2522 Dihedral : 5.350 53.004 1920 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.04 % Favored : 91.90 % Rotamer: Outliers : 3.47 % Allowed : 26.73 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.20), residues: 1704 helix: -1.56 (0.33), residues: 227 sheet: -1.03 (0.33), residues: 258 loop : -1.37 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 659 HIS 0.007 0.001 HIS A 654 PHE 0.017 0.001 PHE A 732 TYR 0.013 0.001 TYR A 534 ARG 0.004 0.000 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 265) hydrogen bonds : angle 6.33982 ( 735) SS BOND : bond 0.00346 ( 42) SS BOND : angle 0.84263 ( 84) covalent geometry : bond 0.00247 (14428) covalent geometry : angle 0.61917 (19514) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 64 time to evaluate : 1.552 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: F 59 MET cc_start: 0.7934 (mpp) cc_final: 0.7448 (mmm) REVERT: C 9 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: A 83 MET cc_start: 0.0272 (mmm) cc_final: -0.0234 (mmm) REVERT: A 656 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7756 (tp) REVERT: B 71 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7578 (tm-30) outliers start: 55 outliers final: 36 residues processed: 113 average time/residue: 0.2176 time to fit residues: 39.6249 Evaluate side-chains 98 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 59 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 147 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 173 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 169 optimal weight: 40.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.097623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.064201 restraints weight = 83809.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.065577 restraints weight = 43648.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.066421 restraints weight = 29742.396| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14470 Z= 0.206 Angle : 0.648 9.512 19598 Z= 0.328 Chirality : 0.045 0.164 2126 Planarity : 0.004 0.048 2522 Dihedral : 5.371 55.036 1918 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 3.97 % Allowed : 26.23 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.20), residues: 1704 helix: -1.50 (0.34), residues: 223 sheet: -1.15 (0.33), residues: 262 loop : -1.34 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 441 HIS 0.005 0.001 HIS B 340 PHE 0.018 0.002 PHE A 509 TYR 0.012 0.001 TYR B 87 ARG 0.004 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 265) hydrogen bonds : angle 6.39176 ( 735) SS BOND : bond 0.00296 ( 42) SS BOND : angle 0.86697 ( 84) covalent geometry : bond 0.00463 (14428) covalent geometry : angle 0.64700 (19514) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 58 time to evaluate : 1.742 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: F 16 PHE cc_start: 0.4253 (OUTLIER) cc_final: 0.3120 (p90) REVERT: C 9 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: A 83 MET cc_start: 0.0529 (mmm) cc_final: -0.0046 (mmm) REVERT: A 656 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7781 (tp) REVERT: B 364 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.8078 (m110) outliers start: 63 outliers final: 45 residues processed: 118 average time/residue: 0.2049 time to fit residues: 39.6439 Evaluate side-chains 107 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 58 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 364 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 30.0000 chunk 0 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 17 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.097557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.066506 restraints weight = 83503.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.066293 restraints weight = 42617.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.067075 restraints weight = 29119.728| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14470 Z= 0.215 Angle : 0.670 9.390 19598 Z= 0.340 Chirality : 0.045 0.211 2126 Planarity : 0.005 0.051 2522 Dihedral : 5.505 55.815 1916 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.27 % Favored : 89.67 % Rotamer: Outliers : 4.60 % Allowed : 25.73 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.20), residues: 1704 helix: -1.52 (0.34), residues: 220 sheet: -1.21 (0.32), residues: 265 loop : -1.37 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 578 HIS 0.005 0.001 HIS B 340 PHE 0.016 0.002 PHE A 409 TYR 0.020 0.001 TYR F 60 ARG 0.005 0.000 ARG F 55 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 265) hydrogen bonds : angle 6.44117 ( 735) SS BOND : bond 0.00354 ( 42) SS BOND : angle 0.94981 ( 84) covalent geometry : bond 0.00482 (14428) covalent geometry : angle 0.66864 (19514) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 59 time to evaluate : 1.555 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: F 16 PHE cc_start: 0.4281 (OUTLIER) cc_final: 0.3140 (p90) REVERT: F 59 MET cc_start: 0.7769 (mpp) cc_final: 0.7237 (mmm) REVERT: C 9 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: A 656 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7844 (tp) REVERT: B 71 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: B 149 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8069 (m-40) REVERT: B 364 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.8070 (m110) REVERT: B 437 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8086 (tp-100) REVERT: B 471 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6971 (pt0) outliers start: 73 outliers final: 52 residues processed: 126 average time/residue: 0.2089 time to fit residues: 42.3191 Evaluate side-chains 116 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 56 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 364 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 103 optimal weight: 1.9990 chunk 19 optimal weight: 40.0000 chunk 113 optimal weight: 5.9990 chunk 68 optimal weight: 0.0870 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 0.0770 chunk 161 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 171 optimal weight: 40.0000 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.099121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.066765 restraints weight = 84670.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.068194 restraints weight = 43287.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.069122 restraints weight = 28882.049| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14470 Z= 0.111 Angle : 0.612 10.214 19598 Z= 0.306 Chirality : 0.044 0.197 2126 Planarity : 0.004 0.054 2522 Dihedral : 5.190 51.836 1916 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 3.59 % Allowed : 26.73 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.20), residues: 1704 helix: -1.47 (0.34), residues: 223 sheet: -1.08 (0.32), residues: 269 loop : -1.34 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 441 HIS 0.006 0.001 HIS A 654 PHE 0.020 0.001 PHE A 509 TYR 0.011 0.001 TYR A 534 ARG 0.003 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 265) hydrogen bonds : angle 6.06026 ( 735) SS BOND : bond 0.00183 ( 42) SS BOND : angle 0.83499 ( 84) covalent geometry : bond 0.00257 (14428) covalent geometry : angle 0.61086 (19514) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 60 time to evaluate : 1.525 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: F 16 PHE cc_start: 0.4184 (OUTLIER) cc_final: 0.3136 (p90) REVERT: F 59 MET cc_start: 0.7683 (mpp) cc_final: 0.7147 (mmm) REVERT: E 45 ASP cc_start: 0.7078 (p0) cc_final: 0.6706 (t0) REVERT: A 83 MET cc_start: 0.0275 (mmm) cc_final: -0.0033 (mmm) REVERT: A 137 MET cc_start: -0.0961 (ttt) cc_final: -0.1860 (tpp) REVERT: A 356 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8357 (pm20) REVERT: A 512 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7819 (mm) REVERT: A 656 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7768 (tp) REVERT: B 71 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: B 149 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7893 (m-40) REVERT: B 606 TYR cc_start: 0.7685 (t80) cc_final: 0.7221 (t80) outliers start: 57 outliers final: 38 residues processed: 113 average time/residue: 0.2148 time to fit residues: 39.9889 Evaluate side-chains 101 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 57 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 25 optimal weight: 5.9990 chunk 125 optimal weight: 0.0270 chunk 157 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 chunk 129 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.099455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.067022 restraints weight = 84470.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.068428 restraints weight = 42270.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.069348 restraints weight = 28449.790| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14470 Z= 0.105 Angle : 0.616 11.377 19598 Z= 0.306 Chirality : 0.044 0.172 2126 Planarity : 0.004 0.054 2522 Dihedral : 5.106 52.997 1916 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.22 % Favored : 91.73 % Rotamer: Outliers : 3.09 % Allowed : 27.30 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.20), residues: 1704 helix: -1.32 (0.35), residues: 218 sheet: -1.15 (0.30), residues: 288 loop : -1.24 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 441 HIS 0.005 0.001 HIS A 654 PHE 0.015 0.001 PHE A 732 TYR 0.010 0.001 TYR F 60 ARG 0.008 0.000 ARG E 50 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 265) hydrogen bonds : angle 5.90019 ( 735) SS BOND : bond 0.00188 ( 42) SS BOND : angle 0.87347 ( 84) covalent geometry : bond 0.00243 (14428) covalent geometry : angle 0.61501 (19514) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 58 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.4050 (OUTLIER) cc_final: 0.3068 (p90) REVERT: F 59 MET cc_start: 0.7699 (mpp) cc_final: 0.7336 (mmm) REVERT: A 83 MET cc_start: 0.0441 (mmm) cc_final: 0.0154 (mmm) REVERT: A 137 MET cc_start: -0.0242 (ttt) cc_final: -0.1113 (tpp) REVERT: A 356 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8353 (pm20) REVERT: A 512 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7741 (mm) REVERT: A 656 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7777 (tp) REVERT: B 149 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7950 (m-40) REVERT: B 606 TYR cc_start: 0.7707 (t80) cc_final: 0.7249 (t80) outliers start: 49 outliers final: 35 residues processed: 101 average time/residue: 0.2099 time to fit residues: 34.9884 Evaluate side-chains 96 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 56 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 43 optimal weight: 10.0000 chunk 117 optimal weight: 0.5980 chunk 143 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 124 optimal weight: 0.0670 chunk 22 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.099217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.067185 restraints weight = 85403.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.068329 restraints weight = 43086.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.068975 restraints weight = 28642.926| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14470 Z= 0.116 Angle : 0.630 11.829 19598 Z= 0.310 Chirality : 0.044 0.162 2126 Planarity : 0.004 0.052 2522 Dihedral : 4.886 42.173 1914 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.39 % Favored : 91.55 % Rotamer: Outliers : 2.71 % Allowed : 27.62 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.20), residues: 1704 helix: -1.28 (0.34), residues: 224 sheet: -1.14 (0.30), residues: 288 loop : -1.23 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 441 HIS 0.004 0.001 HIS A 737 PHE 0.023 0.001 PHE A 509 TYR 0.010 0.001 TYR F 60 ARG 0.002 0.000 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.03267 ( 265) hydrogen bonds : angle 5.86653 ( 735) SS BOND : bond 0.00183 ( 42) SS BOND : angle 0.88324 ( 84) covalent geometry : bond 0.00269 (14428) covalent geometry : angle 0.62833 (19514) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 58 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.4070 (OUTLIER) cc_final: 0.3103 (p90) REVERT: F 59 MET cc_start: 0.7672 (mpp) cc_final: 0.7325 (mmm) REVERT: E 45 ASP cc_start: 0.8059 (t0) cc_final: 0.7709 (p0) REVERT: A 83 MET cc_start: 0.0465 (mmm) cc_final: 0.0187 (mmm) REVERT: A 125 MET cc_start: 0.2847 (tpp) cc_final: 0.2547 (mtt) REVERT: A 137 MET cc_start: -0.0096 (ttt) cc_final: -0.0965 (tpp) REVERT: A 356 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8363 (pm20) REVERT: A 656 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7748 (tp) REVERT: B 149 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7993 (m-40) REVERT: B 606 TYR cc_start: 0.7750 (t80) cc_final: 0.7276 (t80) outliers start: 43 outliers final: 37 residues processed: 97 average time/residue: 0.2010 time to fit residues: 32.8600 Evaluate side-chains 97 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 56 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 76 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 141 optimal weight: 0.2980 chunk 98 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.099515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.067333 restraints weight = 86199.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.068755 restraints weight = 43341.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.069678 restraints weight = 28503.502| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14470 Z= 0.108 Angle : 0.617 11.900 19598 Z= 0.304 Chirality : 0.043 0.167 2126 Planarity : 0.004 0.053 2522 Dihedral : 4.749 37.156 1914 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.75 % Favored : 92.19 % Rotamer: Outliers : 2.59 % Allowed : 27.74 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.20), residues: 1704 helix: -1.38 (0.34), residues: 232 sheet: -0.98 (0.31), residues: 283 loop : -1.24 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 441 HIS 0.004 0.001 HIS A 654 PHE 0.015 0.001 PHE A 732 TYR 0.010 0.001 TYR A 534 ARG 0.005 0.000 ARG E 50 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 265) hydrogen bonds : angle 5.70797 ( 735) SS BOND : bond 0.00185 ( 42) SS BOND : angle 0.76524 ( 84) covalent geometry : bond 0.00250 (14428) covalent geometry : angle 0.61646 (19514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8059.72 seconds wall clock time: 141 minutes 23.60 seconds (8483.60 seconds total)