Starting phenix.real_space_refine on Mon Dec 30 23:25:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xkr_38423/12_2024/8xkr_38423.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xkr_38423/12_2024/8xkr_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_38423/12_2024/8xkr_38423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xkr_38423/12_2024/8xkr_38423.map" model { file = "/net/cci-nas-00/data/ceres_data/8xkr_38423/12_2024/8xkr_38423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xkr_38423/12_2024/8xkr_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-5532/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: 11.33, per 1000 atoms: 0.80 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: 3.30 Conformation dependent library (CDL) restraints added in 2.0 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: 2.05 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: 4.78 Time building geometry restraints manager: 3.94 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: 9.080 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: 0.040 Extract box with map and model: 0.770 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.640 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.390 ------------------------------------------------------------------------------- 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 14428 Z= 0.232 Angle : 0.703 11.339 19514 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 *********************** 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 : 1.604 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: 0.2975 time to fit residues: 33.3894 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 : 1.739 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 14428 Z= 0.252 Angle : 0.654 11.312 19514 Z= 0.335 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 *********************** 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 : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.3432 (OUTLIER) cc_final: 0.2682 (p90) REVERT: A 83 MET cc_start: 0.0175 (mmm) cc_final: -0.0168 (mmm) REVERT: A 114 LEU cc_start: 0.4408 (OUTLIER) cc_final: 0.4155 (mt) REVERT: A 656 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.7425 (tp) REVERT: A 809 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: B 71 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7519 (tm-30) outliers start: 52 outliers final: 24 residues processed: 108 average time/residue: 0.2392 time to fit residues: 41.4046 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 : 1.730 ------------------------------------------------------------------------------- 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 87 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 171 optimal weight: 40.0000 chunk 140 optimal weight: 10.0000 chunk 156 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN B 226 HIS ** B 274 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14428 Z= 0.227 Angle : 0.626 11.394 19514 Z= 0.319 Chirality : 0.044 0.180 2126 Planarity : 0.004 0.050 2522 Dihedral : 5.658 59.691 1926 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.92 % Favored : 90.02 % Rotamer: Outliers : 4.54 % Allowed : 24.84 % Favored : 70.62 % 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: -1.63 (0.33), residues: 237 sheet: -0.79 (0.34), residues: 243 loop : -1.39 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 441 HIS 0.003 0.001 HIS B 226 PHE 0.017 0.001 PHE A 732 TYR 0.010 0.001 TYR F 60 ARG 0.014 0.000 ARG D 56 *********************** 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 132 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 60 time to evaluate : 1.732 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: 0.3566 (OUTLIER) cc_final: 0.2913 (p90) REVERT: C 9 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: A 83 MET cc_start: 0.0266 (mmm) cc_final: -0.0116 (mmm) REVERT: A 114 LEU cc_start: 0.4469 (OUTLIER) cc_final: 0.4212 (mt) REVERT: A 656 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7698 (tp) REVERT: B 149 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8126 (m-40) outliers start: 72 outliers final: 35 residues processed: 126 average time/residue: 0.2274 time to fit residues: 45.9203 Evaluate side-chains 95 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 55 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain E residue 10 LEU 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 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 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 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 591 ILE 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 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 63 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 149 ASN 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 306 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 449 THR 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 156 optimal weight: 0.0060 chunk 119 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 75 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN A 458 ASN ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14428 Z= 0.179 Angle : 0.601 8.876 19514 Z= 0.303 Chirality : 0.044 0.144 2126 Planarity : 0.004 0.055 2522 Dihedral : 5.546 57.638 1926 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.74 % Favored : 91.20 % Rotamer: Outliers : 3.78 % Allowed : 25.35 % Favored : 70.87 % 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: -1.43 (0.34), residues: 223 sheet: -0.95 (0.33), residues: 254 loop : -1.33 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 441 HIS 0.004 0.001 HIS B 226 PHE 0.016 0.001 PHE A 732 TYR 0.011 0.001 TYR A 534 ARG 0.008 0.000 ARG D 56 *********************** 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 120 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 60 time to evaluate : 1.663 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: 0.3674 (OUTLIER) cc_final: 0.2938 (p90) REVERT: C 9 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: A 114 LEU cc_start: 0.4449 (OUTLIER) cc_final: 0.4188 (mt) REVERT: A 656 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7727 (tp) REVERT: B 71 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7548 (tm-30) outliers start: 60 outliers final: 36 residues processed: 116 average time/residue: 0.2350 time to fit residues: 43.9311 Evaluate side-chains 98 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 57 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 10 LEU 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 114 LEU 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 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 512 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 727 SER 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 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 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 404 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 150 optimal weight: 7.9990 chunk 42 optimal weight: 0.0170 chunk 56 optimal weight: 4.9990 overall best weight: 2.9224 ------------------------------------------------------------------------------- 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 458 ASN ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14428 Z= 0.318 Angle : 0.664 8.661 19514 Z= 0.337 Chirality : 0.045 0.193 2126 Planarity : 0.005 0.051 2522 Dihedral : 5.518 58.905 1922 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.56 % Favored : 89.38 % Rotamer: Outliers : 4.60 % Allowed : 24.91 % Favored : 70.49 % 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: -1.93 (0.20), residues: 1704 helix: -1.68 (0.33), residues: 227 sheet: -0.95 (0.34), residues: 242 loop : -1.34 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 578 HIS 0.008 0.001 HIS B 226 PHE 0.023 0.002 PHE A 409 TYR 0.019 0.001 TYR F 60 ARG 0.006 0.000 ARG D 56 *********************** 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 129 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 56 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.3805 (OUTLIER) cc_final: 0.3049 (p90) REVERT: C 9 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: A 83 MET cc_start: 0.0467 (mmm) cc_final: 0.0028 (mmm) REVERT: A 656 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7753 (tp) REVERT: B 71 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7484 (tm-30) REVERT: B 149 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8103 (m-40) REVERT: B 437 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8078 (tp-100) outliers start: 73 outliers final: 48 residues processed: 125 average time/residue: 0.2449 time to fit residues: 47.7630 Evaluate side-chains 106 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 52 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 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 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 595 THR 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 866 ASN 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 93 VAL Chi-restraints excluded: chain B residue 117 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 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 361 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 226 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14428 Z= 0.344 Angle : 0.680 10.296 19514 Z= 0.346 Chirality : 0.045 0.171 2126 Planarity : 0.005 0.059 2522 Dihedral : 5.594 59.853 1918 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.50 % Favored : 89.44 % Rotamer: Outliers : 4.48 % Allowed : 25.16 % Favored : 70.37 % 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: -2.03 (0.20), residues: 1704 helix: -1.70 (0.32), residues: 235 sheet: -1.08 (0.34), residues: 239 loop : -1.40 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 578 HIS 0.007 0.001 HIS B 226 PHE 0.018 0.002 PHE A 409 TYR 0.013 0.001 TYR B 87 ARG 0.010 0.001 ARG E 50 *********************** 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 127 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 56 time to evaluate : 1.659 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: 0.7510 (mmm) cc_final: 0.6982 (mpp) REVERT: E 45 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6776 (t0) REVERT: C 9 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: A 83 MET cc_start: 0.0607 (mmm) cc_final: 0.0388 (mmm) REVERT: A 656 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7813 (tp) REVERT: B 71 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: B 149 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8211 (m-40) outliers start: 71 outliers final: 45 residues processed: 123 average time/residue: 0.2098 time to fit residues: 43.2055 Evaluate side-chains 103 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 53 time to evaluate : 1.726 ------------------------------------------------------------------------------- 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 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 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 591 ILE 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 647 ASP 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 93 VAL Chi-restraints excluded: chain B residue 117 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 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 361 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.0060 chunk 95 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 167 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14428 Z= 0.172 Angle : 0.618 9.514 19514 Z= 0.310 Chirality : 0.044 0.170 2126 Planarity : 0.004 0.053 2522 Dihedral : 5.202 53.271 1916 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 3.34 % Allowed : 26.42 % Favored : 70.24 % 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: -1.95 (0.20), residues: 1704 helix: -1.57 (0.32), residues: 237 sheet: -1.11 (0.32), residues: 267 loop : -1.33 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 441 HIS 0.006 0.001 HIS A 654 PHE 0.019 0.001 PHE A 509 TYR 0.012 0.001 TYR A 534 ARG 0.007 0.000 ARG E 50 *********************** 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 111 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 58 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.3721 (OUTLIER) cc_final: 0.3005 (p90) REVERT: C 9 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: A 83 MET cc_start: 0.0492 (mmm) cc_final: 0.0015 (mmm) REVERT: A 356 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8366 (pm20) REVERT: A 656 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7708 (tp) REVERT: B 71 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: B 149 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7885 (m-40) REVERT: B 236 HIS cc_start: 0.7246 (OUTLIER) cc_final: 0.6892 (t-170) REVERT: B 606 TYR cc_start: 0.7646 (t80) cc_final: 0.7193 (t80) outliers start: 53 outliers final: 39 residues processed: 108 average time/residue: 0.2113 time to fit residues: 38.3132 Evaluate side-chains 102 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 56 time to evaluate : 2.025 ------------------------------------------------------------------------------- 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 59 MET Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain C residue 9 GLU 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 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE 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 236 HIS 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 387 LEU Chi-restraints excluded: chain B residue 458 ASN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 15 optimal weight: 0.0870 chunk 131 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 overall best weight: 1.8762 ------------------------------------------------------------------------------- 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 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14428 Z= 0.232 Angle : 0.625 10.672 19514 Z= 0.312 Chirality : 0.044 0.160 2126 Planarity : 0.004 0.050 2522 Dihedral : 5.189 53.413 1916 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.85 % Allowed : 25.79 % Favored : 70.37 % 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: -1.94 (0.20), residues: 1704 helix: -1.52 (0.33), residues: 233 sheet: -1.13 (0.32), residues: 269 loop : -1.33 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 441 HIS 0.005 0.001 HIS A 737 PHE 0.015 0.001 PHE A 732 TYR 0.011 0.001 TYR F 60 ARG 0.006 0.000 ARG E 50 *********************** 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 120 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 59 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.3796 (OUTLIER) cc_final: 0.3078 (p90) REVERT: F 59 MET cc_start: 0.7347 (mmm) cc_final: 0.6760 (mpp) REVERT: C 9 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: A 293 CYS cc_start: 0.5614 (OUTLIER) cc_final: 0.4794 (m) REVERT: A 356 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8392 (pm20) REVERT: A 656 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7711 (tp) REVERT: B 71 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: B 149 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.7977 (m-40) REVERT: B 236 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.7058 (t-170) REVERT: B 580 MET cc_start: 0.9373 (ppp) cc_final: 0.9162 (ppp) REVERT: B 606 TYR cc_start: 0.7700 (t80) cc_final: 0.7238 (t80) outliers start: 61 outliers final: 42 residues processed: 115 average time/residue: 0.2230 time to fit residues: 41.9823 Evaluate side-chains 108 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 58 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 9 GLU 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 293 CYS 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 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE 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 117 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 236 HIS 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 361 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 437 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.0670 chunk 160 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 165 optimal weight: 20.0000 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14428 Z= 0.270 Angle : 0.646 10.798 19514 Z= 0.324 Chirality : 0.044 0.161 2126 Planarity : 0.004 0.048 2522 Dihedral : 5.297 53.460 1916 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.45 % Favored : 90.49 % Rotamer: Outliers : 3.91 % Allowed : 26.17 % Favored : 69.92 % 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: -1.89 (0.20), residues: 1704 helix: -1.40 (0.34), residues: 226 sheet: -1.22 (0.31), residues: 277 loop : -1.28 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 642 HIS 0.006 0.001 HIS B 226 PHE 0.018 0.001 PHE A 509 TYR 0.011 0.001 TYR B 87 ARG 0.005 0.000 ARG D 56 *********************** 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 120 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 58 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.3864 (OUTLIER) cc_final: 0.3141 (p90) REVERT: C 9 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: A 83 MET cc_start: 0.0335 (mmm) cc_final: 0.0046 (mmm) REVERT: A 137 MET cc_start: 0.0036 (ttt) cc_final: -0.0825 (tpp) REVERT: A 293 CYS cc_start: 0.5624 (OUTLIER) cc_final: 0.4811 (m) REVERT: A 356 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8388 (pm20) REVERT: A 656 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7738 (tp) REVERT: B 71 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: B 149 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.8043 (m-40) REVERT: B 606 TYR cc_start: 0.7787 (t80) cc_final: 0.7310 (t80) outliers start: 62 outliers final: 45 residues processed: 115 average time/residue: 0.2233 time to fit residues: 42.4113 Evaluate side-chains 109 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 57 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 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 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 293 CYS Chi-restraints excluded: chain A residue 301 CYS 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 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE 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 117 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 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 361 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 2.9990 chunk 78 optimal weight: 0.0870 chunk 114 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 14 optimal weight: 50.0000 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 147 optimal weight: 2.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 150 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14428 Z= 0.199 Angle : 0.646 12.396 19514 Z= 0.320 Chirality : 0.044 0.156 2126 Planarity : 0.004 0.050 2522 Dihedral : 5.227 51.751 1916 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 3.40 % Allowed : 26.67 % Favored : 69.92 % 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: -1.93 (0.20), residues: 1704 helix: -1.49 (0.33), residues: 232 sheet: -1.10 (0.32), residues: 269 loop : -1.34 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 441 HIS 0.004 0.001 HIS A 737 PHE 0.015 0.001 PHE A 732 TYR 0.010 0.001 TYR B 87 ARG 0.004 0.000 ARG E 50 ********************** 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 113 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 59 time to evaluate : 1.749 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: 0.3872 (OUTLIER) cc_final: 0.3199 (p90) REVERT: C 9 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: A 83 MET cc_start: 0.0494 (mmm) cc_final: 0.0234 (mmm) REVERT: A 137 MET cc_start: 0.0108 (ttt) cc_final: -0.0760 (tpp) REVERT: A 149 ASN cc_start: 0.6355 (OUTLIER) cc_final: 0.6057 (t0) REVERT: A 356 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: A 656 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7745 (tp) REVERT: B 71 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: B 149 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.7941 (m-40) REVERT: B 580 MET cc_start: 0.8999 (ppp) cc_final: 0.8622 (ppp) REVERT: B 606 TYR cc_start: 0.7755 (t80) cc_final: 0.7297 (t80) outliers start: 54 outliers final: 43 residues processed: 109 average time/residue: 0.2029 time to fit residues: 37.2125 Evaluate side-chains 106 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 56 time to evaluate : 1.988 ------------------------------------------------------------------------------- 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 9 GLU 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 149 ASN 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 301 CYS 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 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE 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 117 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 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 387 LEU Chi-restraints excluded: chain B residue 404 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.5152 > 50: distance: 23 - 102: 9.576 distance: 87 - 89: 6.681 distance: 89 - 90: 4.657 distance: 90 - 91: 4.619 distance: 90 - 93: 10.804 distance: 91 - 95: 3.212 distance: 93 - 94: 3.184 distance: 95 - 96: 10.616 distance: 96 - 97: 4.079 distance: 96 - 99: 9.978 distance: 97 - 98: 17.312 distance: 97 - 102: 15.622 distance: 99 - 100: 5.272 distance: 99 - 101: 7.659 distance: 102 - 103: 12.890 distance: 103 - 104: 4.509 distance: 103 - 106: 10.770 distance: 104 - 105: 20.815 distance: 104 - 113: 20.557 distance: 106 - 107: 8.642 distance: 107 - 108: 8.332 distance: 108 - 109: 7.926 distance: 113 - 114: 8.946 distance: 114 - 117: 6.040 distance: 115 - 116: 19.554 distance: 115 - 121: 16.146 distance: 117 - 118: 5.832 distance: 117 - 119: 8.081 distance: 118 - 120: 3.530 distance: 121 - 122: 8.160 distance: 122 - 123: 9.625 distance: 122 - 125: 6.598 distance: 123 - 124: 18.239 distance: 123 - 130: 26.157 distance: 125 - 126: 8.985 distance: 126 - 127: 3.411 distance: 127 - 129: 3.158 distance: 130 - 131: 18.570 distance: 131 - 132: 7.554 distance: 131 - 134: 8.738 distance: 132 - 133: 22.359 distance: 132 - 139: 35.994 distance: 134 - 135: 20.542 distance: 135 - 136: 8.199 distance: 136 - 137: 11.728 distance: 137 - 138: 6.875 distance: 140 - 141: 23.374 distance: 140 - 143: 50.201 distance: 141 - 142: 33.010 distance: 141 - 147: 28.928 distance: 143 - 144: 29.474 distance: 144 - 145: 29.861 distance: 144 - 146: 49.290 distance: 147 - 148: 24.300 distance: 148 - 149: 12.547 distance: 148 - 151: 10.995 distance: 149 - 150: 6.870 distance: 149 - 155: 12.254 distance: 151 - 152: 31.447 distance: 152 - 153: 25.827 distance: 152 - 154: 51.690 distance: 155 - 156: 14.054 distance: 156 - 157: 7.235 distance: 156 - 159: 10.330 distance: 157 - 158: 5.291 distance: 157 - 164: 3.302 distance: 159 - 160: 5.435 distance: 160 - 161: 6.715