Starting phenix.real_space_refine on Sun Jan 19 20:35:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xkr_38423/01_2025/8xkr_38423.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xkr_38423/01_2025/8xkr_38423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xkr_38423/01_2025/8xkr_38423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xkr_38423/01_2025/8xkr_38423.map" model { file = "/net/cci-nas-00/data/ceres_data/8xkr_38423/01_2025/8xkr_38423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xkr_38423/01_2025/8xkr_38423.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 8924 2.51 5 N 2427 2.21 5 O 2643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 14118 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 311 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 1 Chain: "D" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 254 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain breaks: 1 Chain: "E" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain breaks: 1 Chain: "C" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Chain: "A" Number of atoms: 6544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 813, 6544 Classifications: {'peptide': 813} Link IDs: {'PTRANS': 42, 'TRANS': 770} Chain breaks: 13 Chain: "B" Number of atoms: 6383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6383 Classifications: {'peptide': 795} Link IDs: {'PTRANS': 42, 'TRANS': 752} Chain breaks: 6 Time building chain proxies: 10.04, per 1000 atoms: 0.71 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: 3.16 Conformation dependent library (CDL) restraints added in 1.9 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: 2.04 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: 4.94 Time building geometry restraints manager: 3.66 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: 22.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 34.790 Find NCS groups from input model: 0.640 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: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.080 ------------------------------------------------------------------------------- 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 : 1.736 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: 0.3095 time to fit residues: 34.4765 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 : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 89 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 0.0980 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 ASN A 811 GLN ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.099289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.067699 restraints weight = 83704.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.068744 restraints weight = 43690.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.069532 restraints weight = 29465.315| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 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 : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.3803 (OUTLIER) cc_final: 0.2512 (p90) REVERT: A 83 MET cc_start: 0.0274 (mmm) cc_final: -0.0120 (mmm) REVERT: A 114 LEU cc_start: 0.4006 (OUTLIER) cc_final: 0.3696 (mt) REVERT: A 656 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7436 (tp) REVERT: A 809 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: B 71 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7532 (tm-30) outliers start: 52 outliers final: 24 residues processed: 108 average time/residue: 0.2408 time to fit residues: 41.8509 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 : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 809 GLU Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 117 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 38 optimal weight: 0.0010 chunk 41 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.9392 ------------------------------------------------------------------------------- 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 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.098743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.066446 restraints weight = 83264.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.067880 restraints weight = 42622.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.068691 restraints weight = 28845.756| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14428 Z= 0.236 Angle : 0.629 11.738 19514 Z= 0.320 Chirality : 0.044 0.165 2126 Planarity : 0.004 0.056 2522 Dihedral : 5.676 59.153 1926 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.04 % Favored : 89.91 % Rotamer: Outliers : 4.73 % Allowed : 24.78 % 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: -1.95 (0.20), residues: 1704 helix: -1.64 (0.33), residues: 237 sheet: -0.81 (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 0.004 0.001 HIS B 226 PHE 0.017 0.001 PHE A 732 TYR 0.010 0.001 TYR F 60 ARG 0.011 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 135 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 60 time to evaluate : 1.818 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: 0.3936 (OUTLIER) cc_final: 0.2890 (p90) REVERT: C 9 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: A 83 MET cc_start: 0.0398 (mmm) cc_final: -0.0048 (mmm) REVERT: A 114 LEU cc_start: 0.4008 (OUTLIER) cc_final: 0.3693 (mt) REVERT: A 656 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7694 (tp) REVERT: B 149 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8153 (m-40) outliers start: 75 outliers final: 37 residues processed: 129 average time/residue: 0.2423 time to fit residues: 48.9710 Evaluate side-chains 96 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 54 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 404 VAL 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 114 optimal weight: 3.9990 chunk 164 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 163 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.095836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.062376 restraints weight = 82553.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.063634 restraints weight = 43628.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.064501 restraints weight = 30184.198| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 14428 Z= 0.487 Angle : 0.777 10.330 19514 Z= 0.397 Chirality : 0.048 0.175 2126 Planarity : 0.005 0.061 2522 Dihedral : 6.221 58.613 1926 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.21 % Favored : 87.73 % Rotamer: Outliers : 5.74 % Allowed : 24.65 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.20), residues: 1704 helix: -1.77 (0.32), residues: 232 sheet: -1.13 (0.35), residues: 237 loop : -1.46 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 642 HIS 0.013 0.002 HIS B 226 PHE 0.033 0.002 PHE A 409 TYR 0.018 0.002 TYR F 60 ARG 0.007 0.001 ARG E 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 148 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 57 time to evaluate : 1.704 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: 0.4168 (OUTLIER) cc_final: 0.3086 (p90) REVERT: F 59 MET cc_start: 0.8136 (mpp) cc_final: 0.7630 (mmm) REVERT: C 9 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: A 114 LEU cc_start: 0.3996 (OUTLIER) cc_final: 0.3650 (mt) REVERT: A 656 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7850 (tp) REVERT: A 733 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8441 (tm-30) REVERT: B 71 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7433 (tm-30) REVERT: B 141 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8283 (ttt180) REVERT: B 437 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8125 (tp-100) outliers start: 91 outliers final: 52 residues processed: 145 average time/residue: 0.2409 time to fit residues: 53.7753 Evaluate side-chains 113 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 54 time to evaluate : 1.831 ------------------------------------------------------------------------------- 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 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 367 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 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 508 SER Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 148 optimal weight: 0.0010 chunk 82 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- 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 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.098029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.065957 restraints weight = 83813.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.066988 restraints weight = 42659.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.067715 restraints weight = 28781.052| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14428 Z= 0.223 Angle : 0.645 8.596 19514 Z= 0.327 Chirality : 0.045 0.193 2126 Planarity : 0.004 0.051 2522 Dihedral : 5.600 55.841 1920 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 3.91 % Allowed : 26.73 % Favored : 69.36 % 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: -2.02 (0.20), residues: 1704 helix: -1.61 (0.33), residues: 229 sheet: -1.06 (0.34), residues: 250 loop : -1.42 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 441 HIS 0.006 0.001 HIS A 654 PHE 0.018 0.001 PHE A 732 TYR 0.011 0.001 TYR B 134 ARG 0.004 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 124 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 62 time to evaluate : 1.551 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: 0.4216 (OUTLIER) cc_final: 0.3135 (p90) REVERT: C 9 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: A 83 MET cc_start: 0.0491 (mmm) cc_final: -0.0012 (mmm) REVERT: A 656 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7778 (tp) REVERT: B 71 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: B 149 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7978 (m110) outliers start: 62 outliers final: 40 residues processed: 120 average time/residue: 0.2200 time to fit residues: 42.6489 Evaluate side-chains 105 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 60 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 16 PHE 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 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 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 45 THR 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 149 ASN Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 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 361 THR Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 147 optimal weight: 9.9990 chunk 151 optimal weight: 0.0980 chunk 126 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 169 optimal weight: 50.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 212 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.098268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.066313 restraints weight = 84395.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.066946 restraints weight = 42705.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.067594 restraints weight = 29035.986| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2065 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= 0.214 Angle : 0.626 8.893 19514 Z= 0.316 Chirality : 0.044 0.163 2126 Planarity : 0.004 0.048 2522 Dihedral : 5.438 52.734 1920 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 4.48 % Allowed : 26.10 % Favored : 69.42 % 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: -1.59 (0.33), residues: 230 sheet: -1.14 (0.33), residues: 264 loop : -1.33 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 441 HIS 0.004 0.001 HIS B 226 PHE 0.019 0.001 PHE A 509 TYR 0.014 0.001 TYR F 60 ARG 0.004 0.000 ARG F 55 *********************** 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 134 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 63 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 MET cc_start: 0.7794 (mpp) cc_final: 0.7318 (mmm) REVERT: C 9 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: A 83 MET cc_start: 0.0477 (mmm) cc_final: -0.0088 (mmm) REVERT: A 114 LEU cc_start: 0.4413 (OUTLIER) cc_final: 0.4134 (mt) REVERT: A 656 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7788 (tp) REVERT: B 71 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7561 (tm-30) outliers start: 71 outliers final: 49 residues processed: 129 average time/residue: 0.2294 time to fit residues: 47.3095 Evaluate side-chains 113 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 60 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 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 252 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 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 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 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 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 449 THR Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 113 optimal weight: 0.0980 chunk 144 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 17 optimal weight: 30.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 202 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 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.097655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.064857 restraints weight = 84344.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.066106 restraints weight = 43228.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.066740 restraints weight = 29358.097| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2209 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= 0.269 Angle : 0.642 9.577 19514 Z= 0.325 Chirality : 0.045 0.210 2126 Planarity : 0.004 0.048 2522 Dihedral : 5.375 50.340 1916 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 4.41 % Allowed : 26.10 % Favored : 69.48 % 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: -1.50 (0.34), residues: 220 sheet: -1.15 (0.32), residues: 261 loop : -1.35 (0.18), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 441 HIS 0.006 0.001 HIS B 226 PHE 0.015 0.001 PHE A 732 TYR 0.013 0.001 TYR F 60 ARG 0.003 0.000 ARG B 145 *********************** 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 128 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 58 time to evaluate : 1.725 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: 0.4167 (OUTLIER) cc_final: 0.3034 (p90) REVERT: F 59 MET cc_start: 0.7771 (mpp) cc_final: 0.7280 (mmm) REVERT: C 9 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: A 114 LEU cc_start: 0.4286 (OUTLIER) cc_final: 0.3987 (mt) REVERT: A 656 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7799 (tp) REVERT: B 71 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7546 (tm-30) outliers start: 70 outliers final: 54 residues processed: 123 average time/residue: 0.2087 time to fit residues: 42.3626 Evaluate side-chains 117 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 58 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 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 252 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 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 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 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 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 449 THR Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 103 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 171 optimal weight: 40.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 202 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.098542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.065824 restraints weight = 83949.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.067094 restraints weight = 42584.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.068138 restraints weight = 29192.821| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2322 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= 0.196 Angle : 0.619 10.504 19514 Z= 0.310 Chirality : 0.044 0.204 2126 Planarity : 0.004 0.050 2522 Dihedral : 5.208 50.860 1916 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 4.04 % Allowed : 26.80 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.20), residues: 1704 helix: -1.45 (0.34), residues: 223 sheet: -1.19 (0.31), residues: 275 loop : -1.31 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 441 HIS 0.004 0.001 HIS A 654 PHE 0.020 0.001 PHE A 509 TYR 0.010 0.001 TYR A 534 ARG 0.003 0.000 ARG B 145 *********************** 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 125 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 61 time to evaluate : 1.856 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: 0.4174 (OUTLIER) cc_final: 0.3027 (p90) REVERT: F 59 MET cc_start: 0.7771 (mpp) cc_final: 0.7337 (mmm) REVERT: C 9 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: A 83 MET cc_start: 0.0247 (mmm) cc_final: -0.0081 (mmm) REVERT: A 114 LEU cc_start: 0.4363 (OUTLIER) cc_final: 0.4073 (mt) REVERT: A 356 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8388 (pm20) REVERT: A 656 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7788 (tp) REVERT: B 71 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: B 364 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.8058 (m110) outliers start: 64 outliers final: 47 residues processed: 121 average time/residue: 0.2241 time to fit residues: 44.4604 Evaluate side-chains 112 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 58 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 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 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 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 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 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 364 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 25 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.097835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.066784 restraints weight = 84013.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.066474 restraints weight = 42282.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.067256 restraints weight = 28804.716| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14428 Z= 0.246 Angle : 0.643 10.858 19514 Z= 0.324 Chirality : 0.044 0.194 2126 Planarity : 0.004 0.048 2522 Dihedral : 5.273 51.194 1916 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 4.04 % Allowed : 26.99 % Favored : 68.98 % 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: -1.47 (0.34), residues: 225 sheet: -1.23 (0.31), residues: 277 loop : -1.32 (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 B 226 PHE 0.016 0.001 PHE A 732 TYR 0.012 0.001 TYR F 60 ARG 0.003 0.000 ARG B 145 *********************** 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 121 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 57 time to evaluate : 1.624 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: 0.4137 (OUTLIER) cc_final: 0.3032 (p90) REVERT: F 59 MET cc_start: 0.7738 (mpp) cc_final: 0.7401 (mmm) REVERT: C 9 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: A 83 MET cc_start: 0.0565 (mmm) cc_final: 0.0216 (mmm) REVERT: A 114 LEU cc_start: 0.4383 (OUTLIER) cc_final: 0.4092 (mt) REVERT: A 656 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7765 (tp) REVERT: B 364 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.8057 (m110) outliers start: 64 outliers final: 51 residues processed: 116 average time/residue: 0.2305 time to fit residues: 44.3224 Evaluate side-chains 112 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 56 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 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 114 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 360 CYS 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 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 364 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 22 optimal weight: 0.0070 chunk 50 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.098963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.066523 restraints weight = 84663.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.067946 restraints weight = 42455.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.068853 restraints weight = 28177.407| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14428 Z= 0.171 Angle : 0.640 11.579 19514 Z= 0.316 Chirality : 0.044 0.176 2126 Planarity : 0.004 0.051 2522 Dihedral : 5.129 51.392 1916 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.03 % Allowed : 28.12 % Favored : 68.85 % 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: 225 sheet: -1.15 (0.31), residues: 277 loop : -1.30 (0.18), residues: 1202 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 0.023 0.001 PHE A 509 TYR 0.015 0.001 TYR B 827 ARG 0.003 0.000 ARG F 56 ********************** 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 111 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 63 time to evaluate : 1.677 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: 0.4087 (OUTLIER) cc_final: 0.3045 (p90) REVERT: F 59 MET cc_start: 0.7712 (mpp) cc_final: 0.7350 (mmm) REVERT: C 9 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: A 83 MET cc_start: 0.0617 (mmm) cc_final: 0.0281 (mmm) REVERT: A 114 LEU cc_start: 0.4342 (OUTLIER) cc_final: 0.4070 (mp) REVERT: A 137 MET cc_start: -0.1237 (ttt) cc_final: -0.2158 (tpp) REVERT: A 656 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7809 (tp) REVERT: B 606 TYR cc_start: 0.7750 (t80) cc_final: 0.7270 (t80) outliers start: 48 outliers final: 39 residues processed: 108 average time/residue: 0.2170 time to fit residues: 38.2143 Evaluate side-chains 101 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 58 time to evaluate : 1.895 ------------------------------------------------------------------------------- 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 A residue 67 LYS Chi-restraints excluded: chain A residue 103 PHE 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 252 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 507 THR 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 866 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 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 315 CYS 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 508 SER Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 76 optimal weight: 9.9990 chunk 99 optimal weight: 0.0970 chunk 95 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 73 optimal weight: 0.0970 chunk 105 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.099223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.068477 restraints weight = 84832.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.068373 restraints weight = 42055.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.069151 restraints weight = 28526.196| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14428 Z= 0.165 Angle : 0.628 11.580 19514 Z= 0.310 Chirality : 0.044 0.160 2126 Planarity : 0.004 0.061 2522 Dihedral : 5.027 52.176 1916 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.96 % Allowed : 27.87 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.20), residues: 1704 helix: -1.29 (0.35), residues: 225 sheet: -1.08 (0.31), residues: 278 loop : -1.24 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 441 HIS 0.005 0.001 HIS A 654 PHE 0.016 0.001 PHE A 732 TYR 0.010 0.001 TYR A 534 ARG 0.003 0.000 ARG E 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8004.02 seconds wall clock time: 145 minutes 17.85 seconds (8717.85 seconds total)