Starting phenix.real_space_refine on Thu Jun 12 19:48:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xkr_38423/06_2025/8xkr_38423.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xkr_38423/06_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_38423/06_2025/8xkr_38423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xkr_38423/06_2025/8xkr_38423.map" model { file = "/net/cci-nas-00/data/ceres_data/8xkr_38423/06_2025/8xkr_38423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xkr_38423/06_2025/8xkr_38423.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 8924 2.51 5 N 2427 2.21 5 O 2643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.97, per 1000 atoms: 0.64 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: 2.94 Conformation dependent library (CDL) restraints added in 1.6 seconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3306 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 30 sheets defined 16.4% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 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: 4.58 Time building geometry restraints manager: 3.60 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: 7.340 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: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.510 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14470 Z= 0.180 Angle : 0.704 11.339 19598 Z= 0.370 Chirality : 0.045 0.308 2126 Planarity : 0.004 0.049 2522 Dihedral : 17.123 88.396 5346 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.27 % Favored : 89.61 % Rotamer: Outliers : 0.82 % Allowed : 27.81 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.21), residues: 1704 helix: -1.54 (0.37), residues: 202 sheet: -0.47 (0.37), residues: 231 loop : -1.43 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 441 HIS 0.004 0.001 HIS A 737 PHE 0.022 0.001 PHE A 509 TYR 0.009 0.001 TYR B 87 ARG 0.005 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.27386 ( 265) hydrogen bonds : angle 10.41327 ( 735) SS BOND : bond 0.00475 ( 42) SS BOND : angle 0.85693 ( 84) covalent geometry : bond 0.00352 (14428) covalent geometry : angle 0.70297 (19514) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 1.729 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: 0.2910 time to fit residues: 32.8101 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 : 1.592 ------------------------------------------------------------------------------- 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 = 0.099101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.067367 restraints weight = 83710.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.068677 restraints weight = 42727.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.069466 restraints weight = 28877.227| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14470 Z= 0.173 Angle : 0.657 11.300 19598 Z= 0.336 Chirality : 0.045 0.178 2126 Planarity : 0.005 0.076 2522 Dihedral : 5.754 55.769 1926 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 3.28 % Allowed : 25.98 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1704 helix: -1.42 (0.35), residues: 223 sheet: -0.60 (0.36), residues: 228 loop : -1.41 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 441 HIS 0.005 0.001 HIS A 290 PHE 0.017 0.001 PHE A 732 TYR 0.016 0.001 TYR F 60 ARG 0.006 0.001 ARG A 506 Details of bonding type rmsd hydrogen bonds : bond 0.05092 ( 265) hydrogen bonds : angle 7.63855 ( 735) SS BOND : bond 0.00334 ( 42) SS BOND : angle 1.05924 ( 84) covalent geometry : bond 0.00384 (14428) covalent geometry : angle 0.65487 (19514) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 60 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.3805 (OUTLIER) cc_final: 0.2513 (p90) REVERT: A 83 MET cc_start: 0.0275 (mmm) cc_final: -0.0121 (mmm) REVERT: A 114 LEU cc_start: 0.3986 (OUTLIER) cc_final: 0.3674 (mt) REVERT: A 656 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7440 (tp) REVERT: A 809 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: B 71 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7529 (tm-30) outliers start: 52 outliers final: 24 residues processed: 108 average time/residue: 0.2223 time to fit residues: 38.4905 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 : 1.700 ------------------------------------------------------------------------------- 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: 0.8980 chunk 51 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.097664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.064895 restraints weight = 83548.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.066329 restraints weight = 43032.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.067235 restraints weight = 29076.318| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14470 Z= 0.220 Angle : 0.678 10.748 19598 Z= 0.345 Chirality : 0.045 0.167 2126 Planarity : 0.005 0.062 2522 Dihedral : 5.842 57.915 1926 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.27 % Favored : 88.67 % Rotamer: Outliers : 5.61 % Allowed : 24.78 % 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: -2.00 (0.20), residues: 1704 helix: -1.68 (0.32), residues: 237 sheet: -0.78 (0.35), residues: 231 loop : -1.44 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 578 HIS 0.005 0.001 HIS B 340 PHE 0.017 0.002 PHE B 408 TYR 0.013 0.001 TYR F 60 ARG 0.017 0.001 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.04610 ( 265) hydrogen bonds : angle 7.05756 ( 735) SS BOND : bond 0.00430 ( 42) SS BOND : angle 0.87746 ( 84) covalent geometry : bond 0.00490 (14428) covalent geometry : angle 0.67682 (19514) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 55 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.4036 (OUTLIER) cc_final: 0.2929 (p90) REVERT: C 9 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: A 83 MET cc_start: 0.0460 (mmm) cc_final: 0.0002 (mmm) REVERT: A 656 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7756 (tp) REVERT: B 149 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8272 (m-40) REVERT: B 364 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.8142 (m110) outliers start: 89 outliers final: 43 residues processed: 142 average time/residue: 0.2474 time to fit residues: 54.5086 Evaluate side-chains 100 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 52 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 809 GLU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 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 245 GLN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 364 ASN Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP 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: 10.0000 chunk 164 optimal weight: 30.0000 chunk 87 optimal weight: 0.0040 chunk 121 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 163 optimal weight: 30.0000 chunk 70 optimal weight: 0.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN A 588 GLN ** B 226 HIS ** 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 = 0.4343 r_free = 0.4343 target = 0.098516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.066018 restraints weight = 83903.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.067271 restraints weight = 43636.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.067915 restraints weight = 29523.160| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14470 Z= 0.155 Angle : 0.627 9.322 19598 Z= 0.319 Chirality : 0.044 0.144 2126 Planarity : 0.004 0.052 2522 Dihedral : 5.762 58.830 1926 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 4.41 % Allowed : 25.66 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.20), residues: 1704 helix: -1.51 (0.34), residues: 224 sheet: -0.88 (0.34), residues: 242 loop : -1.37 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 441 HIS 0.004 0.001 HIS A 654 PHE 0.020 0.001 PHE A 409 TYR 0.011 0.001 TYR B 134 ARG 0.003 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 265) hydrogen bonds : angle 6.65717 ( 735) SS BOND : bond 0.00410 ( 42) SS BOND : angle 0.90842 ( 84) covalent geometry : bond 0.00351 (14428) covalent geometry : angle 0.62522 (19514) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 60 time to evaluate : 1.489 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: 0.4159 (OUTLIER) cc_final: 0.3003 (p90) REVERT: C 9 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: A 656 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7753 (tp) REVERT: B 71 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: B 149 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8114 (m-40) REVERT: B 364 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8078 (m110) outliers start: 70 outliers final: 41 residues processed: 127 average time/residue: 0.2123 time to fit residues: 43.0078 Evaluate side-chains 103 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 56 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 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 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 206 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 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 449 THR Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 796 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 151 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 103 optimal weight: 0.0770 overall best weight: 1.3742 ------------------------------------------------------------------------------- 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 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 = 0.4350 r_free = 0.4350 target = 0.098965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.068664 restraints weight = 85409.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.070626 restraints weight = 48298.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.070034 restraints weight = 28593.351| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14470 Z= 0.133 Angle : 0.618 8.617 19598 Z= 0.312 Chirality : 0.044 0.193 2126 Planarity : 0.004 0.050 2522 Dihedral : 5.369 56.448 1920 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 3.59 % Allowed : 26.04 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.20), residues: 1704 helix: -1.53 (0.33), residues: 226 sheet: -1.04 (0.33), residues: 252 loop : -1.35 (0.18), residues: 1226 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 0.019 0.001 PHE A 509 TYR 0.014 0.001 TYR F 60 ARG 0.004 0.000 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 265) hydrogen bonds : angle 6.41897 ( 735) SS BOND : bond 0.00249 ( 42) SS BOND : angle 0.88736 ( 84) covalent geometry : bond 0.00305 (14428) covalent geometry : angle 0.61665 (19514) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 59 time to evaluate : 1.648 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: 0.4071 (OUTLIER) cc_final: 0.3070 (p90) REVERT: F 59 MET cc_start: 0.7894 (mpp) cc_final: 0.7510 (mmm) REVERT: C 9 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: A 83 MET cc_start: 0.0471 (mmm) cc_final: -0.0089 (mmm) REVERT: A 293 CYS cc_start: 0.5333 (OUTLIER) cc_final: 0.4755 (m) REVERT: A 656 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7763 (tp) REVERT: B 71 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: B 149 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8042 (m-40) REVERT: B 364 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.8068 (m110) outliers start: 57 outliers final: 40 residues processed: 113 average time/residue: 0.2295 time to fit residues: 42.0408 Evaluate side-chains 102 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 55 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain 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 293 CYS 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 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 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 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 364 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 147 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 126 optimal weight: 0.0070 chunk 93 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 169 optimal weight: 50.0000 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** 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 = 0.4338 r_free = 0.4338 target = 0.098266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.065327 restraints weight = 84553.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.066764 restraints weight = 43014.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.067674 restraints weight = 29227.750| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14470 Z= 0.162 Angle : 0.620 8.500 19598 Z= 0.313 Chirality : 0.044 0.165 2126 Planarity : 0.004 0.051 2522 Dihedral : 5.354 56.219 1920 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 4.67 % Allowed : 25.28 % Favored : 70.05 % 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: -1.90 (0.20), residues: 1704 helix: -1.36 (0.34), residues: 223 sheet: -1.10 (0.32), residues: 261 loop : -1.34 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 441 HIS 0.004 0.001 HIS B 340 PHE 0.017 0.001 PHE A 409 TYR 0.011 0.001 TYR B 87 ARG 0.003 0.000 ARG F 55 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 265) hydrogen bonds : angle 6.27030 ( 735) SS BOND : bond 0.00270 ( 42) SS BOND : angle 0.83009 ( 84) covalent geometry : bond 0.00368 (14428) covalent geometry : angle 0.61906 (19514) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 58 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 MET cc_start: 0.7832 (mpp) cc_final: 0.7458 (mmm) REVERT: C 9 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: A 356 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8412 (pm20) REVERT: A 656 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7740 (tp) REVERT: B 364 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.8090 (m110) REVERT: B 606 TYR cc_start: 0.7729 (t80) cc_final: 0.7235 (t80) outliers start: 74 outliers final: 49 residues processed: 127 average time/residue: 0.2315 time to fit residues: 48.5986 Evaluate side-chains 109 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 56 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 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 356 GLU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 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 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 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 124 optimal weight: 0.0570 chunk 17 optimal weight: 40.0000 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.098660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.065758 restraints weight = 84649.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.067139 restraints weight = 42941.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.067927 restraints weight = 29000.789| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14470 Z= 0.140 Angle : 0.607 10.035 19598 Z= 0.306 Chirality : 0.044 0.150 2126 Planarity : 0.004 0.051 2522 Dihedral : 5.196 54.015 1916 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 4.41 % Allowed : 25.79 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.20), residues: 1704 helix: -1.34 (0.34), residues: 223 sheet: -1.10 (0.32), residues: 261 loop : -1.33 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 441 HIS 0.004 0.001 HIS A 737 PHE 0.020 0.001 PHE A 509 TYR 0.011 0.001 TYR F 60 ARG 0.004 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 265) hydrogen bonds : angle 6.15824 ( 735) SS BOND : bond 0.00263 ( 42) SS BOND : angle 0.80809 ( 84) covalent geometry : bond 0.00319 (14428) covalent geometry : angle 0.60637 (19514) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 56 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.4037 (OUTLIER) cc_final: 0.2923 (p90) REVERT: F 59 MET cc_start: 0.7874 (mpp) cc_final: 0.7591 (mmm) REVERT: E 45 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6856 (t0) REVERT: C 9 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: A 83 MET cc_start: 0.0360 (mmm) cc_final: -0.0108 (mmm) REVERT: A 293 CYS cc_start: 0.5439 (OUTLIER) cc_final: 0.4662 (m) REVERT: A 356 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8385 (pm20) REVERT: A 656 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7763 (tp) REVERT: B 149 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.7945 (m-40) REVERT: B 236 HIS cc_start: 0.7304 (OUTLIER) cc_final: 0.7027 (t-170) REVERT: B 364 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.8068 (m110) REVERT: B 606 TYR cc_start: 0.7735 (t80) cc_final: 0.7249 (t80) outliers start: 70 outliers final: 50 residues processed: 121 average time/residue: 0.2038 time to fit residues: 40.9859 Evaluate side-chains 114 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 55 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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 E residue 45 ASP Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 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 404 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 103 optimal weight: 2.9990 chunk 19 optimal weight: 40.0000 chunk 113 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 171 optimal weight: 40.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 150 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.098239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.065231 restraints weight = 84427.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.066584 restraints weight = 42904.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.067506 restraints weight = 29097.751| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14470 Z= 0.167 Angle : 0.634 10.668 19598 Z= 0.318 Chirality : 0.044 0.145 2126 Planarity : 0.004 0.050 2522 Dihedral : 5.272 53.316 1916 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 4.35 % Allowed : 26.04 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.20), residues: 1704 helix: -1.42 (0.34), residues: 223 sheet: -1.26 (0.31), residues: 279 loop : -1.30 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 441 HIS 0.005 0.001 HIS A 737 PHE 0.014 0.001 PHE A 732 TYR 0.012 0.001 TYR F 60 ARG 0.003 0.000 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 265) hydrogen bonds : angle 6.17997 ( 735) SS BOND : bond 0.00254 ( 42) SS BOND : angle 1.06261 ( 84) covalent geometry : bond 0.00378 (14428) covalent geometry : angle 0.63109 (19514) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 58 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.4041 (OUTLIER) cc_final: 0.2903 (p90) REVERT: F 59 MET cc_start: 0.7861 (mpp) cc_final: 0.7543 (mmm) REVERT: E 45 ASP cc_start: 0.7210 (p0) cc_final: 0.6871 (t0) REVERT: C 9 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: A 83 MET cc_start: 0.0611 (mmm) cc_final: 0.0116 (mmm) REVERT: A 293 CYS cc_start: 0.5474 (OUTLIER) cc_final: 0.4709 (m) REVERT: A 356 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: A 656 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7762 (tp) REVERT: B 149 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.7997 (m-40) REVERT: B 364 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.8086 (m110) REVERT: B 606 TYR cc_start: 0.7734 (t80) cc_final: 0.7261 (t80) outliers start: 69 outliers final: 52 residues processed: 123 average time/residue: 0.2016 time to fit residues: 40.7491 Evaluate side-chains 116 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 57 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 A residue 67 LYS Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 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 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 25 optimal weight: 8.9990 chunk 125 optimal weight: 0.2980 chunk 157 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 159 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.098627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.065818 restraints weight = 84513.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.067191 restraints weight = 42678.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.068001 restraints weight = 28721.056| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14470 Z= 0.133 Angle : 0.622 11.113 19598 Z= 0.310 Chirality : 0.044 0.244 2126 Planarity : 0.004 0.051 2522 Dihedral : 5.192 51.035 1916 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 4.16 % Allowed : 26.36 % 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: -1.89 (0.20), residues: 1704 helix: -1.39 (0.34), residues: 224 sheet: -1.13 (0.31), residues: 269 loop : -1.31 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 441 HIS 0.004 0.001 HIS A 737 PHE 0.022 0.001 PHE A 509 TYR 0.011 0.001 TYR F 60 ARG 0.003 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 265) hydrogen bonds : angle 6.02470 ( 735) SS BOND : bond 0.00216 ( 42) SS BOND : angle 0.90197 ( 84) covalent geometry : bond 0.00308 (14428) covalent geometry : angle 0.62040 (19514) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 59 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.4017 (OUTLIER) cc_final: 0.2970 (p90) REVERT: F 59 MET cc_start: 0.7865 (mpp) cc_final: 0.7636 (mmm) REVERT: E 45 ASP cc_start: 0.7111 (p0) cc_final: 0.6762 (t0) REVERT: C 9 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: A 137 MET cc_start: -0.1062 (ttt) cc_final: -0.1967 (tpp) REVERT: A 293 CYS cc_start: 0.5504 (OUTLIER) cc_final: 0.4713 (m) REVERT: A 356 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8382 (pm20) REVERT: A 656 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7730 (tp) REVERT: B 149 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7961 (m-40) REVERT: B 236 HIS cc_start: 0.7229 (OUTLIER) cc_final: 0.6888 (t-170) REVERT: B 364 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.8051 (m110) REVERT: B 580 MET cc_start: 0.9108 (ppp) cc_final: 0.8808 (ppp) REVERT: B 606 TYR cc_start: 0.7746 (t80) cc_final: 0.7269 (t80) outliers start: 66 outliers final: 52 residues processed: 121 average time/residue: 0.2056 time to fit residues: 41.0315 Evaluate side-chains 116 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 56 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain 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 A residue 67 LYS Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 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 404 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 43 optimal weight: 0.3980 chunk 117 optimal weight: 0.5980 chunk 143 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.099314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.069670 restraints weight = 85263.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.070954 restraints weight = 51369.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.070397 restraints weight = 35966.000| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14470 Z= 0.117 Angle : 0.629 11.540 19598 Z= 0.312 Chirality : 0.044 0.224 2126 Planarity : 0.004 0.052 2522 Dihedral : 5.082 51.350 1916 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.47 % Allowed : 27.30 % Favored : 69.23 % Cbeta Deviations : 0.06 % 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: -1.82 (0.20), residues: 1704 helix: -1.30 (0.35), residues: 224 sheet: -1.00 (0.32), residues: 263 loop : -1.29 (0.18), residues: 1217 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 0.016 0.001 PHE A 732 TYR 0.010 0.001 TYR A 534 ARG 0.005 0.000 ARG E 50 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 265) hydrogen bonds : angle 5.89627 ( 735) SS BOND : bond 0.00178 ( 42) SS BOND : angle 0.80089 ( 84) covalent geometry : bond 0.00268 (14428) covalent geometry : angle 0.62852 (19514) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 60 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.3967 (OUTLIER) cc_final: 0.3046 (p90) REVERT: D 6 CYS cc_start: 0.2903 (p) cc_final: 0.2678 (m) REVERT: E 45 ASP cc_start: 0.7833 (p0) cc_final: 0.7331 (t0) REVERT: C 9 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: A 83 MET cc_start: 0.0677 (mmm) cc_final: 0.0198 (mmm) REVERT: A 137 MET cc_start: -0.1807 (ttt) cc_final: -0.2753 (tpp) REVERT: A 356 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: A 656 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7744 (tp) REVERT: B 149 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.7954 (m-40) REVERT: B 236 HIS cc_start: 0.7320 (OUTLIER) cc_final: 0.6963 (t-170) REVERT: B 364 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.8053 (m110) REVERT: B 580 MET cc_start: 0.9220 (ppp) cc_final: 0.8952 (ppp) REVERT: B 606 TYR cc_start: 0.8230 (t80) cc_final: 0.7719 (t80) outliers start: 55 outliers final: 42 residues processed: 111 average time/residue: 0.2055 time to fit residues: 37.9007 Evaluate side-chains 107 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 58 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 103 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL 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 727 SER Chi-restraints excluded: chain A residue 866 ASN 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 149 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 315 CYS 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 404 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 76 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 141 optimal weight: 0.0020 chunk 98 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.099852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.067308 restraints weight = 85910.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.068729 restraints weight = 43605.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.069430 restraints weight = 29330.758| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14470 Z= 0.106 Angle : 0.624 11.497 19598 Z= 0.306 Chirality : 0.044 0.195 2126 Planarity : 0.004 0.054 2522 Dihedral : 4.938 52.133 1916 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.46 % Allowed : 28.18 % 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: -1.68 (0.20), residues: 1704 helix: -1.09 (0.36), residues: 218 sheet: -0.84 (0.32), residues: 260 loop : -1.24 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 441 HIS 0.004 0.001 HIS A 654 PHE 0.024 0.001 PHE A 509 TYR 0.014 0.001 TYR F 60 ARG 0.006 0.000 ARG E 50 Details of bonding type rmsd hydrogen bonds : bond 0.03034 ( 265) hydrogen bonds : angle 5.71046 ( 735) SS BOND : bond 0.00188 ( 42) SS BOND : angle 0.85207 ( 84) covalent geometry : bond 0.00247 (14428) covalent geometry : angle 0.62245 (19514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8296.99 seconds wall clock time: 143 minutes 59.91 seconds (8639.91 seconds total)