Starting phenix.real_space_refine on Thu Sep 18 05:07:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xkr_38423/09_2025/8xkr_38423.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xkr_38423/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xkr_38423/09_2025/8xkr_38423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xkr_38423/09_2025/8xkr_38423.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xkr_38423/09_2025/8xkr_38423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xkr_38423/09_2025/8xkr_38423.map" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.49, per 1000 atoms: 0.25 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: 0.95 Conformation dependent library (CDL) restraints added in 647.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.54 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: 2.60 Time building geometry restraints manager: 1.34 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: 11.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.090 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.320 ------------------------------------------------------------------------------- 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 : 23.66 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG B 41 TYR 0.009 0.001 TYR B 87 PHE 0.022 0.001 PHE A 509 TRP 0.014 0.001 TRP A 441 HIS 0.004 0.001 HIS A 737 Details of bonding type rmsd covalent geometry : bond 0.00352 (14428) covalent geometry : angle 0.70297 (19514) SS BOND : bond 0.00475 ( 42) SS BOND : angle 0.85693 ( 84) hydrogen bonds : bond 0.27386 ( 265) hydrogen bonds : angle 10.41327 ( 735) *********************** 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 : 0.553 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: 0.1433 time to fit residues: 15.9791 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 : 0.603 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.099100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.067244 restraints weight = 83698.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.068601 restraints weight = 42914.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.069516 restraints weight = 28665.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.070023 restraints weight = 22855.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.070219 restraints weight = 20268.584| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14470 Z= 0.183 Angle : 0.668 11.525 19598 Z= 0.341 Chirality : 0.045 0.173 2126 Planarity : 0.005 0.076 2522 Dihedral : 5.783 55.502 1926 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 3.59 % Allowed : 25.85 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.20), residues: 1704 helix: -1.45 (0.35), residues: 223 sheet: -0.60 (0.36), residues: 228 loop : -1.42 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 506 TYR 0.016 0.001 TYR F 60 PHE 0.017 0.001 PHE A 732 TRP 0.011 0.001 TRP A 441 HIS 0.005 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00409 (14428) covalent geometry : angle 0.66501 (19514) SS BOND : bond 0.00326 ( 42) SS BOND : angle 1.11647 ( 84) hydrogen bonds : bond 0.05079 ( 265) hydrogen bonds : angle 7.63724 ( 735) *********************** 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 116 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 59 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.3831 (OUTLIER) cc_final: 0.2485 (p90) REVERT: A 83 MET cc_start: 0.0297 (mmm) cc_final: -0.0114 (mmm) REVERT: A 114 LEU cc_start: 0.3912 (OUTLIER) cc_final: 0.3579 (mt) REVERT: A 656 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.7419 (tp) REVERT: A 809 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7361 (mt-10) REVERT: B 71 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7544 (tm-30) outliers start: 57 outliers final: 24 residues processed: 112 average time/residue: 0.1032 time to fit residues: 18.4182 Evaluate side-chains 84 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 55 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 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 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 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 68 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 167 optimal weight: 0.0040 chunk 41 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN B 226 HIS ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.099645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.067642 restraints weight = 84184.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.069119 restraints weight = 42608.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.069775 restraints weight = 28720.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.070300 restraints weight = 23281.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.070879 restraints weight = 20489.845| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14470 Z= 0.125 Angle : 0.616 11.642 19598 Z= 0.314 Chirality : 0.044 0.162 2126 Planarity : 0.004 0.053 2522 Dihedral : 5.602 59.085 1926 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.45 % Favored : 91.49 % Rotamer: Outliers : 3.53 % Allowed : 25.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.20), residues: 1704 helix: -1.47 (0.34), residues: 226 sheet: -0.91 (0.33), residues: 254 loop : -1.38 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 56 TYR 0.011 0.001 TYR A 534 PHE 0.018 0.001 PHE A 509 TRP 0.013 0.001 TRP A 441 HIS 0.004 0.001 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00275 (14428) covalent geometry : angle 0.61436 (19514) SS BOND : bond 0.00288 ( 42) SS BOND : angle 0.90270 ( 84) hydrogen bonds : bond 0.04292 ( 265) hydrogen bonds : angle 6.89054 ( 735) *********************** 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 116 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 60 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 PHE cc_start: 0.3867 (OUTLIER) cc_final: 0.2587 (p90) REVERT: C 9 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: A 83 MET cc_start: 0.0183 (mmm) cc_final: -0.0222 (mmm) REVERT: A 114 LEU cc_start: 0.4106 (OUTLIER) cc_final: 0.3798 (mt) REVERT: A 656 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7674 (tp) REVERT: B 149 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8000 (m-40) outliers start: 56 outliers final: 25 residues processed: 112 average time/residue: 0.1117 time to fit residues: 19.7463 Evaluate side-chains 85 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 809 GLU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 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 339 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 130 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 102 optimal weight: 0.0030 chunk 98 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 172 optimal weight: 50.0000 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.099529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.068125 restraints weight = 85384.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.069119 restraints weight = 42802.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.069903 restraints weight = 28547.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.070487 restraints weight = 22896.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.070661 restraints weight = 20343.790| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1558 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= 0.127 Angle : 0.601 9.151 19598 Z= 0.304 Chirality : 0.044 0.158 2126 Planarity : 0.004 0.055 2522 Dihedral : 5.528 56.384 1926 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.92 % Favored : 91.02 % Rotamer: Outliers : 4.22 % Allowed : 24.72 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.20), residues: 1704 helix: -1.42 (0.34), residues: 231 sheet: -0.99 (0.33), residues: 260 loop : -1.36 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 56 TYR 0.010 0.001 TYR A 534 PHE 0.015 0.001 PHE A 732 TRP 0.012 0.001 TRP A 441 HIS 0.003 0.001 HIS A 737 Details of bonding type rmsd covalent geometry : bond 0.00289 (14428) covalent geometry : angle 0.59984 (19514) SS BOND : bond 0.00244 ( 42) SS BOND : angle 0.84725 ( 84) hydrogen bonds : bond 0.03839 ( 265) hydrogen bonds : angle 6.51833 ( 735) *********************** 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 125 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 58 time to evaluate : 0.593 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: 0.3873 (OUTLIER) cc_final: 0.2915 (p90) REVERT: C 9 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: A 114 LEU cc_start: 0.4070 (OUTLIER) cc_final: 0.3758 (mt) REVERT: A 656 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7689 (tp) REVERT: B 71 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7545 (tm-30) outliers start: 67 outliers final: 40 residues processed: 121 average time/residue: 0.0998 time to fit residues: 19.5472 Evaluate side-chains 102 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 57 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 10 LEU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 809 GLU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 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 514 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 824 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 30 optimal weight: 40.0000 chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 73 optimal weight: 50.0000 chunk 161 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4346 r_free = 0.4346 target = 0.098728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.067129 restraints weight = 84252.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.068009 restraints weight = 42917.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.068677 restraints weight = 28824.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.069225 restraints weight = 23410.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.069745 restraints weight = 20707.944| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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= 0.163 Angle : 0.617 8.756 19598 Z= 0.313 Chirality : 0.044 0.182 2126 Planarity : 0.004 0.051 2522 Dihedral : 5.314 56.450 1922 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.39 % Favored : 90.55 % Rotamer: Outliers : 4.16 % Allowed : 24.84 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.20), residues: 1704 helix: -1.52 (0.33), residues: 231 sheet: -0.98 (0.33), residues: 258 loop : -1.36 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 41 TYR 0.011 0.001 TYR B 87 PHE 0.016 0.001 PHE A 103 TRP 0.010 0.001 TRP A 441 HIS 0.004 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00368 (14428) covalent geometry : angle 0.61534 (19514) SS BOND : bond 0.00263 ( 42) SS BOND : angle 0.95636 ( 84) hydrogen bonds : bond 0.03710 ( 265) hydrogen bonds : angle 6.38635 ( 735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 58 time to evaluate : 0.695 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: 0.4090 (OUTLIER) cc_final: 0.2958 (p90) REVERT: F 59 MET cc_start: 0.8038 (mpp) cc_final: 0.7343 (mmm) REVERT: C 9 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: A 83 MET cc_start: 0.0374 (mmm) cc_final: -0.0115 (mmm) REVERT: A 114 LEU cc_start: 0.4000 (OUTLIER) cc_final: 0.3668 (mt) REVERT: A 356 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8386 (pm20) REVERT: A 656 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7703 (tp) REVERT: B 71 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: B 149 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8048 (m-40) outliers start: 66 outliers final: 47 residues processed: 119 average time/residue: 0.1020 time to fit residues: 19.9484 Evaluate side-chains 111 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 57 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 809 GLU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 449 THR 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 13 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 14 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 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 = 0.4349 r_free = 0.4349 target = 0.098867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.066869 restraints weight = 83990.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.068265 restraints weight = 42709.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.069150 restraints weight = 28536.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.069481 restraints weight = 23004.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.069485 restraints weight = 20597.725| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1830 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= 0.143 Angle : 0.607 9.119 19598 Z= 0.306 Chirality : 0.044 0.164 2126 Planarity : 0.004 0.052 2522 Dihedral : 5.251 55.413 1920 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.98 % Favored : 90.96 % Rotamer: Outliers : 4.35 % Allowed : 25.03 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.20), residues: 1704 helix: -1.56 (0.33), residues: 233 sheet: -1.01 (0.33), residues: 260 loop : -1.34 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 56 TYR 0.011 0.001 TYR F 60 PHE 0.019 0.001 PHE A 509 TRP 0.012 0.001 TRP A 441 HIS 0.003 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00324 (14428) covalent geometry : angle 0.60538 (19514) SS BOND : bond 0.00230 ( 42) SS BOND : angle 0.83273 ( 84) hydrogen bonds : bond 0.03530 ( 265) hydrogen bonds : angle 6.23079 ( 735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 58 time to evaluate : 0.699 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: C 9 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: A 114 LEU cc_start: 0.4180 (OUTLIER) cc_final: 0.3870 (mt) REVERT: A 356 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8367 (pm20) REVERT: A 656 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7722 (tp) REVERT: B 71 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: B 149 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.7995 (m-40) REVERT: B 287 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.9003 (mm-40) REVERT: B 606 TYR cc_start: 0.7536 (t80) cc_final: 0.7092 (t80) outliers start: 69 outliers final: 44 residues processed: 123 average time/residue: 0.1051 time to fit residues: 21.0807 Evaluate side-chains 108 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 57 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 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 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 809 GLU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 287 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 387 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 107 optimal weight: 4.9990 chunk 169 optimal weight: 50.0000 chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 164 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.097174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.066598 restraints weight = 83081.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.066079 restraints weight = 44930.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.066879 restraints weight = 29609.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.067257 restraints weight = 23272.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.067625 restraints weight = 20352.049| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14470 Z= 0.226 Angle : 0.673 9.895 19598 Z= 0.341 Chirality : 0.045 0.165 2126 Planarity : 0.004 0.046 2522 Dihedral : 5.451 58.601 1916 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.56 % Favored : 89.38 % Rotamer: Outliers : 4.54 % Allowed : 25.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.20), residues: 1704 helix: -1.61 (0.34), residues: 226 sheet: -1.02 (0.33), residues: 247 loop : -1.35 (0.18), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 55 TYR 0.019 0.001 TYR F 60 PHE 0.018 0.002 PHE A 409 TRP 0.012 0.001 TRP A 578 HIS 0.006 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00504 (14428) covalent geometry : angle 0.67174 (19514) SS BOND : bond 0.00364 ( 42) SS BOND : angle 0.96131 ( 84) hydrogen bonds : bond 0.03941 ( 265) hydrogen bonds : angle 6.45607 ( 735) *********************** 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 130 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 58 time to evaluate : 0.593 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: 0.4145 (OUTLIER) cc_final: 0.2965 (p90) REVERT: F 59 MET cc_start: 0.7736 (mpp) cc_final: 0.7125 (mmm) REVERT: C 9 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: A 83 MET cc_start: 0.0289 (mmm) cc_final: -0.0096 (mmm) REVERT: A 114 LEU cc_start: 0.4017 (OUTLIER) cc_final: 0.3685 (mt) REVERT: A 293 CYS cc_start: 0.5425 (OUTLIER) cc_final: 0.4674 (m) REVERT: A 656 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7767 (tp) REVERT: A 733 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8461 (tp30) REVERT: B 71 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: B 149 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.8155 (m-40) REVERT: B 437 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8070 (tp-100) REVERT: B 606 TYR cc_start: 0.7762 (t80) cc_final: 0.7315 (t80) outliers start: 72 outliers final: 50 residues processed: 126 average time/residue: 0.0923 time to fit residues: 19.3631 Evaluate side-chains 113 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 55 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 45 ASP Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 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 507 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 0.3980 chunk 131 optimal weight: 0.0970 chunk 21 optimal weight: 7.9990 chunk 108 optimal weight: 0.3980 chunk 88 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 136 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 ASN ** 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 = 0.4360 r_free = 0.4360 target = 0.099570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.067405 restraints weight = 84621.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.068841 restraints weight = 42706.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.069782 restraints weight = 28747.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.070258 restraints weight = 22837.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.070479 restraints weight = 20161.348| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14470 Z= 0.107 Angle : 0.622 10.543 19598 Z= 0.309 Chirality : 0.044 0.161 2126 Planarity : 0.004 0.057 2522 Dihedral : 5.143 51.393 1916 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.69 % Favored : 92.25 % Rotamer: Outliers : 3.09 % Allowed : 26.61 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.20), residues: 1704 helix: -1.41 (0.34), residues: 221 sheet: -1.11 (0.31), residues: 274 loop : -1.27 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 581 TYR 0.012 0.001 TYR A 534 PHE 0.021 0.001 PHE A 509 TRP 0.015 0.001 TRP A 441 HIS 0.006 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00243 (14428) covalent geometry : angle 0.62121 (19514) SS BOND : bond 0.00188 ( 42) SS BOND : angle 0.85344 ( 84) hydrogen bonds : bond 0.03439 ( 265) hydrogen bonds : angle 6.02103 ( 735) *********************** 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 109 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 60 time to evaluate : 0.525 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: 0.4014 (OUTLIER) cc_final: 0.2912 (p90) REVERT: F 59 MET cc_start: 0.7673 (mpp) cc_final: 0.7112 (mmm) REVERT: E 45 ASP cc_start: 0.6891 (p0) cc_final: 0.6655 (t0) REVERT: C 9 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: A 83 MET cc_start: 0.0302 (mmm) cc_final: -0.0064 (mmm) REVERT: A 293 CYS cc_start: 0.5432 (OUTLIER) cc_final: 0.4670 (m) REVERT: A 356 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: A 656 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7716 (tp) REVERT: B 71 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: B 149 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7868 (m-40) REVERT: B 606 TYR cc_start: 0.7603 (t80) cc_final: 0.7185 (t80) outliers start: 49 outliers final: 33 residues processed: 108 average time/residue: 0.0976 time to fit residues: 17.2759 Evaluate side-chains 98 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 58 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 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 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 136 optimal weight: 0.0370 chunk 4 optimal weight: 6.9990 chunk 170 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 overall best weight: 2.3664 ------------------------------------------------------------------------------- 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 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 = 0.4334 r_free = 0.4334 target = 0.098029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.067577 restraints weight = 84103.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.069224 restraints weight = 47854.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.069063 restraints weight = 30618.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.069287 restraints weight = 23553.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.069326 restraints weight = 23744.279| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2241 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= 0.183 Angle : 0.647 11.347 19598 Z= 0.323 Chirality : 0.044 0.163 2126 Planarity : 0.004 0.049 2522 Dihedral : 5.218 52.790 1916 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.03 % Allowed : 26.86 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.20), residues: 1704 helix: -1.37 (0.34), residues: 222 sheet: -1.22 (0.31), residues: 283 loop : -1.19 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 50 TYR 0.013 0.001 TYR F 60 PHE 0.015 0.001 PHE B 408 TRP 0.013 0.002 TRP A 642 HIS 0.004 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00413 (14428) covalent geometry : angle 0.64574 (19514) SS BOND : bond 0.00287 ( 42) SS BOND : angle 0.90386 ( 84) hydrogen bonds : bond 0.03489 ( 265) hydrogen bonds : angle 6.12434 ( 735) *********************** 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 106 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 58 time to evaluate : 0.606 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: 0.4073 (OUTLIER) cc_final: 0.3039 (p90) REVERT: F 59 MET cc_start: 0.7679 (mpp) cc_final: 0.7401 (mmm) REVERT: E 45 ASP cc_start: 0.7130 (p0) cc_final: 0.6746 (t0) REVERT: C 9 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: A 83 MET cc_start: 0.0543 (mmm) cc_final: 0.0109 (mmm) REVERT: A 137 MET cc_start: -0.2225 (ttt) cc_final: -0.3125 (tpp) REVERT: A 293 CYS cc_start: 0.5363 (OUTLIER) cc_final: 0.4686 (m) REVERT: A 656 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7739 (tp) REVERT: B 71 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: B 149 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8064 (m-40) REVERT: B 606 TYR cc_start: 0.8024 (t80) cc_final: 0.7504 (t80) outliers start: 48 outliers final: 38 residues processed: 103 average time/residue: 0.0896 time to fit residues: 15.9058 Evaluate side-chains 101 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 57 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain C residue 9 GLU 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 360 CYS Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 96 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.097568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.065038 restraints weight = 84448.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.066341 restraints weight = 44067.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.067271 restraints weight = 29757.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.067672 restraints weight = 23615.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.067839 restraints weight = 21063.173| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2412 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= 0.191 Angle : 0.665 12.439 19598 Z= 0.334 Chirality : 0.045 0.162 2126 Planarity : 0.004 0.053 2522 Dihedral : 5.352 51.731 1916 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 3.22 % Allowed : 26.80 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.20), residues: 1704 helix: -1.50 (0.34), residues: 223 sheet: -1.28 (0.30), residues: 286 loop : -1.31 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 50 TYR 0.013 0.001 TYR F 60 PHE 0.019 0.002 PHE A 509 TRP 0.016 0.002 TRP A 578 HIS 0.004 0.001 HIS A 737 Details of bonding type rmsd covalent geometry : bond 0.00429 (14428) covalent geometry : angle 0.66416 (19514) SS BOND : bond 0.00317 ( 42) SS BOND : angle 0.90598 ( 84) hydrogen bonds : bond 0.03597 ( 265) hydrogen bonds : angle 6.18587 ( 735) ********************** 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 109 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 58 time to evaluate : 0.539 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: 0.4217 (OUTLIER) cc_final: 0.3093 (p90) REVERT: F 59 MET cc_start: 0.7613 (mpp) cc_final: 0.7191 (mmm) REVERT: C 9 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: A 83 MET cc_start: 0.0615 (mmm) cc_final: 0.0244 (mmm) REVERT: A 114 LEU cc_start: 0.4265 (OUTLIER) cc_final: 0.3984 (mp) REVERT: A 137 MET cc_start: -0.1267 (ttt) cc_final: -0.2212 (tpp) REVERT: A 293 CYS cc_start: 0.5467 (OUTLIER) cc_final: 0.4688 (m) REVERT: A 656 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7736 (tp) REVERT: B 71 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: B 149 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8019 (m-40) REVERT: B 606 TYR cc_start: 0.7764 (t80) cc_final: 0.7319 (t80) outliers start: 51 outliers final: 41 residues processed: 107 average time/residue: 0.0907 time to fit residues: 16.6243 Evaluate side-chains 105 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 57 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 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 360 CYS Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 586 TRP Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 868 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.097640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.066825 restraints weight = 84668.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.066447 restraints weight = 43236.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.067257 restraints weight = 29320.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.067781 restraints weight = 23638.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.067936 restraints weight = 21042.321| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14470 Z= 0.181 Angle : 0.661 11.921 19598 Z= 0.329 Chirality : 0.044 0.160 2126 Planarity : 0.004 0.050 2522 Dihedral : 5.313 52.053 1916 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 3.22 % Allowed : 26.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.20), residues: 1704 helix: -1.51 (0.34), residues: 220 sheet: -1.26 (0.31), residues: 283 loop : -1.30 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 50 TYR 0.012 0.001 TYR F 60 PHE 0.015 0.001 PHE B 408 TRP 0.010 0.001 TRP A 642 HIS 0.006 0.001 HIS A 737 Details of bonding type rmsd covalent geometry : bond 0.00411 (14428) covalent geometry : angle 0.65937 (19514) SS BOND : bond 0.00304 ( 42) SS BOND : angle 1.00060 ( 84) hydrogen bonds : bond 0.03475 ( 265) hydrogen bonds : angle 6.12228 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4962.41 seconds wall clock time: 85 minutes 38.02 seconds (5138.02 seconds total)