Starting phenix.real_space_refine on Thu Mar 5 14:18:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tlb_25986/03_2026/7tlb_25986.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tlb_25986/03_2026/7tlb_25986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tlb_25986/03_2026/7tlb_25986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tlb_25986/03_2026/7tlb_25986.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tlb_25986/03_2026/7tlb_25986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tlb_25986/03_2026/7tlb_25986.map" } resolution = 3.06 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= 0.003 sd= 0.085 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 105 5.16 5 C 14580 2.51 5 N 3786 2.21 5 O 4335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22806 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "B" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "C" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Time building chain proxies: 4.86, per 1000 atoms: 0.21 Number of scatterers: 22806 At special positions: 0 Unit cell: (129.076, 134.366, 171.396, 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 105 16.00 O 4335 8.00 N 3786 7.00 C 14580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS C 383 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 985 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.01 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: 1.75 Conformation dependent library (CDL) restraints added in 946.1 milliseconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 47 sheets defined 27.1% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.608A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.388A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.708A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.679A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.575A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.725A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.554A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.571A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.709A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.660A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.330A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.642A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.911A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.464A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.314A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.780A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.530A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.564A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.756A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.622A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.625A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.600A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.897A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.151A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.080A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.300A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.634A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.547A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.622A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.635A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.813A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.555A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.325A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.248A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.507A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.527A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.912A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.527A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.019A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.151A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.151A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.851A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.605A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.694A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.848A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.422A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.225A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.701A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.416A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.812A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.699A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.290A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.579A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.788A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.501A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.653A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.948A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.500A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.572A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.631A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.878A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.481A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.295A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.958A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.958A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.998A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.567A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.546A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.894A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.639A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 2877 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 2.42 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: 6197 1.33 - 1.46: 4307 1.46 - 1.58: 12677 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 23310 Sorted by residual: bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.540 -0.023 6.70e-03 2.23e+04 1.19e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.540 -0.023 6.70e-03 2.23e+04 1.19e+01 bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.539 -0.022 6.70e-03 2.23e+04 1.11e+01 bond pdb=" CZ ARG C1000 " pdb=" NH2 ARG C1000 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" CZ ARG A1039 " pdb=" NH2 ARG A1039 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.00e+01 ... (remaining 23305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 22548 1.81 - 3.63: 7959 3.63 - 5.44: 1103 5.44 - 7.26: 88 7.26 - 9.07: 9 Bond angle restraints: 31707 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 119.30 -8.60 1.22e+00 6.72e-01 4.97e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 118.45 -7.75 1.22e+00 6.72e-01 4.03e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 118.44 -7.74 1.22e+00 6.72e-01 4.03e+01 angle pdb=" CA PHE A 565 " pdb=" CB PHE A 565 " pdb=" CG PHE A 565 " ideal model delta sigma weight residual 113.80 119.34 -5.54 1.00e+00 1.00e+00 3.07e+01 angle pdb=" OE1 GLN C 965 " pdb=" CD GLN C 965 " pdb=" NE2 GLN C 965 " ideal model delta sigma weight residual 122.60 117.07 5.53 1.00e+00 1.00e+00 3.05e+01 ... (remaining 31702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 12882 17.45 - 34.90: 812 34.90 - 52.35: 134 52.35 - 69.79: 53 69.79 - 87.24: 30 Dihedral angle restraints: 13911 sinusoidal: 5421 harmonic: 8490 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -162.57 76.57 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.39 71.39 1 1.00e+01 1.00e-02 6.54e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 159.97 -66.97 1 1.00e+01 1.00e-02 5.84e+01 ... (remaining 13908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2403 0.087 - 0.174: 1084 0.174 - 0.261: 121 0.261 - 0.349: 18 0.349 - 0.436: 7 Chirality restraints: 3633 Sorted by residual: chirality pdb=" CA PRO A 986 " pdb=" N PRO A 986 " pdb=" C PRO A 986 " pdb=" CB PRO A 986 " both_signs ideal model delta sigma weight residual False 2.72 2.28 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CA PRO C 986 " pdb=" N PRO C 986 " pdb=" C PRO C 986 " pdb=" CB PRO C 986 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ASP C 571 " pdb=" N ASP C 571 " pdb=" C ASP C 571 " pdb=" CB ASP C 571 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 3630 not shown) Planarity restraints: 4098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 396 " -0.181 2.00e-02 2.50e+03 1.00e-01 2.00e+02 pdb=" CG TYR C 396 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR C 396 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TYR C 396 " 0.084 2.00e-02 2.50e+03 pdb=" CE1 TYR C 396 " 0.058 2.00e-02 2.50e+03 pdb=" CE2 TYR C 396 " 0.055 2.00e-02 2.50e+03 pdb=" CZ TYR C 396 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR C 396 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 269 " 0.127 2.00e-02 2.50e+03 6.56e-02 8.62e+01 pdb=" CG TYR C 269 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR C 269 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TYR C 269 " -0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR C 269 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR C 269 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR C 269 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR C 269 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 396 " 0.118 2.00e-02 2.50e+03 6.36e-02 8.10e+01 pdb=" CG TYR B 396 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 396 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR B 396 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR B 396 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR B 396 " -0.034 2.00e-02 2.50e+03 pdb=" CZ TYR B 396 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 396 " 0.095 2.00e-02 2.50e+03 ... (remaining 4095 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 11438 3.00 - 3.48: 22223 3.48 - 3.95: 38597 3.95 - 4.43: 43146 4.43 - 4.90: 73387 Nonbonded interactions: 188791 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.531 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.541 3.040 nonbonded pdb=" OH TYR A 396 " pdb=" OE1 GLU A 516 " model vdw 2.543 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.552 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.552 3.040 ... (remaining 188786 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 individual isotropic 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.320 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5484 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 : 0.012 0.043 23349 Z= 0.725 Angle : 1.743 9.069 31785 Z= 1.183 Chirality : 0.091 0.436 3633 Planarity : 0.014 0.197 4098 Dihedral : 13.142 87.243 8310 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.27 % Favored : 94.66 % Rotamer: Outliers : 0.82 % Allowed : 2.43 % Favored : 96.75 % Cbeta Deviations : 0.04 % 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 are not related in a simple way. whole: -1.00 (0.14), residues: 2844 helix: -0.57 (0.17), residues: 629 sheet: 0.01 (0.20), residues: 583 loop : -0.93 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1019 TYR 0.181 0.022 TYR C 396 PHE 0.095 0.012 PHE A 718 TRP 0.074 0.023 TRP C1102 HIS 0.010 0.003 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.01238 (23310) covalent geometry : angle 1.74185 (31707) SS BOND : bond 0.01348 ( 39) SS BOND : angle 2.08852 ( 78) hydrogen bonds : bond 0.14185 ( 1046) hydrogen bonds : angle 8.46453 ( 2877) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 524 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.6568 (m-30) cc_final: 0.6300 (m-30) REVERT: A 129 LYS cc_start: 0.5133 (mttm) cc_final: 0.4910 (tptp) REVERT: A 200 TYR cc_start: 0.7084 (m-80) cc_final: 0.6334 (m-80) REVERT: A 316 SER cc_start: 0.7330 (t) cc_final: 0.7070 (p) REVERT: A 359 SER cc_start: 0.8288 (p) cc_final: 0.7803 (t) REVERT: A 383 CYS cc_start: 0.5999 (t) cc_final: 0.5599 (t) REVERT: A 389 ASP cc_start: 0.6825 (t0) cc_final: 0.6500 (m-30) REVERT: A 394 ASN cc_start: 0.7185 (m-40) cc_final: 0.6678 (m-40) REVERT: A 396 TYR cc_start: 0.6255 (m-80) cc_final: 0.5530 (m-80) REVERT: A 453 TYR cc_start: 0.6299 (p90) cc_final: 0.6000 (p90) REVERT: A 493 GLN cc_start: 0.3922 (OUTLIER) cc_final: 0.3687 (mp10) REVERT: A 497 PHE cc_start: 0.3874 (m-80) cc_final: 0.3297 (m-10) REVERT: A 529 LYS cc_start: 0.8402 (mttt) cc_final: 0.7806 (ptmt) REVERT: A 558 LYS cc_start: 0.8234 (tttt) cc_final: 0.7962 (mttp) REVERT: A 572 THR cc_start: 0.5445 (p) cc_final: 0.5232 (p) REVERT: A 581 THR cc_start: 0.6460 (t) cc_final: 0.6223 (t) REVERT: A 614 ASP cc_start: 0.8022 (t0) cc_final: 0.7795 (m-30) REVERT: A 661 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6716 (mm-30) REVERT: A 675 GLN cc_start: 0.5899 (mm-40) cc_final: 0.5671 (tt0) REVERT: A 697 MET cc_start: 0.6430 (ptm) cc_final: 0.6163 (ptm) REVERT: A 748 GLU cc_start: 0.7127 (mp0) cc_final: 0.6806 (mp0) REVERT: A 750 SER cc_start: 0.6309 (t) cc_final: 0.6099 (m) REVERT: A 752 LEU cc_start: 0.6661 (mt) cc_final: 0.6139 (mt) REVERT: A 755 GLN cc_start: 0.6534 (mt0) cc_final: 0.5876 (pt0) REVERT: A 790 LYS cc_start: 0.7175 (pttt) cc_final: 0.6903 (pttp) REVERT: A 823 PHE cc_start: 0.6827 (m-80) cc_final: 0.6574 (m-80) REVERT: A 825 LYS cc_start: 0.6783 (mmtt) cc_final: 0.6395 (mtpt) REVERT: A 855 PHE cc_start: 0.6827 (m-80) cc_final: 0.6445 (m-10) REVERT: A 987 PRO cc_start: 0.8654 (Cg_exo) cc_final: 0.8194 (Cg_endo) REVERT: A 988 GLU cc_start: 0.7317 (tp30) cc_final: 0.6996 (pm20) REVERT: A 994 ASP cc_start: 0.5791 (t0) cc_final: 0.5435 (t0) REVERT: A 1002 GLN cc_start: 0.6155 (tt0) cc_final: 0.5574 (tp-100) REVERT: A 1005 GLN cc_start: 0.6567 (mt0) cc_final: 0.6060 (tp-100) REVERT: A 1119 ASN cc_start: 0.6452 (m-40) cc_final: 0.6123 (m110) REVERT: A 1142 GLN cc_start: 0.6722 (tp40) cc_final: 0.6112 (tp-100) REVERT: B 32 PHE cc_start: 0.5577 (m-80) cc_final: 0.5348 (m-80) REVERT: B 48 LEU cc_start: 0.6566 (mt) cc_final: 0.6344 (mt) REVERT: B 63 THR cc_start: 0.5581 (m) cc_final: 0.5151 (p) REVERT: B 65 PHE cc_start: 0.6906 (m-80) cc_final: 0.6598 (m-80) REVERT: B 88 ASP cc_start: 0.6453 (m-30) cc_final: 0.6019 (m-30) REVERT: B 133 PHE cc_start: 0.5183 (m-80) cc_final: 0.4586 (m-80) REVERT: B 221 SER cc_start: 0.6362 (t) cc_final: 0.5795 (p) REVERT: B 269 TYR cc_start: 0.7232 (m-80) cc_final: 0.6625 (m-80) REVERT: B 289 VAL cc_start: 0.4665 (t) cc_final: 0.4430 (t) REVERT: B 302 THR cc_start: 0.6613 (m) cc_final: 0.6218 (p) REVERT: B 351 TYR cc_start: 0.7737 (p90) cc_final: 0.7279 (p90) REVERT: B 365 TYR cc_start: 0.6554 (m-80) cc_final: 0.6054 (m-80) REVERT: B 370 ASN cc_start: 0.6938 (m-40) cc_final: 0.6491 (p0) REVERT: B 408 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8146 (ttp-170) REVERT: B 417 LYS cc_start: 0.8210 (ptpt) cc_final: 0.7989 (mmmt) REVERT: B 448 ASN cc_start: 0.6613 (t0) cc_final: 0.6171 (t0) REVERT: B 558 LYS cc_start: 0.7768 (tttt) cc_final: 0.7357 (mtmm) REVERT: B 651 ILE cc_start: 0.7645 (mt) cc_final: 0.7397 (mp) REVERT: B 702 GLU cc_start: 0.7016 (tt0) cc_final: 0.6375 (tm-30) REVERT: B 776 LYS cc_start: 0.4833 (tttt) cc_final: 0.4322 (ttpt) REVERT: B 804 GLN cc_start: 0.6106 (mm-40) cc_final: 0.5760 (mp10) REVERT: B 868 GLU cc_start: 0.6647 (tt0) cc_final: 0.6014 (mp0) REVERT: B 998 THR cc_start: 0.6322 (m) cc_final: 0.5862 (p) REVERT: B 1045 LYS cc_start: 0.7419 (ttpp) cc_final: 0.6570 (mppt) REVERT: C 52 GLN cc_start: 0.7457 (tt0) cc_final: 0.6891 (tt0) REVERT: C 105 ILE cc_start: 0.5767 (mt) cc_final: 0.5467 (mp) REVERT: C 140 PHE cc_start: 0.4409 (p90) cc_final: 0.4205 (p90) REVERT: C 197 ILE cc_start: 0.6853 (mt) cc_final: 0.6573 (tt) REVERT: C 200 TYR cc_start: 0.5387 (m-80) cc_final: 0.5019 (m-80) REVERT: C 221 SER cc_start: 0.7394 (t) cc_final: 0.7142 (p) REVERT: C 237 ARG cc_start: 0.6191 (mtt90) cc_final: 0.5964 (mtp85) REVERT: C 239 GLN cc_start: 0.5712 (tt0) cc_final: 0.5307 (tt0) REVERT: C 316 SER cc_start: 0.5970 (t) cc_final: 0.5729 (p) REVERT: C 360 ASN cc_start: 0.8155 (m-40) cc_final: 0.7777 (t0) REVERT: C 383 CYS cc_start: 0.6736 (t) cc_final: 0.6406 (t) REVERT: C 537 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8544 (ttpp) REVERT: C 558 LYS cc_start: 0.7819 (tttt) cc_final: 0.7146 (mttp) REVERT: C 614 ASP cc_start: 0.7984 (t0) cc_final: 0.7719 (m-30) REVERT: C 658 ASN cc_start: 0.6809 (m-40) cc_final: 0.6411 (t0) REVERT: C 740 MET cc_start: 0.7112 (ttt) cc_final: 0.6853 (ttm) REVERT: C 755 GLN cc_start: 0.5393 (mt0) cc_final: 0.5137 (mm-40) REVERT: C 790 LYS cc_start: 0.7183 (pttt) cc_final: 0.6371 (mtpp) REVERT: C 875 SER cc_start: 0.6548 (t) cc_final: 0.6108 (m) REVERT: C 994 ASP cc_start: 0.6083 (t70) cc_final: 0.5784 (t0) REVERT: C 1073 LYS cc_start: 0.6931 (mttt) cc_final: 0.6624 (mtpt) REVERT: C 1119 ASN cc_start: 0.6965 (m-40) cc_final: 0.6666 (m110) outliers start: 21 outliers final: 6 residues processed: 539 average time/residue: 0.1505 time to fit residues: 127.3570 Evaluate side-chains 305 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 298 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 422 ASN A 607 GLN A 901 GLN A 955 ASN B 207 HIS B 394 ASN B 580 GLN B 784 GLN B 955 ASN C 207 HIS C 613 GLN C 965 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.161976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.111138 restraints weight = 30206.895| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.90 r_work: 0.3152 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 23349 Z= 0.165 Angle : 0.645 12.596 31785 Z= 0.348 Chirality : 0.048 0.214 3633 Planarity : 0.004 0.044 4098 Dihedral : 5.758 56.099 3109 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.29 % Favored : 97.64 % Rotamer: Outliers : 1.96 % Allowed : 7.51 % Favored : 90.53 % 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 are not related in a simple way. whole: -0.04 (0.15), residues: 2844 helix: 1.44 (0.20), residues: 645 sheet: 0.02 (0.18), residues: 657 loop : -0.65 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 577 TYR 0.017 0.002 TYR C1067 PHE 0.025 0.002 PHE C 400 TRP 0.020 0.002 TRP C 353 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00375 (23310) covalent geometry : angle 0.63821 (31707) SS BOND : bond 0.00257 ( 39) SS BOND : angle 2.02758 ( 78) hydrogen bonds : bond 0.04476 ( 1046) hydrogen bonds : angle 6.37713 ( 2877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 333 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7010 (m-30) cc_final: 0.6785 (m-30) REVERT: A 129 LYS cc_start: 0.6759 (mttm) cc_final: 0.6417 (tptp) REVERT: A 200 TYR cc_start: 0.6815 (m-80) cc_final: 0.6409 (m-80) REVERT: A 334 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7163 (p0) REVERT: A 396 TYR cc_start: 0.7745 (m-80) cc_final: 0.7128 (m-80) REVERT: A 453 TYR cc_start: 0.6323 (p90) cc_final: 0.5669 (p90) REVERT: A 516 GLU cc_start: 0.6774 (tt0) cc_final: 0.6347 (tt0) REVERT: A 697 MET cc_start: 0.8530 (ptm) cc_final: 0.8229 (ptm) REVERT: A 752 LEU cc_start: 0.8236 (mt) cc_final: 0.7883 (mp) REVERT: A 755 GLN cc_start: 0.8280 (mt0) cc_final: 0.7969 (pt0) REVERT: A 1142 GLN cc_start: 0.7702 (tp40) cc_final: 0.7021 (tp-100) REVERT: B 63 THR cc_start: 0.7837 (m) cc_final: 0.7092 (p) REVERT: B 88 ASP cc_start: 0.7053 (m-30) cc_final: 0.6793 (m-30) REVERT: B 133 PHE cc_start: 0.6654 (m-80) cc_final: 0.6365 (m-80) REVERT: B 221 SER cc_start: 0.7561 (t) cc_final: 0.7176 (p) REVERT: B 237 ARG cc_start: 0.7168 (mtp85) cc_final: 0.6891 (mtp85) REVERT: B 319 ARG cc_start: 0.7390 (mtp-110) cc_final: 0.7115 (ttm-80) REVERT: B 351 TYR cc_start: 0.8266 (p90) cc_final: 0.8027 (p90) REVERT: B 370 ASN cc_start: 0.7292 (m-40) cc_final: 0.6681 (p0) REVERT: B 408 ARG cc_start: 0.8332 (ttp80) cc_final: 0.8121 (ptt90) REVERT: B 425 LEU cc_start: 0.8368 (mp) cc_final: 0.8080 (mt) REVERT: B 429 PHE cc_start: 0.8320 (t80) cc_final: 0.8100 (t80) REVERT: B 448 ASN cc_start: 0.6231 (t0) cc_final: 0.5935 (t0) REVERT: B 776 LYS cc_start: 0.8145 (tttt) cc_final: 0.7822 (ttpt) REVERT: B 878 LEU cc_start: 0.8992 (tp) cc_final: 0.8726 (tp) REVERT: B 979 ASP cc_start: 0.7724 (m-30) cc_final: 0.7502 (m-30) REVERT: B 994 ASP cc_start: 0.7858 (t70) cc_final: 0.7383 (m-30) REVERT: B 998 THR cc_start: 0.8678 (m) cc_final: 0.8345 (p) REVERT: C 132 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6076 (pm20) REVERT: C 207 HIS cc_start: 0.7127 (m-70) cc_final: 0.6524 (m-70) REVERT: C 269 TYR cc_start: 0.8568 (m-10) cc_final: 0.8207 (m-10) REVERT: C 392 PHE cc_start: 0.8135 (m-80) cc_final: 0.7784 (m-10) REVERT: C 511 VAL cc_start: 0.7863 (t) cc_final: 0.7491 (p) REVERT: C 790 LYS cc_start: 0.8333 (pttt) cc_final: 0.7971 (mtpp) REVERT: C 990 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7557 (mt-10) REVERT: C 1142 GLN cc_start: 0.8058 (tp40) cc_final: 0.7713 (tp40) outliers start: 50 outliers final: 29 residues processed: 371 average time/residue: 0.1477 time to fit residues: 87.3515 Evaluate side-chains 262 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 220 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 281 optimal weight: 1.9990 chunk 152 optimal weight: 0.2980 chunk 116 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 762 GLN A 955 ASN A1119 ASN B 207 HIS B 317 ASN B 437 ASN C 607 GLN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.161388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112134 restraints weight = 30277.374| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.07 r_work: 0.3159 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 23349 Z= 0.172 Angle : 0.601 10.842 31785 Z= 0.321 Chirality : 0.046 0.211 3633 Planarity : 0.004 0.052 4098 Dihedral : 4.951 28.447 3101 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.39 % Allowed : 9.47 % Favored : 88.15 % 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 are not related in a simple way. whole: -0.01 (0.15), residues: 2844 helix: 1.58 (0.20), residues: 651 sheet: -0.17 (0.18), residues: 680 loop : -0.60 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 577 TYR 0.023 0.002 TYR C1067 PHE 0.023 0.002 PHE B 400 TRP 0.021 0.002 TRP C 353 HIS 0.010 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00387 (23310) covalent geometry : angle 0.59542 (31707) SS BOND : bond 0.00753 ( 39) SS BOND : angle 1.74575 ( 78) hydrogen bonds : bond 0.04326 ( 1046) hydrogen bonds : angle 6.01036 ( 2877) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 280 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7216 (m-30) cc_final: 0.6887 (m-30) REVERT: A 129 LYS cc_start: 0.6934 (mttm) cc_final: 0.6401 (tptp) REVERT: A 200 TYR cc_start: 0.6835 (m-80) cc_final: 0.6576 (m-80) REVERT: A 237 ARG cc_start: 0.6516 (mtt90) cc_final: 0.6315 (mtp85) REVERT: A 334 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.7185 (p0) REVERT: A 507 PRO cc_start: 0.6555 (Cg_exo) cc_final: 0.6322 (Cg_endo) REVERT: A 528 LYS cc_start: 0.8383 (tttp) cc_final: 0.7671 (tttm) REVERT: A 804 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7328 (mm110) REVERT: A 1142 GLN cc_start: 0.7552 (tp40) cc_final: 0.6880 (tp40) REVERT: B 133 PHE cc_start: 0.6709 (m-80) cc_final: 0.6263 (m-80) REVERT: B 221 SER cc_start: 0.7918 (t) cc_final: 0.7390 (p) REVERT: B 237 ARG cc_start: 0.7471 (mtp85) cc_final: 0.7166 (mtp85) REVERT: B 319 ARG cc_start: 0.7421 (mtp-110) cc_final: 0.7067 (ttm-80) REVERT: B 351 TYR cc_start: 0.8482 (p90) cc_final: 0.8227 (p90) REVERT: B 393 THR cc_start: 0.7436 (p) cc_final: 0.6867 (t) REVERT: B 394 ASN cc_start: 0.7620 (m-40) cc_final: 0.6656 (m-40) REVERT: B 448 ASN cc_start: 0.6116 (t0) cc_final: 0.5818 (t0) REVERT: B 776 LYS cc_start: 0.8628 (tttt) cc_final: 0.8259 (ttpt) REVERT: B 868 GLU cc_start: 0.8498 (tt0) cc_final: 0.8275 (mp0) REVERT: B 957 GLN cc_start: 0.8314 (tp-100) cc_final: 0.7996 (tt0) REVERT: C 102 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6863 (mtp85) REVERT: C 190 ARG cc_start: 0.6239 (mtt180) cc_final: 0.5874 (mtt180) REVERT: C 205 SER cc_start: 0.7792 (t) cc_final: 0.7504 (t) REVERT: C 380 TYR cc_start: 0.7624 (m-80) cc_final: 0.7372 (m-80) REVERT: C 508 TYR cc_start: 0.7579 (m-80) cc_final: 0.7208 (m-80) REVERT: C 804 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7601 (mp10) outliers start: 61 outliers final: 37 residues processed: 327 average time/residue: 0.1416 time to fit residues: 74.5043 Evaluate side-chains 259 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 140 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 264 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 147 optimal weight: 0.2980 chunk 135 optimal weight: 10.0000 chunk 223 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 314 GLN A 755 GLN B 207 HIS C 901 GLN C1002 GLN C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.157978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107964 restraints weight = 30210.697| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.03 r_work: 0.3115 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 23349 Z= 0.242 Angle : 0.609 8.426 31785 Z= 0.322 Chirality : 0.047 0.187 3633 Planarity : 0.004 0.048 4098 Dihedral : 5.002 35.746 3101 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.78 % Allowed : 11.11 % Favored : 86.11 % 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 are not related in a simple way. whole: -0.13 (0.15), residues: 2844 helix: 1.49 (0.21), residues: 654 sheet: -0.19 (0.18), residues: 629 loop : -0.71 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1039 TYR 0.022 0.002 TYR A1067 PHE 0.020 0.002 PHE B 400 TRP 0.017 0.002 TRP B 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00578 (23310) covalent geometry : angle 0.60274 (31707) SS BOND : bond 0.00604 ( 39) SS BOND : angle 1.81091 ( 78) hydrogen bonds : bond 0.04433 ( 1046) hydrogen bonds : angle 6.08633 ( 2877) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 217 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7354 (m-30) cc_final: 0.7034 (m-30) REVERT: A 129 LYS cc_start: 0.6952 (mttm) cc_final: 0.6358 (tptt) REVERT: A 200 TYR cc_start: 0.6886 (m-80) cc_final: 0.6568 (m-80) REVERT: A 334 ASN cc_start: 0.7703 (OUTLIER) cc_final: 0.7206 (p0) REVERT: A 453 TYR cc_start: 0.5222 (p90) cc_final: 0.4740 (p90) REVERT: A 565 PHE cc_start: 0.6490 (m-10) cc_final: 0.6251 (m-10) REVERT: A 869 MET cc_start: 0.8997 (mtt) cc_final: 0.8771 (mtt) REVERT: A 1142 GLN cc_start: 0.7577 (tp40) cc_final: 0.6915 (tp40) REVERT: B 99 ASN cc_start: 0.6693 (t0) cc_final: 0.6473 (t0) REVERT: B 133 PHE cc_start: 0.6815 (m-80) cc_final: 0.6290 (m-80) REVERT: B 200 TYR cc_start: 0.6157 (m-10) cc_final: 0.5928 (m-80) REVERT: B 221 SER cc_start: 0.8084 (t) cc_final: 0.7679 (p) REVERT: B 237 ARG cc_start: 0.7737 (mtp85) cc_final: 0.7429 (mtp85) REVERT: B 319 ARG cc_start: 0.7620 (mtp-110) cc_final: 0.7235 (ttm-80) REVERT: B 334 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7449 (p0) REVERT: B 351 TYR cc_start: 0.8576 (p90) cc_final: 0.8214 (p90) REVERT: B 357 ARG cc_start: 0.8104 (mtp180) cc_final: 0.7336 (mtp85) REVERT: B 380 TYR cc_start: 0.8448 (m-80) cc_final: 0.7872 (m-80) REVERT: B 393 THR cc_start: 0.7921 (p) cc_final: 0.7277 (t) REVERT: B 394 ASN cc_start: 0.7991 (m-40) cc_final: 0.6795 (m-40) REVERT: B 646 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7653 (tpp80) REVERT: B 776 LYS cc_start: 0.8884 (tttt) cc_final: 0.8594 (ttpt) REVERT: B 957 GLN cc_start: 0.8348 (tp-100) cc_final: 0.8136 (tt0) REVERT: C 53 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.6746 (m-30) REVERT: C 198 ASP cc_start: 0.7119 (m-30) cc_final: 0.6872 (t0) REVERT: C 237 ARG cc_start: 0.7706 (mtp85) cc_final: 0.7330 (mtm-85) REVERT: C 380 TYR cc_start: 0.7675 (m-80) cc_final: 0.7387 (m-80) REVERT: C 508 TYR cc_start: 0.7652 (m-80) cc_final: 0.7095 (m-80) REVERT: C 558 LYS cc_start: 0.8306 (mttm) cc_final: 0.7829 (ptpp) REVERT: C 646 ARG cc_start: 0.7697 (ttp80) cc_final: 0.7373 (mtm180) REVERT: C 804 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7825 (mp10) outliers start: 71 outliers final: 46 residues processed: 270 average time/residue: 0.1380 time to fit residues: 60.1469 Evaluate side-chains 233 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 169 optimal weight: 0.5980 chunk 280 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 190 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 213 optimal weight: 0.3980 chunk 36 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS C1002 GLN C1106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.160255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111423 restraints weight = 30169.275| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.00 r_work: 0.3158 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23349 Z= 0.121 Angle : 0.521 8.655 31785 Z= 0.274 Chirality : 0.044 0.171 3633 Planarity : 0.004 0.036 4098 Dihedral : 4.644 31.359 3101 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.23 % Allowed : 12.32 % Favored : 85.45 % 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 are not related in a simple way. whole: 0.05 (0.15), residues: 2844 helix: 1.77 (0.21), residues: 653 sheet: -0.12 (0.18), residues: 635 loop : -0.64 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.019 0.001 TYR C1067 PHE 0.022 0.001 PHE C 400 TRP 0.013 0.001 TRP C 353 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00272 (23310) covalent geometry : angle 0.51740 (31707) SS BOND : bond 0.00249 ( 39) SS BOND : angle 1.37657 ( 78) hydrogen bonds : bond 0.03746 ( 1046) hydrogen bonds : angle 5.75533 ( 2877) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 223 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6956 (mttm) cc_final: 0.6385 (tptt) REVERT: A 200 TYR cc_start: 0.6850 (m-80) cc_final: 0.6556 (m-80) REVERT: A 271 GLN cc_start: 0.8279 (mt0) cc_final: 0.7940 (mm-40) REVERT: A 380 TYR cc_start: 0.7282 (m-10) cc_final: 0.7045 (m-10) REVERT: A 453 TYR cc_start: 0.5102 (p90) cc_final: 0.4761 (p90) REVERT: A 565 PHE cc_start: 0.6416 (m-10) cc_final: 0.6168 (m-10) REVERT: A 567 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7540 (mtt-85) REVERT: A 762 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: A 869 MET cc_start: 0.8966 (mtt) cc_final: 0.8749 (mtt) REVERT: A 1142 GLN cc_start: 0.7514 (tp40) cc_final: 0.6870 (tp40) REVERT: B 99 ASN cc_start: 0.6719 (t0) cc_final: 0.5982 (m110) REVERT: B 133 PHE cc_start: 0.6740 (m-80) cc_final: 0.6256 (m-80) REVERT: B 221 SER cc_start: 0.7986 (t) cc_final: 0.7598 (p) REVERT: B 237 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7432 (mtp85) REVERT: B 319 ARG cc_start: 0.7571 (mtp-110) cc_final: 0.7219 (ttm-80) REVERT: B 351 TYR cc_start: 0.8611 (p90) cc_final: 0.8269 (p90) REVERT: B 360 ASN cc_start: 0.8691 (m-40) cc_final: 0.8300 (m-40) REVERT: B 393 THR cc_start: 0.7776 (p) cc_final: 0.7206 (t) REVERT: B 646 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7553 (tpp80) REVERT: B 776 LYS cc_start: 0.8871 (tttt) cc_final: 0.8549 (ttpt) REVERT: B 957 GLN cc_start: 0.8274 (tp-100) cc_final: 0.8063 (tt0) REVERT: C 102 ARG cc_start: 0.7145 (mtt180) cc_final: 0.6694 (mtp85) REVERT: C 237 ARG cc_start: 0.7640 (mtp85) cc_final: 0.7342 (mtm-85) REVERT: C 305 SER cc_start: 0.9091 (t) cc_final: 0.8678 (p) REVERT: C 380 TYR cc_start: 0.7737 (m-80) cc_final: 0.7505 (m-80) REVERT: C 508 TYR cc_start: 0.7547 (m-80) cc_final: 0.7019 (m-80) REVERT: C 558 LYS cc_start: 0.8295 (mttm) cc_final: 0.7827 (ptpp) REVERT: C 646 ARG cc_start: 0.7661 (ttp80) cc_final: 0.7349 (mtm180) REVERT: C 804 GLN cc_start: 0.8406 (mm-40) cc_final: 0.7840 (mp10) REVERT: C 902 MET cc_start: 0.8686 (tpt) cc_final: 0.8238 (mmt) REVERT: C 994 ASP cc_start: 0.8247 (t70) cc_final: 0.7876 (m-30) outliers start: 57 outliers final: 34 residues processed: 268 average time/residue: 0.1497 time to fit residues: 64.4034 Evaluate side-chains 238 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 204 optimal weight: 20.0000 chunk 232 optimal weight: 0.0030 chunk 120 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 55 optimal weight: 0.3980 chunk 8 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 overall best weight: 3.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B1002 GLN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.155559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105578 restraints weight = 30430.110| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.03 r_work: 0.3062 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 23349 Z= 0.316 Angle : 0.649 10.610 31785 Z= 0.339 Chirality : 0.049 0.190 3633 Planarity : 0.004 0.046 4098 Dihedral : 5.028 41.078 3100 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.21 % Allowed : 11.85 % Favored : 84.94 % 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 are not related in a simple way. whole: -0.33 (0.15), residues: 2844 helix: 1.36 (0.20), residues: 666 sheet: -0.33 (0.18), residues: 628 loop : -0.86 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 190 TYR 0.024 0.002 TYR B1067 PHE 0.021 0.002 PHE C 898 TRP 0.016 0.002 TRP C 353 HIS 0.021 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00769 (23310) covalent geometry : angle 0.64179 (31707) SS BOND : bond 0.00475 ( 39) SS BOND : angle 2.08379 ( 78) hydrogen bonds : bond 0.04708 ( 1046) hydrogen bonds : angle 6.13634 ( 2877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 196 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7714 (m-80) cc_final: 0.7294 (m-80) REVERT: A 129 LYS cc_start: 0.6975 (mttm) cc_final: 0.6286 (tptt) REVERT: A 200 TYR cc_start: 0.6991 (m-80) cc_final: 0.6598 (m-80) REVERT: A 271 GLN cc_start: 0.8523 (mt0) cc_final: 0.8110 (mm-40) REVERT: A 309 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: A 334 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7329 (p0) REVERT: A 453 TYR cc_start: 0.5355 (p90) cc_final: 0.5000 (p90) REVERT: A 507 PRO cc_start: 0.7003 (Cg_exo) cc_final: 0.6792 (Cg_endo) REVERT: A 528 LYS cc_start: 0.8392 (tttp) cc_final: 0.7932 (tttm) REVERT: A 567 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7610 (mtt-85) REVERT: A 702 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8184 (tp30) REVERT: A 869 MET cc_start: 0.8984 (mtt) cc_final: 0.8763 (mtt) REVERT: A 1142 GLN cc_start: 0.7583 (tp40) cc_final: 0.6877 (tp40) REVERT: B 99 ASN cc_start: 0.6967 (t0) cc_final: 0.6118 (m110) REVERT: B 221 SER cc_start: 0.8101 (t) cc_final: 0.7801 (p) REVERT: B 237 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7452 (mtp85) REVERT: B 319 ARG cc_start: 0.7818 (mtp-110) cc_final: 0.7307 (tpt90) REVERT: B 334 ASN cc_start: 0.7167 (OUTLIER) cc_final: 0.6896 (p0) REVERT: B 351 TYR cc_start: 0.8683 (p90) cc_final: 0.8262 (p90) REVERT: B 360 ASN cc_start: 0.8756 (m-40) cc_final: 0.8528 (m110) REVERT: B 528 LYS cc_start: 0.7645 (tttt) cc_final: 0.7432 (tttm) REVERT: B 646 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7629 (tpp80) REVERT: B 776 LYS cc_start: 0.8996 (tttt) cc_final: 0.8701 (ttpt) REVERT: B 1145 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6385 (mp) REVERT: C 32 PHE cc_start: 0.8849 (m-10) cc_final: 0.8558 (m-10) REVERT: C 53 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.6655 (m-30) REVERT: C 305 SER cc_start: 0.9211 (t) cc_final: 0.8722 (p) REVERT: C 380 TYR cc_start: 0.7612 (m-80) cc_final: 0.7250 (m-80) REVERT: C 646 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7506 (mtm180) REVERT: C 804 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7955 (mp10) REVERT: C 902 MET cc_start: 0.8855 (tpt) cc_final: 0.8573 (mmt) REVERT: C 994 ASP cc_start: 0.8237 (t70) cc_final: 0.7944 (t70) outliers start: 82 outliers final: 54 residues processed: 262 average time/residue: 0.1431 time to fit residues: 60.7553 Evaluate side-chains 242 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 180 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.1980 chunk 131 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 134 optimal weight: 0.0020 chunk 236 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 185 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN A 935 GLN C1005 GLN C1119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.159748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.110408 restraints weight = 30328.556| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.94 r_work: 0.3150 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 23349 Z= 0.114 Angle : 0.517 9.469 31785 Z= 0.272 Chirality : 0.044 0.195 3633 Planarity : 0.004 0.041 4098 Dihedral : 4.537 33.425 3100 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.76 % Allowed : 13.50 % Favored : 84.74 % 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 are not related in a simple way. whole: -0.05 (0.15), residues: 2844 helix: 1.71 (0.21), residues: 667 sheet: -0.14 (0.18), residues: 629 loop : -0.76 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 190 TYR 0.019 0.001 TYR C1067 PHE 0.027 0.001 PHE C 400 TRP 0.017 0.001 TRP C 353 HIS 0.002 0.000 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00256 (23310) covalent geometry : angle 0.51129 (31707) SS BOND : bond 0.00335 ( 39) SS BOND : angle 1.63684 ( 78) hydrogen bonds : bond 0.03655 ( 1046) hydrogen bonds : angle 5.71513 ( 2877) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7682 (m-80) cc_final: 0.7131 (m-80) REVERT: A 129 LYS cc_start: 0.7007 (mttm) cc_final: 0.6349 (tptt) REVERT: A 200 TYR cc_start: 0.6892 (m-80) cc_final: 0.6611 (m-80) REVERT: A 271 GLN cc_start: 0.8407 (mt0) cc_final: 0.8051 (mm-40) REVERT: A 453 TYR cc_start: 0.5706 (p90) cc_final: 0.5304 (p90) REVERT: A 507 PRO cc_start: 0.6920 (Cg_exo) cc_final: 0.6519 (Cg_endo) REVERT: A 508 TYR cc_start: 0.7006 (m-80) cc_final: 0.6308 (m-80) REVERT: A 528 LYS cc_start: 0.8310 (tttp) cc_final: 0.7949 (tttm) REVERT: A 761 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8330 (p) REVERT: A 1142 GLN cc_start: 0.7531 (tp40) cc_final: 0.6973 (tp-100) REVERT: B 99 ASN cc_start: 0.6997 (t0) cc_final: 0.6144 (m110) REVERT: B 133 PHE cc_start: 0.6873 (m-80) cc_final: 0.6595 (m-80) REVERT: B 221 SER cc_start: 0.8153 (t) cc_final: 0.7885 (p) REVERT: B 237 ARG cc_start: 0.7807 (mtp85) cc_final: 0.7451 (mtp85) REVERT: B 319 ARG cc_start: 0.7708 (mtp-110) cc_final: 0.7387 (ttt90) REVERT: B 351 TYR cc_start: 0.8648 (p90) cc_final: 0.8266 (p90) REVERT: B 528 LYS cc_start: 0.7643 (tttt) cc_final: 0.7372 (tttm) REVERT: B 646 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7595 (tpp80) REVERT: B 776 LYS cc_start: 0.8907 (tttt) cc_final: 0.8573 (ttpt) REVERT: C 32 PHE cc_start: 0.8861 (m-10) cc_final: 0.8620 (m-10) REVERT: C 305 SER cc_start: 0.9112 (t) cc_final: 0.8660 (p) REVERT: C 558 LYS cc_start: 0.8286 (mttm) cc_final: 0.7930 (ptpt) REVERT: C 646 ARG cc_start: 0.7747 (ttp80) cc_final: 0.7409 (mtm180) REVERT: C 804 GLN cc_start: 0.8384 (mm-40) cc_final: 0.7852 (mp10) REVERT: C 902 MET cc_start: 0.8720 (tpt) cc_final: 0.8214 (mmt) REVERT: C 988 GLU cc_start: 0.8297 (mp0) cc_final: 0.8092 (mp0) REVERT: C 994 ASP cc_start: 0.8109 (t70) cc_final: 0.7794 (m-30) REVERT: C 1005 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8049 (mt0) outliers start: 45 outliers final: 34 residues processed: 239 average time/residue: 0.1581 time to fit residues: 59.5197 Evaluate side-chains 224 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 4 optimal weight: 20.0000 chunk 215 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 247 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 217 optimal weight: 0.0070 chunk 245 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 360 ASN B 506 GLN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.158832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109581 restraints weight = 30166.353| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.04 r_work: 0.3135 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 23349 Z= 0.151 Angle : 0.537 17.750 31785 Z= 0.280 Chirality : 0.045 0.302 3633 Planarity : 0.004 0.037 4098 Dihedral : 4.495 32.577 3100 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.96 % Allowed : 13.73 % Favored : 84.31 % 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 are not related in a simple way. whole: 0.01 (0.15), residues: 2844 helix: 1.81 (0.21), residues: 665 sheet: -0.09 (0.19), residues: 615 loop : -0.74 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 237 TYR 0.022 0.001 TYR C 508 PHE 0.018 0.001 PHE A 400 TRP 0.017 0.001 TRP C 353 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00357 (23310) covalent geometry : angle 0.52920 (31707) SS BOND : bond 0.00463 ( 39) SS BOND : angle 1.91090 ( 78) hydrogen bonds : bond 0.03748 ( 1046) hydrogen bonds : angle 5.70383 ( 2877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7000 (mttm) cc_final: 0.6332 (tptt) REVERT: A 200 TYR cc_start: 0.6904 (m-80) cc_final: 0.6594 (m-80) REVERT: A 271 GLN cc_start: 0.8421 (mt0) cc_final: 0.8076 (mm-40) REVERT: A 453 TYR cc_start: 0.5744 (p90) cc_final: 0.5366 (p90) REVERT: A 507 PRO cc_start: 0.6994 (Cg_exo) cc_final: 0.6589 (Cg_endo) REVERT: A 508 TYR cc_start: 0.7061 (m-80) cc_final: 0.6362 (m-80) REVERT: A 528 LYS cc_start: 0.8331 (tttp) cc_final: 0.7944 (tttm) REVERT: A 761 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8350 (p) REVERT: A 1142 GLN cc_start: 0.7542 (tp40) cc_final: 0.6800 (tp-100) REVERT: B 133 PHE cc_start: 0.6837 (m-80) cc_final: 0.6555 (m-80) REVERT: B 221 SER cc_start: 0.8157 (t) cc_final: 0.7894 (p) REVERT: B 237 ARG cc_start: 0.7807 (mtp85) cc_final: 0.7409 (mtp85) REVERT: B 319 ARG cc_start: 0.7705 (mtp-110) cc_final: 0.7456 (ttt90) REVERT: B 351 TYR cc_start: 0.8691 (p90) cc_final: 0.8311 (p90) REVERT: B 528 LYS cc_start: 0.7647 (tttt) cc_final: 0.7366 (tttm) REVERT: B 646 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7653 (tpp80) REVERT: B 776 LYS cc_start: 0.8952 (tttt) cc_final: 0.8621 (ttpt) REVERT: C 32 PHE cc_start: 0.8817 (m-10) cc_final: 0.8564 (m-10) REVERT: C 305 SER cc_start: 0.9113 (t) cc_final: 0.8649 (p) REVERT: C 646 ARG cc_start: 0.7851 (ttp80) cc_final: 0.7484 (mtm180) REVERT: C 804 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7874 (mp10) REVERT: C 994 ASP cc_start: 0.8128 (t70) cc_final: 0.7810 (m-30) REVERT: C 1005 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8179 (mt0) outliers start: 50 outliers final: 41 residues processed: 228 average time/residue: 0.1435 time to fit residues: 53.0357 Evaluate side-chains 227 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 28 optimal weight: 7.9990 chunk 279 optimal weight: 0.5980 chunk 219 optimal weight: 0.0000 chunk 55 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 200 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 247 optimal weight: 0.7980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 360 ASN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.157249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107835 restraints weight = 30460.303| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.12 r_work: 0.3095 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 23349 Z= 0.221 Angle : 0.581 15.094 31785 Z= 0.303 Chirality : 0.046 0.261 3633 Planarity : 0.004 0.037 4098 Dihedral : 4.655 36.361 3100 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.07 % Allowed : 13.77 % Favored : 84.15 % 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 are not related in a simple way. whole: -0.16 (0.15), residues: 2844 helix: 1.59 (0.20), residues: 671 sheet: -0.18 (0.18), residues: 635 loop : -0.83 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 237 TYR 0.021 0.002 TYR A1067 PHE 0.018 0.002 PHE C 168 TRP 0.019 0.001 TRP C 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00533 (23310) covalent geometry : angle 0.57054 (31707) SS BOND : bond 0.00489 ( 39) SS BOND : angle 2.23800 ( 78) hydrogen bonds : bond 0.04118 ( 1046) hydrogen bonds : angle 5.83603 ( 2877) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7777 (m-80) cc_final: 0.7208 (m-80) REVERT: A 129 LYS cc_start: 0.7005 (mttm) cc_final: 0.6280 (tptt) REVERT: A 200 TYR cc_start: 0.6938 (m-80) cc_final: 0.6552 (m-80) REVERT: A 271 GLN cc_start: 0.8509 (mt0) cc_final: 0.8161 (mm-40) REVERT: A 400 PHE cc_start: 0.8857 (p90) cc_final: 0.8623 (p90) REVERT: A 453 TYR cc_start: 0.5806 (p90) cc_final: 0.5405 (p90) REVERT: A 498 GLN cc_start: 0.7951 (mt0) cc_final: 0.7338 (mm-40) REVERT: A 507 PRO cc_start: 0.7031 (Cg_exo) cc_final: 0.6560 (Cg_endo) REVERT: A 508 TYR cc_start: 0.7087 (m-80) cc_final: 0.6362 (m-80) REVERT: A 528 LYS cc_start: 0.8423 (tttp) cc_final: 0.7988 (tttm) REVERT: A 761 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8336 (p) REVERT: A 762 GLN cc_start: 0.7869 (pt0) cc_final: 0.7575 (tt0) REVERT: A 1142 GLN cc_start: 0.7541 (tp40) cc_final: 0.6784 (tp-100) REVERT: B 99 ASN cc_start: 0.7128 (t0) cc_final: 0.6148 (m-40) REVERT: B 133 PHE cc_start: 0.6961 (m-80) cc_final: 0.6615 (m-80) REVERT: B 221 SER cc_start: 0.8193 (t) cc_final: 0.7964 (p) REVERT: B 237 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7469 (mtp85) REVERT: B 319 ARG cc_start: 0.7802 (mtp-110) cc_final: 0.7573 (tpt90) REVERT: B 351 TYR cc_start: 0.8711 (p90) cc_final: 0.8296 (p90) REVERT: B 646 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7674 (tpp80) REVERT: B 776 LYS cc_start: 0.8996 (tttt) cc_final: 0.8634 (ttpt) REVERT: C 32 PHE cc_start: 0.8807 (m-10) cc_final: 0.8566 (m-10) REVERT: C 305 SER cc_start: 0.9157 (t) cc_final: 0.8659 (p) REVERT: C 430 THR cc_start: 0.8782 (m) cc_final: 0.8372 (t) REVERT: C 646 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7559 (mtm180) REVERT: C 994 ASP cc_start: 0.8254 (t70) cc_final: 0.7976 (t70) REVERT: C 1005 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8106 (mt0) outliers start: 53 outliers final: 44 residues processed: 227 average time/residue: 0.1479 time to fit residues: 54.6522 Evaluate side-chains 229 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 108 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 250 optimal weight: 0.3980 chunk 169 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 253 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 268 optimal weight: 0.5980 chunk 233 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 360 ASN C1002 GLN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.159367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110104 restraints weight = 30243.910| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.97 r_work: 0.3141 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 23349 Z= 0.126 Angle : 0.544 14.191 31785 Z= 0.282 Chirality : 0.044 0.234 3633 Planarity : 0.004 0.038 4098 Dihedral : 4.443 32.327 3100 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.80 % Allowed : 13.93 % Favored : 84.27 % 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 are not related in a simple way. whole: -0.00 (0.15), residues: 2844 helix: 1.77 (0.21), residues: 671 sheet: -0.09 (0.18), residues: 635 loop : -0.76 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 237 TYR 0.018 0.001 TYR C1067 PHE 0.016 0.001 PHE B 643 TRP 0.020 0.001 TRP C 353 HIS 0.002 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00294 (23310) covalent geometry : angle 0.53574 (31707) SS BOND : bond 0.00435 ( 39) SS BOND : angle 1.93185 ( 78) hydrogen bonds : bond 0.03657 ( 1046) hydrogen bonds : angle 5.65629 ( 2877) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7750 (m-80) cc_final: 0.7127 (m-80) REVERT: A 129 LYS cc_start: 0.7103 (mttm) cc_final: 0.6371 (tptt) REVERT: A 200 TYR cc_start: 0.6860 (m-80) cc_final: 0.6492 (m-80) REVERT: A 271 GLN cc_start: 0.8471 (mt0) cc_final: 0.8136 (mm-40) REVERT: A 453 TYR cc_start: 0.5799 (p90) cc_final: 0.5434 (p90) REVERT: A 498 GLN cc_start: 0.7852 (mt0) cc_final: 0.7264 (mm-40) REVERT: A 528 LYS cc_start: 0.8358 (tttp) cc_final: 0.7950 (tttm) REVERT: A 761 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8245 (p) REVERT: A 1142 GLN cc_start: 0.7575 (tp40) cc_final: 0.6999 (tp-100) REVERT: B 99 ASN cc_start: 0.7270 (t0) cc_final: 0.6233 (m-40) REVERT: B 133 PHE cc_start: 0.6739 (m-80) cc_final: 0.6410 (m-80) REVERT: B 221 SER cc_start: 0.8120 (t) cc_final: 0.7887 (p) REVERT: B 237 ARG cc_start: 0.7856 (mtp85) cc_final: 0.7491 (mtp85) REVERT: B 351 TYR cc_start: 0.8684 (p90) cc_final: 0.8294 (p90) REVERT: B 646 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7618 (tpp80) REVERT: B 776 LYS cc_start: 0.8924 (tttt) cc_final: 0.8599 (ttpt) REVERT: C 215 ASP cc_start: 0.6872 (t0) cc_final: 0.6153 (p0) REVERT: C 305 SER cc_start: 0.9127 (t) cc_final: 0.8667 (p) REVERT: C 430 THR cc_start: 0.8768 (m) cc_final: 0.8338 (t) REVERT: C 646 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7495 (mtm180) REVERT: C 994 ASP cc_start: 0.8091 (t70) cc_final: 0.7781 (m-30) REVERT: C 1005 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8177 (mt0) outliers start: 46 outliers final: 37 residues processed: 225 average time/residue: 0.1508 time to fit residues: 54.8656 Evaluate side-chains 220 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 55 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 282 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 264 optimal weight: 0.6980 chunk 266 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 163 optimal weight: 0.2980 chunk 155 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 214 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 506 GLN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.160179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110938 restraints weight = 30243.330| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.00 r_work: 0.3155 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23349 Z= 0.113 Angle : 0.520 13.838 31785 Z= 0.270 Chirality : 0.044 0.226 3633 Planarity : 0.004 0.041 4098 Dihedral : 4.311 29.050 3100 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.96 % Allowed : 13.77 % Favored : 84.27 % 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 are not related in a simple way. whole: 0.12 (0.15), residues: 2844 helix: 1.87 (0.21), residues: 671 sheet: -0.02 (0.19), residues: 640 loop : -0.68 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 237 TYR 0.025 0.001 TYR A 508 PHE 0.021 0.001 PHE C 168 TRP 0.020 0.001 TRP C 353 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00256 (23310) covalent geometry : angle 0.51479 (31707) SS BOND : bond 0.00419 ( 39) SS BOND : angle 1.51059 ( 78) hydrogen bonds : bond 0.03515 ( 1046) hydrogen bonds : angle 5.55238 ( 2877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7241.11 seconds wall clock time: 123 minutes 54.72 seconds (7434.72 seconds total)