Starting phenix.real_space_refine on Thu Jun 19 23:28:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tlb_25986/06_2025/7tlb_25986.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tlb_25986/06_2025/7tlb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tlb_25986/06_2025/7tlb_25986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tlb_25986/06_2025/7tlb_25986.map" model { file = "/net/cci-nas-00/data/ceres_data/7tlb_25986/06_2025/7tlb_25986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tlb_25986/06_2025/7tlb_25986.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.37, per 1000 atoms: 0.63 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: 5.94 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.37 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: 10.92 Time building geometry restraints manager: 7.11 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: 0.08 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 56.680 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (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 TRP 0.074 0.023 TRP C1102 HIS 0.010 0.003 HIS B1083 PHE 0.095 0.012 PHE A 718 TYR 0.181 0.022 TYR C 396 ARG 0.012 0.001 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.14185 ( 1046) hydrogen bonds : angle 8.46453 ( 2877) SS BOND : bond 0.01348 ( 39) SS BOND : angle 2.08852 ( 78) covalent geometry : bond 0.01238 (23310) covalent geometry : angle 1.74185 (31707) *********************** 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 : 2.509 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: 0.5600 (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: 0.6162 (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: 0.6138 (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: 0.6377 (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: 0.6113 (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: 0.5153 (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: 0.6021 (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: 0.6623 (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: 0.6374 (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: 0.5393 (mp) REVERT: C 140 PHE cc_start: 0.4409 (p90) cc_final: 0.4204 (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: 0.5171 (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: 0.6372 (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: 0.6665 (m110) outliers start: 21 outliers final: 6 residues processed: 539 average time/residue: 0.3484 time to fit residues: 292.9186 Evaluate side-chains 304 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 297 time to evaluate : 2.380 ------------------------------------------------------------------------------- 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 245 optimal weight: 0.5980 chunk 220 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 138 optimal weight: 0.3980 chunk 169 optimal weight: 0.9990 chunk 264 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 955 ASN B 207 HIS B 394 ASN B 955 ASN C 87 ASN C 207 HIS C 613 GLN C 965 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.162715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112720 restraints weight = 30110.978| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.76 r_work: 0.3152 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23349 Z= 0.146 Angle : 0.635 13.446 31785 Z= 0.342 Chirality : 0.047 0.206 3633 Planarity : 0.004 0.043 4098 Dihedral : 5.776 56.816 3109 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.54 % Rotamer: Outliers : 1.88 % Allowed : 7.51 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 2844 helix: 1.50 (0.20), residues: 645 sheet: 0.06 (0.19), residues: 643 loop : -0.64 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 353 HIS 0.007 0.001 HIS B 207 PHE 0.027 0.002 PHE C 400 TYR 0.018 0.002 TYR C1067 ARG 0.005 0.001 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 1046) hydrogen bonds : angle 6.36454 ( 2877) SS BOND : bond 0.00275 ( 39) SS BOND : angle 2.10718 ( 78) covalent geometry : bond 0.00317 (23310) covalent geometry : angle 0.62708 (31707) *********************** 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 388 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 340 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.6930 (m-30) cc_final: 0.6710 (m-30) REVERT: A 129 LYS cc_start: 0.6736 (mttm) cc_final: 0.6366 (tptp) REVERT: A 200 TYR cc_start: 0.6808 (m-80) cc_final: 0.6430 (m-80) REVERT: A 334 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7129 (p0) REVERT: A 396 TYR cc_start: 0.7745 (m-80) cc_final: 0.7225 (m-80) REVERT: A 453 TYR cc_start: 0.6308 (p90) cc_final: 0.5608 (p90) REVERT: A 516 GLU cc_start: 0.6750 (tt0) cc_final: 0.6350 (tt0) REVERT: A 697 MET cc_start: 0.8447 (ptm) cc_final: 0.8170 (ptm) REVERT: A 752 LEU cc_start: 0.8142 (mt) cc_final: 0.7843 (mp) REVERT: A 755 GLN cc_start: 0.8121 (mt0) cc_final: 0.7906 (pt0) REVERT: A 1142 GLN cc_start: 0.7709 (tp40) cc_final: 0.6973 (tp-100) REVERT: B 36 VAL cc_start: 0.6367 (t) cc_final: 0.6142 (t) REVERT: B 63 THR cc_start: 0.7870 (m) cc_final: 0.7166 (p) REVERT: B 88 ASP cc_start: 0.7064 (m-30) cc_final: 0.6815 (m-30) REVERT: B 133 PHE cc_start: 0.6825 (m-80) cc_final: 0.6588 (m-80) REVERT: B 221 SER cc_start: 0.7338 (t) cc_final: 0.7017 (p) REVERT: B 237 ARG cc_start: 0.7037 (mtp85) cc_final: 0.6785 (mtp85) REVERT: B 319 ARG cc_start: 0.7351 (mtp-110) cc_final: 0.7089 (ttm-80) REVERT: B 351 TYR cc_start: 0.8284 (p90) cc_final: 0.8081 (p90) REVERT: B 365 TYR cc_start: 0.7801 (m-80) cc_final: 0.7574 (m-80) REVERT: B 370 ASN cc_start: 0.7275 (m-40) cc_final: 0.6690 (p0) REVERT: B 408 ARG cc_start: 0.8293 (ttp80) cc_final: 0.8062 (ptt90) REVERT: B 425 LEU cc_start: 0.8309 (mp) cc_final: 0.7996 (mt) REVERT: B 429 PHE cc_start: 0.8298 (t80) cc_final: 0.8083 (t80) REVERT: B 448 ASN cc_start: 0.6212 (t0) cc_final: 0.5915 (t0) REVERT: B 776 LYS cc_start: 0.7834 (tttt) cc_final: 0.7536 (ttpt) REVERT: B 878 LEU cc_start: 0.8851 (tp) cc_final: 0.8606 (tp) REVERT: B 994 ASP cc_start: 0.7650 (t70) cc_final: 0.7315 (m-30) REVERT: B 998 THR cc_start: 0.8497 (m) cc_final: 0.8220 (p) REVERT: C 132 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6031 (pm20) REVERT: C 190 ARG cc_start: 0.7076 (mtt90) cc_final: 0.6685 (mtt180) REVERT: C 207 HIS cc_start: 0.6922 (m-70) cc_final: 0.6574 (m-70) REVERT: C 269 TYR cc_start: 0.8500 (m-10) cc_final: 0.8026 (m-10) REVERT: C 392 PHE cc_start: 0.8105 (m-80) cc_final: 0.7884 (m-10) REVERT: C 790 LYS cc_start: 0.8245 (pttt) cc_final: 0.7918 (mtpp) REVERT: C 990 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7583 (mt-10) REVERT: C 1105 THR cc_start: 0.8559 (t) cc_final: 0.8348 (t) REVERT: C 1142 GLN cc_start: 0.8076 (tp40) cc_final: 0.7698 (tp40) outliers start: 48 outliers final: 29 residues processed: 375 average time/residue: 0.3407 time to fit residues: 202.2496 Evaluate side-chains 265 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR 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 517 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 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 859 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 112 SER 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 878 LEU Chi-restraints excluded: chain C residue 969 ASN 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 237 optimal weight: 9.9990 chunk 231 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 233 optimal weight: 9.9990 chunk 240 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 655 HIS A 901 GLN A 955 ASN A1010 GLN B 207 HIS B 317 ASN B 580 GLN B 901 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 901 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.158883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.106880 restraints weight = 30120.087| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.82 r_work: 0.3092 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 23349 Z= 0.282 Angle : 0.709 12.473 31785 Z= 0.375 Chirality : 0.050 0.211 3633 Planarity : 0.005 0.052 4098 Dihedral : 5.432 24.930 3100 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.70 % Allowed : 9.70 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 2844 helix: 1.27 (0.20), residues: 633 sheet: -0.25 (0.18), residues: 633 loop : -0.76 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 353 HIS 0.007 0.002 HIS B 207 PHE 0.022 0.002 PHE B 400 TYR 0.027 0.002 TYR C1067 ARG 0.005 0.001 ARG C 328 Details of bonding type rmsd hydrogen bonds : bond 0.05132 ( 1046) hydrogen bonds : angle 6.41763 ( 2877) SS BOND : bond 0.00551 ( 39) SS BOND : angle 2.16292 ( 78) covalent geometry : bond 0.00674 (23310) covalent geometry : angle 0.70207 (31707) *********************** 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 315 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 246 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7462 (m-30) cc_final: 0.7128 (m-30) REVERT: A 129 LYS cc_start: 0.6813 (mttm) cc_final: 0.6234 (tptt) REVERT: A 200 TYR cc_start: 0.6938 (m-80) cc_final: 0.6677 (m-80) REVERT: A 334 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7093 (p0) REVERT: A 565 PHE cc_start: 0.6627 (m-10) cc_final: 0.6406 (m-10) REVERT: A 571 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: A 869 MET cc_start: 0.9015 (mtt) cc_final: 0.8792 (mtt) REVERT: A 1142 GLN cc_start: 0.7599 (tp40) cc_final: 0.6902 (tp40) REVERT: B 133 PHE cc_start: 0.6731 (m-80) cc_final: 0.6238 (m-80) REVERT: B 221 SER cc_start: 0.8339 (t) cc_final: 0.8001 (p) REVERT: B 237 ARG cc_start: 0.7728 (mtp85) cc_final: 0.7375 (mtp85) REVERT: B 319 ARG cc_start: 0.7639 (mtp-110) cc_final: 0.7131 (ttm-80) REVERT: B 334 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7451 (p0) REVERT: B 351 TYR cc_start: 0.8552 (p90) cc_final: 0.8272 (p90) REVERT: B 394 ASN cc_start: 0.8181 (m-40) cc_final: 0.7027 (m-40) REVERT: B 776 LYS cc_start: 0.8985 (tttt) cc_final: 0.8664 (ttpt) REVERT: B 868 GLU cc_start: 0.8485 (tt0) cc_final: 0.8244 (mp0) REVERT: B 957 GLN cc_start: 0.8456 (tp-100) cc_final: 0.8166 (tt0) REVERT: C 32 PHE cc_start: 0.8782 (m-80) cc_final: 0.8564 (m-10) REVERT: C 102 ARG cc_start: 0.7287 (mtt180) cc_final: 0.6866 (mtp85) REVERT: C 205 SER cc_start: 0.8241 (t) cc_final: 0.8030 (t) REVERT: C 207 HIS cc_start: 0.7192 (m-70) cc_final: 0.6771 (m90) REVERT: C 223 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7888 (mt) REVERT: C 380 TYR cc_start: 0.7652 (m-80) cc_final: 0.7125 (m-80) REVERT: C 508 TYR cc_start: 0.7669 (m-80) cc_final: 0.7159 (m-80) REVERT: C 804 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8393 (mm110) REVERT: C 990 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7854 (mt-10) outliers start: 69 outliers final: 44 residues processed: 302 average time/residue: 0.3537 time to fit residues: 171.1338 Evaluate side-chains 236 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 188 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 571 ASP 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 772 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 289 VAL 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 613 GLN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1094 VAL 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 236 THR Chi-restraints excluded: chain C residue 336 CYS 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 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 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 266 optimal weight: 0.6980 chunk 109 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 B 207 HIS B 901 GLN C 87 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.159334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110366 restraints weight = 30390.200| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.11 r_work: 0.3123 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5146 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= 0.165 Angle : 0.572 9.521 31785 Z= 0.301 Chirality : 0.045 0.177 3633 Planarity : 0.004 0.042 4098 Dihedral : 4.934 23.544 3099 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.15 % Allowed : 11.78 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 2844 helix: 1.55 (0.21), residues: 648 sheet: -0.17 (0.18), residues: 638 loop : -0.76 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 353 HIS 0.005 0.001 HIS B 207 PHE 0.025 0.002 PHE C 168 TYR 0.021 0.001 TYR B1067 ARG 0.004 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 1046) hydrogen bonds : angle 6.02988 ( 2877) SS BOND : bond 0.00336 ( 39) SS BOND : angle 1.79779 ( 78) covalent geometry : bond 0.00387 (23310) covalent geometry : angle 0.56547 (31707) *********************** 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 273 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7515 (m-80) cc_final: 0.7179 (m-80) REVERT: A 88 ASP cc_start: 0.7451 (m-30) cc_final: 0.7105 (m-30) REVERT: A 129 LYS cc_start: 0.6935 (mttm) cc_final: 0.6321 (tptt) REVERT: A 200 TYR cc_start: 0.6905 (m-80) cc_final: 0.6587 (m-80) REVERT: A 334 ASN cc_start: 0.7635 (OUTLIER) cc_final: 0.7142 (p0) REVERT: A 516 GLU cc_start: 0.7373 (tt0) cc_final: 0.7140 (mt-10) REVERT: A 528 LYS cc_start: 0.8351 (tttp) cc_final: 0.7924 (tttm) REVERT: A 565 PHE cc_start: 0.6432 (m-10) cc_final: 0.6193 (m-10) REVERT: A 761 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8347 (p) REVERT: A 869 MET cc_start: 0.9007 (mtt) cc_final: 0.8783 (mtt) REVERT: A 1142 GLN cc_start: 0.7565 (tp40) cc_final: 0.6908 (tp40) REVERT: B 133 PHE cc_start: 0.6795 (m-80) cc_final: 0.6286 (m-80) REVERT: B 200 TYR cc_start: 0.6229 (m-10) cc_final: 0.5996 (m-80) REVERT: B 221 SER cc_start: 0.8213 (t) cc_final: 0.7881 (p) REVERT: B 237 ARG cc_start: 0.7768 (mtp85) cc_final: 0.7405 (mtp85) REVERT: B 319 ARG cc_start: 0.7643 (mtp-110) cc_final: 0.7280 (ttm-80) REVERT: B 351 TYR cc_start: 0.8614 (p90) cc_final: 0.8262 (p90) REVERT: B 357 ARG cc_start: 0.8119 (mtp180) cc_final: 0.7610 (mmm160) REVERT: B 394 ASN cc_start: 0.7704 (m-40) cc_final: 0.7382 (m110) REVERT: B 776 LYS cc_start: 0.8903 (tttt) cc_final: 0.8601 (ttpt) REVERT: C 102 ARG cc_start: 0.7112 (mtt180) cc_final: 0.6682 (mtp85) REVERT: C 190 ARG cc_start: 0.6531 (mtt180) cc_final: 0.5980 (mtt180) REVERT: C 205 SER cc_start: 0.8198 (t) cc_final: 0.7960 (t) REVERT: C 207 HIS cc_start: 0.7079 (m-70) cc_final: 0.6721 (m90) REVERT: C 223 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7768 (mt) REVERT: C 305 SER cc_start: 0.9159 (t) cc_final: 0.8713 (m) REVERT: C 380 TYR cc_start: 0.7698 (m-80) cc_final: 0.7142 (m-80) REVERT: C 646 ARG cc_start: 0.7687 (ttp80) cc_final: 0.7366 (mtm180) REVERT: C 804 GLN cc_start: 0.8504 (mm-40) cc_final: 0.7966 (mp10) outliers start: 55 outliers final: 33 residues processed: 256 average time/residue: 0.3360 time to fit residues: 137.1345 Evaluate side-chains 219 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR 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 368 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 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 B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 334 ASN 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 791 THR Chi-restraints excluded: chain B residue 859 THR 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 223 LEU 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 568 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 286 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 180 optimal weight: 0.0770 chunk 154 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 217 optimal weight: 0.1980 chunk 212 optimal weight: 5.9990 overall best weight: 1.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN B 207 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.159333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.109994 restraints weight = 30366.960| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.03 r_work: 0.3126 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23349 Z= 0.157 Angle : 0.542 8.763 31785 Z= 0.285 Chirality : 0.045 0.152 3633 Planarity : 0.004 0.071 4098 Dihedral : 4.706 22.311 3099 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.43 % Allowed : 12.36 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 2844 helix: 1.71 (0.21), residues: 652 sheet: -0.15 (0.18), residues: 610 loop : -0.74 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 353 HIS 0.003 0.001 HIS C1083 PHE 0.022 0.001 PHE C 400 TYR 0.021 0.001 TYR B1067 ARG 0.006 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 1046) hydrogen bonds : angle 5.87333 ( 2877) SS BOND : bond 0.00276 ( 39) SS BOND : angle 1.66910 ( 78) covalent geometry : bond 0.00371 (23310) covalent geometry : angle 0.53595 (31707) *********************** 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 259 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 197 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7586 (m-80) cc_final: 0.7139 (m-80) REVERT: A 88 ASP cc_start: 0.7463 (m-30) cc_final: 0.7131 (m-30) REVERT: A 129 LYS cc_start: 0.6995 (mttm) cc_final: 0.6357 (tptt) REVERT: A 200 TYR cc_start: 0.6890 (m-80) cc_final: 0.6583 (m-80) REVERT: A 334 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7148 (p0) REVERT: A 394 ASN cc_start: 0.8128 (m-40) cc_final: 0.7793 (m-40) REVERT: A 400 PHE cc_start: 0.8769 (p90) cc_final: 0.8461 (p90) REVERT: A 565 PHE cc_start: 0.6481 (m-10) cc_final: 0.6247 (m-10) REVERT: A 567 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7556 (mtt-85) REVERT: A 761 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8332 (p) REVERT: A 804 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7474 (mm110) REVERT: A 1142 GLN cc_start: 0.7548 (tp40) cc_final: 0.6885 (tp40) REVERT: B 99 ASN cc_start: 0.6796 (t0) cc_final: 0.6035 (m110) REVERT: B 133 PHE cc_start: 0.6793 (m-80) cc_final: 0.6281 (m-80) REVERT: B 221 SER cc_start: 0.8096 (t) cc_final: 0.7814 (p) REVERT: B 237 ARG cc_start: 0.7748 (mtp85) cc_final: 0.7404 (mtp85) REVERT: B 319 ARG cc_start: 0.7613 (mtp-110) cc_final: 0.7293 (ttt90) REVERT: B 334 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7387 (p0) REVERT: B 351 TYR cc_start: 0.8658 (p90) cc_final: 0.8308 (p90) REVERT: B 776 LYS cc_start: 0.8968 (tttt) cc_final: 0.8600 (ttpt) REVERT: B 1145 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6433 (mp) REVERT: C 53 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.6625 (m-30) REVERT: C 190 ARG cc_start: 0.6611 (mtt180) cc_final: 0.6024 (mtt180) REVERT: C 205 SER cc_start: 0.8266 (t) cc_final: 0.8038 (t) REVERT: C 207 HIS cc_start: 0.7127 (m-70) cc_final: 0.6690 (m90) REVERT: C 223 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7735 (mt) REVERT: C 305 SER cc_start: 0.9131 (t) cc_final: 0.8713 (p) REVERT: C 380 TYR cc_start: 0.7726 (m-80) cc_final: 0.7269 (m-80) REVERT: C 508 TYR cc_start: 0.7731 (m-80) cc_final: 0.7111 (m-80) REVERT: C 540 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7794 (m-40) REVERT: C 646 ARG cc_start: 0.7725 (ttp80) cc_final: 0.7401 (mtm180) REVERT: C 804 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8019 (mp10) REVERT: C 988 GLU cc_start: 0.8293 (mp0) cc_final: 0.7980 (pm20) outliers start: 62 outliers final: 41 residues processed: 245 average time/residue: 0.3335 time to fit residues: 131.4631 Evaluate side-chains 232 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 183 time to evaluate : 2.344 ------------------------------------------------------------------------------- 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 334 ASN 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 453 TYR 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 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 B residue 88 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE 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 615 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 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 223 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 549 THR 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 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 72 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 244 optimal weight: 0.7980 chunk 211 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A1142 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.155534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.114393 restraints weight = 30117.542| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.72 r_work: 0.3044 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 23349 Z= 0.367 Angle : 0.681 10.218 31785 Z= 0.357 Chirality : 0.050 0.189 3633 Planarity : 0.005 0.071 4098 Dihedral : 5.181 22.777 3099 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.17 % Allowed : 12.05 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 2844 helix: 1.22 (0.20), residues: 664 sheet: -0.37 (0.18), residues: 626 loop : -0.96 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 353 HIS 0.006 0.002 HIS A1048 PHE 0.024 0.002 PHE C 898 TYR 0.026 0.002 TYR B 265 ARG 0.010 0.001 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.04962 ( 1046) hydrogen bonds : angle 6.25321 ( 2877) SS BOND : bond 0.00529 ( 39) SS BOND : angle 1.89072 ( 78) covalent geometry : bond 0.00886 (23310) covalent geometry : angle 0.67549 (31707) *********************** 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 271 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 190 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7888 (m-80) cc_final: 0.7574 (m-80) REVERT: A 88 ASP cc_start: 0.7545 (m-30) cc_final: 0.7267 (m-30) REVERT: A 129 LYS cc_start: 0.7302 (mttm) cc_final: 0.6691 (tptt) REVERT: A 200 TYR cc_start: 0.7020 (m-80) cc_final: 0.6619 (m-80) REVERT: A 309 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: A 334 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7433 (p0) REVERT: A 337 PRO cc_start: 0.8682 (Cg_exo) cc_final: 0.7967 (Cg_endo) REVERT: A 400 PHE cc_start: 0.8877 (p90) cc_final: 0.8670 (p90) REVERT: A 552 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8708 (mt) REVERT: A 1142 GLN cc_start: 0.7688 (tp-100) cc_final: 0.7142 (tp40) REVERT: B 99 ASN cc_start: 0.7001 (t0) cc_final: 0.6200 (m110) REVERT: B 237 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7734 (mtp85) REVERT: B 319 ARG cc_start: 0.8061 (mtp-110) cc_final: 0.7680 (ttt90) REVERT: B 351 TYR cc_start: 0.8666 (p90) cc_final: 0.8353 (p90) REVERT: B 1145 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6532 (mp) REVERT: C 53 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.6685 (m-30) REVERT: C 223 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8110 (mt) REVERT: C 804 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8379 (mm110) REVERT: C 988 GLU cc_start: 0.8335 (mp0) cc_final: 0.8106 (pm20) outliers start: 81 outliers final: 59 residues processed: 257 average time/residue: 0.3327 time to fit residues: 137.4981 Evaluate side-chains 234 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 169 time to evaluate : 2.684 ------------------------------------------------------------------------------- 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 195 LYS 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 430 THR Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 615 VAL 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 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 205 SER 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 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 727 LEU 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 135 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 389 ASP 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 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 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 241 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 185 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 221 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 210 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN B 207 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.158723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.109928 restraints weight = 30372.763| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.06 r_work: 0.3135 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 23349 Z= 0.132 Angle : 0.544 12.695 31785 Z= 0.285 Chirality : 0.044 0.155 3633 Planarity : 0.004 0.072 4098 Dihedral : 4.658 22.711 3099 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.96 % Allowed : 13.38 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 2844 helix: 1.60 (0.20), residues: 671 sheet: -0.25 (0.18), residues: 626 loop : -0.85 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 353 HIS 0.008 0.001 HIS C 207 PHE 0.022 0.001 PHE C 168 TYR 0.019 0.001 TYR C 508 ARG 0.009 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 1046) hydrogen bonds : angle 5.85266 ( 2877) SS BOND : bond 0.00273 ( 39) SS BOND : angle 2.17379 ( 78) covalent geometry : bond 0.00310 (23310) covalent geometry : angle 0.53433 (31707) *********************** 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 237 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7763 (m-80) cc_final: 0.7284 (m-80) REVERT: A 88 ASP cc_start: 0.7497 (m-30) cc_final: 0.6991 (m-30) REVERT: A 129 LYS cc_start: 0.6988 (mttm) cc_final: 0.6277 (tptt) REVERT: A 200 TYR cc_start: 0.6915 (m-80) cc_final: 0.6639 (m-80) REVERT: A 507 PRO cc_start: 0.6904 (Cg_exo) cc_final: 0.6694 (Cg_endo) REVERT: A 567 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7572 (mtt-85) REVERT: A 761 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8357 (p) REVERT: A 1142 GLN cc_start: 0.7539 (tp-100) cc_final: 0.6922 (tp-100) REVERT: B 99 ASN cc_start: 0.6936 (t0) cc_final: 0.6106 (m110) REVERT: B 235 ILE cc_start: 0.7289 (mt) cc_final: 0.7066 (mm) REVERT: B 237 ARG cc_start: 0.7805 (mtp85) cc_final: 0.7430 (mtp85) REVERT: B 319 ARG cc_start: 0.7763 (mtp-110) cc_final: 0.7460 (tpt90) REVERT: B 351 TYR cc_start: 0.8738 (p90) cc_final: 0.8316 (p90) REVERT: B 740 MET cc_start: 0.8987 (ttt) cc_final: 0.8660 (ttm) REVERT: B 1145 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6538 (mp) REVERT: C 32 PHE cc_start: 0.8807 (m-10) cc_final: 0.8525 (m-10) REVERT: C 380 TYR cc_start: 0.7718 (m-80) cc_final: 0.7282 (m-80) REVERT: C 646 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7507 (mtm180) REVERT: C 804 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8242 (mm110) outliers start: 50 outliers final: 32 residues processed: 224 average time/residue: 0.3250 time to fit residues: 117.5384 Evaluate side-chains 205 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 2.583 ------------------------------------------------------------------------------- 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 430 THR 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 874 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 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 B residue 1145 LEU 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 389 ASP 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 576 VAL 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 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 47 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 253 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 207 HIS B 360 ASN B 506 GLN C 207 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.157497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110504 restraints weight = 30287.193| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.66 r_work: 0.3102 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.5934 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= 0.212 Angle : 0.588 17.308 31785 Z= 0.306 Chirality : 0.046 0.298 3633 Planarity : 0.004 0.078 4098 Dihedral : 4.713 22.827 3099 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.27 % Allowed : 13.54 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 2844 helix: 1.57 (0.20), residues: 671 sheet: -0.30 (0.18), residues: 638 loop : -0.90 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 353 HIS 0.003 0.001 HIS A 519 PHE 0.021 0.002 PHE A 400 TYR 0.021 0.002 TYR B1067 ARG 0.010 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 1046) hydrogen bonds : angle 5.90883 ( 2877) SS BOND : bond 0.00534 ( 39) SS BOND : angle 2.19035 ( 78) covalent geometry : bond 0.00513 (23310) covalent geometry : angle 0.57831 (31707) *********************** 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 237 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 179 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7768 (m-80) cc_final: 0.7249 (m-80) REVERT: A 88 ASP cc_start: 0.7404 (m-30) cc_final: 0.6901 (m-30) REVERT: A 129 LYS cc_start: 0.7104 (mttm) cc_final: 0.6361 (tptt) REVERT: A 200 TYR cc_start: 0.6975 (m-80) cc_final: 0.6597 (m-80) REVERT: A 309 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: A 552 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8547 (mt) REVERT: A 567 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7641 (mtt-85) REVERT: A 761 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8338 (p) REVERT: A 994 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: A 1142 GLN cc_start: 0.7565 (tp-100) cc_final: 0.6922 (tp-100) REVERT: B 99 ASN cc_start: 0.7070 (t0) cc_final: 0.6276 (m-40) REVERT: B 237 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7477 (mtp85) REVERT: B 319 ARG cc_start: 0.7837 (mtp-110) cc_final: 0.7535 (tpt90) REVERT: B 351 TYR cc_start: 0.8741 (p90) cc_final: 0.8332 (p90) REVERT: B 740 MET cc_start: 0.9015 (ttt) cc_final: 0.8680 (ttm) REVERT: B 1145 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6465 (mp) REVERT: C 32 PHE cc_start: 0.8784 (m-10) cc_final: 0.8523 (m-10) REVERT: C 200 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6627 (t80) REVERT: C 380 TYR cc_start: 0.7579 (m-80) cc_final: 0.7177 (m-80) REVERT: C 646 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7491 (mtm180) REVERT: C 804 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8226 (mm110) REVERT: C 1005 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8325 (mt0) outliers start: 58 outliers final: 42 residues processed: 221 average time/residue: 0.3127 time to fit residues: 112.6655 Evaluate side-chains 223 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 2.793 ------------------------------------------------------------------------------- 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 309 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 705 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 994 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 534 VAL 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 B residue 1145 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 221 SER 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 568 ASP Chi-restraints excluded: chain C residue 576 VAL 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 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1005 GLN 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 186 optimal weight: 2.9990 chunk 256 optimal weight: 0.6980 chunk 105 optimal weight: 8.9990 chunk 243 optimal weight: 2.9990 chunk 116 optimal weight: 0.2980 chunk 126 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 229 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 158 optimal weight: 0.8980 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 B 641 ASN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.159141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109771 restraints weight = 30249.100| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.96 r_work: 0.3152 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23349 Z= 0.126 Angle : 0.541 15.300 31785 Z= 0.283 Chirality : 0.044 0.256 3633 Planarity : 0.004 0.075 4098 Dihedral : 4.509 21.566 3099 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.00 % Allowed : 14.12 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 2844 helix: 1.74 (0.20), residues: 673 sheet: -0.18 (0.18), residues: 626 loop : -0.82 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 353 HIS 0.007 0.001 HIS C 207 PHE 0.024 0.001 PHE C 168 TYR 0.018 0.001 TYR A 313 ARG 0.006 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 1046) hydrogen bonds : angle 5.74603 ( 2877) SS BOND : bond 0.00457 ( 39) SS BOND : angle 1.85944 ( 78) covalent geometry : bond 0.00291 (23310) covalent geometry : angle 0.53404 (31707) *********************** 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 238 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7757 (m-80) cc_final: 0.7209 (m-80) REVERT: A 88 ASP cc_start: 0.7436 (m-30) cc_final: 0.6955 (m-30) REVERT: A 129 LYS cc_start: 0.7091 (mttm) cc_final: 0.6363 (tptt) REVERT: A 200 TYR cc_start: 0.6731 (m-80) cc_final: 0.6491 (m-80) REVERT: A 552 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8535 (mt) REVERT: A 567 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7593 (mtt-85) REVERT: A 761 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8283 (p) REVERT: A 994 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7912 (m-30) REVERT: A 1142 GLN cc_start: 0.7539 (tp-100) cc_final: 0.6915 (tp-100) REVERT: B 99 ASN cc_start: 0.7066 (t0) cc_final: 0.6243 (m-40) REVERT: B 237 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7488 (mtp85) REVERT: B 319 ARG cc_start: 0.7741 (mtp-110) cc_final: 0.7478 (tpt90) REVERT: B 351 TYR cc_start: 0.8748 (p90) cc_final: 0.8394 (p90) REVERT: B 740 MET cc_start: 0.8964 (ttt) cc_final: 0.8640 (ttm) REVERT: B 1145 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6443 (mp) REVERT: C 32 PHE cc_start: 0.8771 (m-10) cc_final: 0.8524 (m-10) REVERT: C 200 TYR cc_start: 0.7184 (m-80) cc_final: 0.6883 (t80) REVERT: C 380 TYR cc_start: 0.7495 (m-80) cc_final: 0.7149 (m-80) REVERT: C 430 THR cc_start: 0.8650 (m) cc_final: 0.8273 (t) REVERT: C 646 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7436 (mtm180) REVERT: C 804 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8253 (mm110) REVERT: C 994 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7646 (t0) REVERT: C 1005 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8278 (mt0) outliers start: 51 outliers final: 38 residues processed: 225 average time/residue: 0.3131 time to fit residues: 114.3690 Evaluate side-chains 226 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 2.419 ------------------------------------------------------------------------------- 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 359 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 705 VAL 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 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL 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 B residue 1145 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 240 THR 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 568 ASP Chi-restraints excluded: chain C residue 576 VAL 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 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1005 GLN 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 14 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 172 optimal weight: 0.7980 chunk 270 optimal weight: 0.2980 chunk 5 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 212 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 209 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN B 207 HIS B 360 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.158732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110368 restraints weight = 30391.850| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.09 r_work: 0.3137 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23349 Z= 0.150 Angle : 0.544 14.457 31785 Z= 0.283 Chirality : 0.045 0.238 3633 Planarity : 0.004 0.074 4098 Dihedral : 4.452 21.192 3099 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.84 % Allowed : 14.16 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 2844 helix: 1.78 (0.21), residues: 671 sheet: -0.12 (0.18), residues: 622 loop : -0.79 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 353 HIS 0.003 0.001 HIS A 519 PHE 0.021 0.001 PHE A 400 TYR 0.019 0.001 TYR B1067 ARG 0.005 0.000 ARG B 408 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 1046) hydrogen bonds : angle 5.69936 ( 2877) SS BOND : bond 0.00473 ( 39) SS BOND : angle 1.72032 ( 78) covalent geometry : bond 0.00356 (23310) covalent geometry : angle 0.53825 (31707) ********************** 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 229 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7584 (m-30) cc_final: 0.7114 (m-30) REVERT: A 129 LYS cc_start: 0.7112 (mttm) cc_final: 0.6359 (tptt) REVERT: A 200 TYR cc_start: 0.6892 (m-80) cc_final: 0.6497 (m-80) REVERT: A 507 PRO cc_start: 0.6875 (Cg_exo) cc_final: 0.6422 (Cg_endo) REVERT: A 508 TYR cc_start: 0.6996 (m-80) cc_final: 0.6319 (m-80) REVERT: A 552 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8542 (mt) REVERT: A 761 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8288 (p) REVERT: A 804 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7648 (mm-40) REVERT: A 904 TYR cc_start: 0.8125 (m-10) cc_final: 0.7890 (m-10) REVERT: A 941 THR cc_start: 0.6952 (m) cc_final: 0.6485 (p) REVERT: A 994 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: A 1142 GLN cc_start: 0.7562 (tp-100) cc_final: 0.6935 (tp-100) REVERT: B 237 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7444 (mtp85) REVERT: B 319 ARG cc_start: 0.7733 (mtp-110) cc_final: 0.7494 (tpt90) REVERT: B 351 TYR cc_start: 0.8764 (p90) cc_final: 0.8419 (p90) REVERT: B 436 TRP cc_start: 0.7165 (p90) cc_final: 0.6857 (p90) REVERT: B 740 MET cc_start: 0.9028 (ttt) cc_final: 0.8712 (ttm) REVERT: B 1145 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6356 (mp) REVERT: C 32 PHE cc_start: 0.8799 (m-10) cc_final: 0.8564 (m-10) REVERT: C 200 TYR cc_start: 0.7394 (m-80) cc_final: 0.7002 (t80) REVERT: C 380 TYR cc_start: 0.7495 (m-80) cc_final: 0.6980 (m-80) REVERT: C 430 THR cc_start: 0.8583 (m) cc_final: 0.8194 (t) REVERT: C 804 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8289 (mm110) REVERT: C 994 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7693 (t0) REVERT: C 1005 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8313 (mt0) outliers start: 47 outliers final: 38 residues processed: 217 average time/residue: 0.3957 time to fit residues: 139.1810 Evaluate side-chains 217 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 4.168 ------------------------------------------------------------------------------- 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 359 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 705 VAL 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 A residue 1081 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 510 VAL 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 B residue 1145 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 PHE 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 568 ASP Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR 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 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1005 GLN 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 199 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 chunk 237 optimal weight: 10.0000 chunk 273 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 286 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 264 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 207 HIS C 239 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.155398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107727 restraints weight = 30330.587| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.62 r_work: 0.3073 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.112 23349 Z= 0.351 Angle : 0.676 14.944 31785 Z= 0.351 Chirality : 0.050 0.249 3633 Planarity : 0.005 0.073 4098 Dihedral : 4.950 22.306 3099 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.31 % Allowed : 13.89 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 2844 helix: 1.36 (0.20), residues: 666 sheet: -0.34 (0.18), residues: 653 loop : -1.02 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 353 HIS 0.007 0.002 HIS A1048 PHE 0.021 0.002 PHE C 898 TYR 0.029 0.002 TYR B 508 ARG 0.007 0.001 ARG B1039 Details of bonding type rmsd hydrogen bonds : bond 0.04747 ( 1046) hydrogen bonds : angle 6.10851 ( 2877) SS BOND : bond 0.00640 ( 39) SS BOND : angle 2.31305 ( 78) covalent geometry : bond 0.00848 (23310) covalent geometry : angle 0.66670 (31707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15459.16 seconds wall clock time: 270 minutes 4.34 seconds (16204.34 seconds total)