Starting phenix.real_space_refine on Fri Jun 20 10:23:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8csa_26961/06_2025/8csa_26961.cif Found real_map, /net/cci-nas-00/data/ceres_data/8csa_26961/06_2025/8csa_26961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8csa_26961/06_2025/8csa_26961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8csa_26961/06_2025/8csa_26961.map" model { file = "/net/cci-nas-00/data/ceres_data/8csa_26961/06_2025/8csa_26961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8csa_26961/06_2025/8csa_26961.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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 14979 2.51 5 N 3894 2.21 5 O 4464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23442 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7814 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "B" Number of atoms: 7814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7814 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "C" Number of atoms: 7814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7814 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Time building chain proxies: 12.83, per 1000 atoms: 0.55 Number of scatterers: 23442 At special positions: 0 Unit cell: (129.349, 137.901, 175.316, 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 4464 8.00 N 3894 7.00 C 14979 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.01 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.01 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 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: 5.60 Conformation dependent library (CDL) restraints added in 2.9 seconds 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 49 sheets defined 27.5% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.512A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.711A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.308A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.824A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.684A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.275A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.644A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.775A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.432A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.618A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.769A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.525A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.328A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.738A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.521A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.462A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.537A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 890 removed outlier: 4.052A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.932A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) 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 966 removed outlier: 3.686A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.720A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.226A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.126A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 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: 4.112A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.263A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.727A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 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: 3.887A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.038A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 9.418A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.142A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 7.195A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (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: 6.780A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.180A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.415A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.622A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.853A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.255A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.305A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.896A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.906A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.903A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 7.084A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.963A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.692A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.886A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.886A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.648A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.306A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.789A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.283A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.062A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.573A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.868A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.631A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE4, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.717A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.911A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.402A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.834A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.323A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 1036 hydrogen bonds defined for protein. 2808 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: 15.73 Time building geometry restraints manager: 6.52 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: 6293 1.33 - 1.46: 4669 1.46 - 1.58: 12873 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 23964 Sorted by residual: bond pdb=" CZ ARG B 457 " pdb=" NH2 ARG B 457 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.00e+01 bond pdb=" CZ ARG B1039 " pdb=" NH2 ARG B1039 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.35e+00 bond pdb=" CZ ARG C1039 " pdb=" NH2 ARG C1039 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.33e+00 bond pdb=" CZ ARG C 44 " pdb=" NH2 ARG C 44 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.13e+00 bond pdb=" CA PRO C 792 " pdb=" C PRO C 792 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 9.02e+00 ... (remaining 23959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 22004 1.67 - 3.33: 8595 3.33 - 5.00: 1803 5.00 - 6.67: 185 6.67 - 8.33: 14 Bond angle restraints: 32601 Sorted by residual: angle pdb=" CA PHE A 106 " pdb=" CB PHE A 106 " pdb=" CG PHE A 106 " ideal model delta sigma weight residual 113.80 120.68 -6.88 1.00e+00 1.00e+00 4.73e+01 angle pdb=" CA ASP A 985 " pdb=" CB ASP A 985 " pdb=" CG ASP A 985 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.00e+00 1.00e+00 3.07e+01 angle pdb=" CA PHE B 32 " pdb=" C PHE B 32 " pdb=" N THR B 33 " ideal model delta sigma weight residual 119.52 115.38 4.14 7.90e-01 1.60e+00 2.75e+01 angle pdb=" CA PHE C 392 " pdb=" CB PHE C 392 " pdb=" CG PHE C 392 " ideal model delta sigma weight residual 113.80 118.98 -5.18 1.00e+00 1.00e+00 2.69e+01 angle pdb=" C ASP B1139 " pdb=" N PRO B1140 " pdb=" CA PRO B1140 " ideal model delta sigma weight residual 119.56 124.79 -5.23 1.02e+00 9.61e-01 2.63e+01 ... (remaining 32596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 13133 17.65 - 35.30: 915 35.30 - 52.95: 150 52.95 - 70.60: 50 70.60 - 88.25: 35 Dihedral angle restraints: 14283 sinusoidal: 5550 harmonic: 8733 Sorted by residual: dihedral pdb=" CA ASN B 211 " pdb=" C ASN B 211 " pdb=" N LEU B 212 " pdb=" CA LEU B 212 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA LYS B 97 " pdb=" C LYS B 97 " pdb=" N SER B 98 " pdb=" CA SER B 98 " ideal model delta harmonic sigma weight residual 180.00 -150.01 -29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA LEU B 461 " pdb=" C LEU B 461 " pdb=" N LYS B 462 " pdb=" CA LYS B 462 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 14280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2150 0.075 - 0.150: 1272 0.150 - 0.224: 253 0.224 - 0.299: 38 0.299 - 0.374: 13 Chirality restraints: 3726 Sorted by residual: chirality pdb=" CA ASP B1041 " pdb=" N ASP B1041 " pdb=" C ASP B1041 " pdb=" CB ASP B1041 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA ASP A1041 " pdb=" N ASP A1041 " pdb=" C ASP A1041 " pdb=" CB ASP A1041 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA ASP A 571 " pdb=" N ASP A 571 " pdb=" C ASP A 571 " pdb=" CB ASP A 571 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 3723 not shown) Planarity restraints: 4221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 904 " 0.234 2.00e-02 2.50e+03 1.25e-01 3.14e+02 pdb=" CG TYR B 904 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TYR B 904 " -0.096 2.00e-02 2.50e+03 pdb=" CD2 TYR B 904 " -0.108 2.00e-02 2.50e+03 pdb=" CE1 TYR B 904 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR B 904 " -0.065 2.00e-02 2.50e+03 pdb=" CZ TYR B 904 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 904 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 707 " 0.199 2.00e-02 2.50e+03 1.05e-01 2.20e+02 pdb=" CG TYR B 707 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR B 707 " -0.086 2.00e-02 2.50e+03 pdb=" CD2 TYR B 707 " -0.096 2.00e-02 2.50e+03 pdb=" CE1 TYR B 707 " -0.054 2.00e-02 2.50e+03 pdb=" CE2 TYR B 707 " -0.047 2.00e-02 2.50e+03 pdb=" CZ TYR B 707 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 707 " 0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 917 " 0.180 2.00e-02 2.50e+03 1.03e-01 2.11e+02 pdb=" CG TYR C 917 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR C 917 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR C 917 " -0.104 2.00e-02 2.50e+03 pdb=" CE1 TYR C 917 " -0.082 2.00e-02 2.50e+03 pdb=" CE2 TYR C 917 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR C 917 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 917 " 0.163 2.00e-02 2.50e+03 ... (remaining 4218 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 12660 3.00 - 3.48: 24725 3.48 - 3.95: 39405 3.95 - 4.43: 44548 4.43 - 4.90: 72889 Nonbonded interactions: 194227 Sorted by model distance: nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.527 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.529 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.538 3.040 nonbonded pdb=" OG1 THR A 581 " pdb=" OE1 GLU A 583 " model vdw 2.538 3.040 nonbonded pdb=" OG SER A 383 " pdb=" OD1 ASP B 985 " model vdw 2.538 3.040 ... (remaining 194222 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: 0.11 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.830 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 59.420 Find NCS groups from input model: 2.750 Set up NCS constraints: 0.330 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: 0.030 Load rotamer database and sin/cos tables:5.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 0.041 24003 Z= 0.718 Angle : 1.750 8.333 32679 Z= 1.174 Chirality : 0.091 0.374 3726 Planarity : 0.015 0.205 4221 Dihedral : 13.740 88.245 8544 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.99 % Favored : 93.77 % Rotamer: Outliers : 1.18 % Allowed : 3.43 % Favored : 95.39 % Cbeta Deviations : 0.11 % 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: -1.46 (0.14), residues: 2955 helix: -0.97 (0.17), residues: 676 sheet: -0.18 (0.24), residues: 417 loop : -1.17 (0.13), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.121 0.026 TRP A1102 HIS 0.014 0.004 HIS C1048 PHE 0.069 0.013 PHE C 718 TYR 0.234 0.027 TYR B 904 ARG 0.009 0.001 ARG C 273 Details of bonding type rmsd hydrogen bonds : bond 0.14297 ( 1034) hydrogen bonds : angle 8.63395 ( 2808) SS BOND : bond 0.01282 ( 39) SS BOND : angle 1.69551 ( 78) covalent geometry : bond 0.01249 (23964) covalent geometry : angle 1.75012 (32601) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.6549 (mttt) cc_final: 0.6119 (ttmt) REVERT: A 731 MET cc_start: 0.8322 (ptp) cc_final: 0.8028 (ptp) REVERT: A 902 MET cc_start: 0.8680 (mmm) cc_final: 0.8385 (mmm) REVERT: B 383 SER cc_start: 0.9190 (t) cc_final: 0.7958 (p) REVERT: B 455 LEU cc_start: 0.9000 (tp) cc_final: 0.8796 (tt) REVERT: B 912 THR cc_start: 0.7441 (m) cc_final: 0.7147 (p) REVERT: B 1050 MET cc_start: 0.8360 (ttp) cc_final: 0.8140 (ttp) REVERT: C 58 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8603 (m-80) REVERT: C 119 ILE cc_start: 0.9445 (mt) cc_final: 0.9102 (pt) REVERT: C 529 LYS cc_start: 0.8879 (mttt) cc_final: 0.8629 (mmmt) REVERT: C 984 LEU cc_start: 0.8618 (mt) cc_final: 0.8289 (mp) outliers start: 31 outliers final: 14 residues processed: 298 average time/residue: 0.4813 time to fit residues: 217.9794 Evaluate side-chains 134 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 121 ASN A 658 ASN A 955 ASN B 52 GLN B 207 HIS B 218 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 856 ASN B1058 HIS C 544 ASN C 613 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.071391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.053609 restraints weight = 131956.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.054931 restraints weight = 73911.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.055703 restraints weight = 49689.762| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 24003 Z= 0.145 Angle : 0.673 11.548 32679 Z= 0.361 Chirality : 0.047 0.201 3726 Planarity : 0.004 0.048 4221 Dihedral : 7.193 80.373 3234 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.91 % Allowed : 7.25 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 2955 helix: 1.17 (0.20), residues: 675 sheet: -0.32 (0.20), residues: 590 loop : -0.58 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 436 HIS 0.005 0.001 HIS B1048 PHE 0.022 0.002 PHE A 106 TYR 0.029 0.002 TYR C 369 ARG 0.007 0.001 ARG A 34 Details of bonding type rmsd hydrogen bonds : bond 0.04794 ( 1034) hydrogen bonds : angle 6.35266 ( 2808) SS BOND : bond 0.00440 ( 39) SS BOND : angle 2.33150 ( 78) covalent geometry : bond 0.00307 (23964) covalent geometry : angle 0.66421 (32601) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 LYS cc_start: 0.8839 (tttt) cc_final: 0.8345 (tmtt) REVERT: A 780 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7750 (mt-10) REVERT: A 902 MET cc_start: 0.8670 (mmm) cc_final: 0.8221 (mmm) REVERT: A 1005 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 492 LEU cc_start: 0.7568 (mt) cc_final: 0.7290 (tp) REVERT: B 912 THR cc_start: 0.7579 (m) cc_final: 0.7356 (p) REVERT: B 988 GLU cc_start: 0.8463 (mp0) cc_final: 0.8241 (pm20) REVERT: C 53 ASP cc_start: 0.8402 (t0) cc_final: 0.7971 (t0) REVERT: C 58 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8638 (m-80) REVERT: C 119 ILE cc_start: 0.9423 (mt) cc_final: 0.9022 (pt) REVERT: C 224 GLU cc_start: 0.8886 (pt0) cc_final: 0.8545 (pm20) REVERT: C 529 LYS cc_start: 0.8904 (mttt) cc_final: 0.8672 (mmmt) outliers start: 50 outliers final: 27 residues processed: 201 average time/residue: 0.4189 time to fit residues: 133.2168 Evaluate side-chains 134 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 213 optimal weight: 9.9990 chunk 155 optimal weight: 0.0980 chunk 140 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 97 optimal weight: 0.0870 chunk 210 optimal weight: 30.0000 chunk 96 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 overall best weight: 1.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN B 755 GLN B 784 GLN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS ** C1010 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 = 0.3781 r_free = 0.3781 target = 0.070582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.052962 restraints weight = 131322.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.054244 restraints weight = 73812.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.055049 restraints weight = 49739.868| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24003 Z= 0.137 Angle : 0.596 11.140 32679 Z= 0.316 Chirality : 0.045 0.217 3726 Planarity : 0.004 0.048 4221 Dihedral : 6.205 75.712 3222 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.83 % Allowed : 9.50 % Favored : 88.67 % 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: -0.05 (0.15), residues: 2955 helix: 1.44 (0.20), residues: 681 sheet: -0.50 (0.20), residues: 626 loop : -0.42 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 PHE 0.022 0.001 PHE B 392 TYR 0.022 0.001 TYR C 369 ARG 0.008 0.001 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 1034) hydrogen bonds : angle 5.95835 ( 2808) SS BOND : bond 0.00355 ( 39) SS BOND : angle 1.33678 ( 78) covalent geometry : bond 0.00290 (23964) covalent geometry : angle 0.59284 (32601) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 121 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8434 (ptp) cc_final: 0.8165 (ptp) REVERT: A 902 MET cc_start: 0.8729 (mmm) cc_final: 0.8316 (mmm) REVERT: A 983 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8707 (ttm170) REVERT: A 1005 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7608 (tm-30) REVERT: B 206 LYS cc_start: 0.9127 (tppt) cc_final: 0.8732 (tptp) REVERT: B 912 THR cc_start: 0.7307 (m) cc_final: 0.7093 (p) REVERT: C 53 ASP cc_start: 0.8328 (t0) cc_final: 0.7964 (t0) REVERT: C 58 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8605 (m-80) REVERT: C 224 GLU cc_start: 0.8735 (pt0) cc_final: 0.8420 (pm20) REVERT: C 278 LYS cc_start: 0.8673 (tptp) cc_final: 0.8382 (tmtt) REVERT: C 392 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7012 (m-80) REVERT: C 529 LYS cc_start: 0.8971 (mttt) cc_final: 0.8665 (mmmt) REVERT: C 907 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8024 (m110) outliers start: 48 outliers final: 24 residues processed: 160 average time/residue: 0.3881 time to fit residues: 99.9910 Evaluate side-chains 122 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 48 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 195 optimal weight: 7.9990 chunk 122 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 179 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 251 optimal weight: 0.9990 chunk 200 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN B 450 ASN B 784 GLN C 655 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 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 = 0.3803 r_free = 0.3803 target = 0.071475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.053867 restraints weight = 132380.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.055188 restraints weight = 73198.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.056026 restraints weight = 48743.574| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 24003 Z= 0.104 Angle : 0.550 13.095 32679 Z= 0.291 Chirality : 0.044 0.189 3726 Planarity : 0.004 0.047 4221 Dihedral : 5.446 54.617 3217 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.68 % Allowed : 9.84 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2955 helix: 1.56 (0.20), residues: 683 sheet: -0.41 (0.20), residues: 621 loop : -0.38 (0.16), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 436 HIS 0.003 0.001 HIS A1101 PHE 0.019 0.001 PHE B 515 TYR 0.021 0.001 TYR C 369 ARG 0.006 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 1034) hydrogen bonds : angle 5.67111 ( 2808) SS BOND : bond 0.00721 ( 39) SS BOND : angle 2.40348 ( 78) covalent geometry : bond 0.00217 (23964) covalent geometry : angle 0.53781 (32601) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 120 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8482 (ptp) cc_final: 0.8164 (ptp) REVERT: A 776 LYS cc_start: 0.8220 (tmtt) cc_final: 0.6990 (tmtt) REVERT: A 902 MET cc_start: 0.8667 (mmm) cc_final: 0.8225 (mmm) REVERT: A 983 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8597 (ttm170) REVERT: A 985 ASP cc_start: 0.9382 (t0) cc_final: 0.9146 (p0) REVERT: A 1005 GLN cc_start: 0.8335 (tm-30) cc_final: 0.8127 (tm-30) REVERT: B 206 LYS cc_start: 0.9116 (tppt) cc_final: 0.8723 (tptp) REVERT: B 492 LEU cc_start: 0.7746 (tp) cc_final: 0.7517 (tp) REVERT: B 1010 GLN cc_start: 0.7642 (pp30) cc_final: 0.7164 (pp30) REVERT: C 53 ASP cc_start: 0.8186 (t0) cc_final: 0.7867 (t0) REVERT: C 58 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8619 (m-80) REVERT: C 224 GLU cc_start: 0.8713 (pt0) cc_final: 0.8460 (pm20) REVERT: C 392 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7270 (m-80) REVERT: C 529 LYS cc_start: 0.8907 (mttt) cc_final: 0.8572 (mmmt) REVERT: C 907 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.7963 (m110) outliers start: 44 outliers final: 23 residues processed: 158 average time/residue: 0.3324 time to fit residues: 86.1070 Evaluate side-chains 122 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 261 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 chunk 46 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 481 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 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 = 0.3773 r_free = 0.3773 target = 0.070356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.052729 restraints weight = 133149.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.054016 restraints weight = 73682.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.054836 restraints weight = 49348.213| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 24003 Z= 0.158 Angle : 0.574 13.591 32679 Z= 0.303 Chirality : 0.043 0.221 3726 Planarity : 0.004 0.059 4221 Dihedral : 5.338 56.294 3216 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.14 % Allowed : 10.87 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.03 (0.16), residues: 2955 helix: 1.48 (0.20), residues: 680 sheet: -0.50 (0.20), residues: 625 loop : -0.41 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.004 0.001 HIS C1048 PHE 0.017 0.001 PHE C1089 TYR 0.020 0.001 TYR C 369 ARG 0.010 0.000 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 1034) hydrogen bonds : angle 5.69095 ( 2808) SS BOND : bond 0.00397 ( 39) SS BOND : angle 2.41495 ( 78) covalent geometry : bond 0.00344 (23964) covalent geometry : angle 0.56271 (32601) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 106 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8532 (ptp) cc_final: 0.8140 (ptp) REVERT: A 763 LEU cc_start: 0.9388 (mp) cc_final: 0.9186 (tt) REVERT: A 776 LYS cc_start: 0.8340 (tmtt) cc_final: 0.7789 (tmtt) REVERT: A 902 MET cc_start: 0.8740 (mmm) cc_final: 0.8340 (mmm) REVERT: A 1005 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7714 (tm-30) REVERT: B 206 LYS cc_start: 0.9074 (tppt) cc_final: 0.8863 (tmtt) REVERT: B 492 LEU cc_start: 0.7854 (tp) cc_final: 0.7525 (tp) REVERT: C 58 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8703 (m-80) REVERT: C 224 GLU cc_start: 0.8809 (pt0) cc_final: 0.8538 (pm20) REVERT: C 392 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: C 529 LYS cc_start: 0.8869 (mttt) cc_final: 0.8564 (mmmt) REVERT: C 907 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8008 (m110) outliers start: 56 outliers final: 35 residues processed: 152 average time/residue: 0.3369 time to fit residues: 84.6367 Evaluate side-chains 131 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 88 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 299 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 258 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 755 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.069808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.052088 restraints weight = 132775.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.053346 restraints weight = 74145.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.054158 restraints weight = 50019.106| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24003 Z= 0.173 Angle : 0.588 13.630 32679 Z= 0.309 Chirality : 0.044 0.195 3726 Planarity : 0.004 0.044 4221 Dihedral : 5.365 56.643 3214 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.95 % Allowed : 11.75 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.12 (0.15), residues: 2955 helix: 1.45 (0.20), residues: 676 sheet: -0.63 (0.20), residues: 579 loop : -0.46 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.004 0.001 HIS C1048 PHE 0.018 0.001 PHE B1089 TYR 0.020 0.001 TYR C 369 ARG 0.021 0.001 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 1034) hydrogen bonds : angle 5.82691 ( 2808) SS BOND : bond 0.00451 ( 39) SS BOND : angle 1.73901 ( 78) covalent geometry : bond 0.00371 (23964) covalent geometry : angle 0.58291 (32601) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 103 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8468 (ptp) cc_final: 0.8225 (ptp) REVERT: A 776 LYS cc_start: 0.8228 (tmtt) cc_final: 0.7680 (tmtt) REVERT: A 780 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 902 MET cc_start: 0.8753 (mmm) cc_final: 0.8366 (mmm) REVERT: A 1005 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7713 (tm-30) REVERT: B 206 LYS cc_start: 0.9042 (tppt) cc_final: 0.8813 (tmtt) REVERT: B 492 LEU cc_start: 0.8084 (tp) cc_final: 0.7721 (tp) REVERT: B 755 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8090 (pm20) REVERT: C 224 GLU cc_start: 0.8770 (pt0) cc_final: 0.8509 (pm20) REVERT: C 392 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7067 (m-80) REVERT: C 529 LYS cc_start: 0.8830 (mttt) cc_final: 0.8584 (mmmt) REVERT: C 985 ASP cc_start: 0.7968 (p0) cc_final: 0.5785 (p0) outliers start: 51 outliers final: 38 residues processed: 141 average time/residue: 0.3195 time to fit residues: 75.8656 Evaluate side-chains 130 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 90 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 235 optimal weight: 0.6980 chunk 295 optimal weight: 7.9990 chunk 240 optimal weight: 9.9990 chunk 267 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 196 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 209 optimal weight: 9.9990 chunk 236 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1125 ASN B 901 GLN C 134 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 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 = 0.3738 r_free = 0.3738 target = 0.068913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.051176 restraints weight = 135257.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.052398 restraints weight = 75635.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.053172 restraints weight = 51164.870| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 24003 Z= 0.225 Angle : 0.643 13.707 32679 Z= 0.336 Chirality : 0.045 0.197 3726 Planarity : 0.004 0.046 4221 Dihedral : 5.427 57.004 3212 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.91 % Allowed : 12.43 % Favored : 85.66 % 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: -0.37 (0.15), residues: 2955 helix: 1.12 (0.20), residues: 686 sheet: -0.70 (0.20), residues: 601 loop : -0.60 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 436 HIS 0.005 0.001 HIS C1048 PHE 0.023 0.002 PHE B1089 TYR 0.020 0.002 TYR C 369 ARG 0.008 0.001 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 1034) hydrogen bonds : angle 6.03554 ( 2808) SS BOND : bond 0.00481 ( 39) SS BOND : angle 2.31394 ( 78) covalent geometry : bond 0.00482 (23964) covalent geometry : angle 0.63369 (32601) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 92 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8518 (ptp) cc_final: 0.8261 (ptp) REVERT: A 776 LYS cc_start: 0.8263 (tmtt) cc_final: 0.8057 (tmtt) REVERT: A 902 MET cc_start: 0.8803 (mmm) cc_final: 0.8431 (mmm) REVERT: A 1005 GLN cc_start: 0.8441 (tm-30) cc_final: 0.7865 (tm-30) REVERT: B 492 LEU cc_start: 0.8185 (tp) cc_final: 0.7848 (tp) REVERT: B 1010 GLN cc_start: 0.7812 (pp30) cc_final: 0.7514 (pp30) REVERT: C 224 GLU cc_start: 0.8839 (pt0) cc_final: 0.8541 (pm20) REVERT: C 436 TRP cc_start: 0.8617 (p90) cc_final: 0.8105 (p90) REVERT: C 529 LYS cc_start: 0.8867 (mttt) cc_final: 0.8593 (mmmt) REVERT: C 985 ASP cc_start: 0.8359 (p0) cc_final: 0.7885 (p0) outliers start: 50 outliers final: 45 residues processed: 133 average time/residue: 0.3454 time to fit residues: 76.9784 Evaluate side-chains 130 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 85 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 917 TYR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 231 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 148 optimal weight: 0.0370 chunk 31 optimal weight: 9.9990 chunk 276 optimal weight: 4.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN B 314 GLN B 901 GLN C 895 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 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 = 0.3759 r_free = 0.3759 target = 0.069882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.052131 restraints weight = 135015.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.053366 restraints weight = 75579.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.054173 restraints weight = 50894.679| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 24003 Z= 0.148 Angle : 0.576 12.521 32679 Z= 0.301 Chirality : 0.044 0.190 3726 Planarity : 0.004 0.045 4221 Dihedral : 5.171 55.227 3212 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.98 % Allowed : 12.66 % Favored : 85.35 % 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: -0.23 (0.16), residues: 2955 helix: 1.38 (0.20), residues: 681 sheet: -0.71 (0.20), residues: 596 loop : -0.54 (0.16), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.003 0.001 HIS B 655 PHE 0.021 0.001 PHE C 823 TYR 0.019 0.001 TYR C 369 ARG 0.007 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 1034) hydrogen bonds : angle 5.81979 ( 2808) SS BOND : bond 0.00409 ( 39) SS BOND : angle 1.91499 ( 78) covalent geometry : bond 0.00322 (23964) covalent geometry : angle 0.56905 (32601) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 92 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8431 (ptp) cc_final: 0.8122 (ptp) REVERT: A 764 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8438 (t0) REVERT: A 902 MET cc_start: 0.8767 (mmm) cc_final: 0.8385 (mmm) REVERT: A 1005 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7776 (tm-30) REVERT: B 492 LEU cc_start: 0.8113 (tp) cc_final: 0.7771 (tp) REVERT: B 1010 GLN cc_start: 0.7724 (pp30) cc_final: 0.7468 (pp30) REVERT: C 224 GLU cc_start: 0.8768 (pt0) cc_final: 0.8486 (pm20) REVERT: C 392 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7028 (m-80) REVERT: C 436 TRP cc_start: 0.8643 (p90) cc_final: 0.8132 (p90) REVERT: C 529 LYS cc_start: 0.8850 (mttt) cc_final: 0.8590 (mmmt) REVERT: C 1050 MET cc_start: 0.7040 (ptp) cc_final: 0.6785 (mtm) REVERT: C 1101 HIS cc_start: 0.5494 (OUTLIER) cc_final: 0.5277 (m90) outliers start: 52 outliers final: 43 residues processed: 138 average time/residue: 0.3025 time to fit residues: 71.2247 Evaluate side-chains 128 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 82 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 764 ASN Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 100 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 205 optimal weight: 9.9990 chunk 249 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 chunk 51 optimal weight: 0.0670 chunk 64 optimal weight: 2.9990 chunk 194 optimal weight: 0.3980 chunk 23 optimal weight: 20.0000 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.071037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.053447 restraints weight = 131783.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.054757 restraints weight = 73452.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.055576 restraints weight = 49103.663| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 24003 Z= 0.101 Angle : 0.536 12.594 32679 Z= 0.280 Chirality : 0.043 0.210 3726 Planarity : 0.003 0.045 4221 Dihedral : 4.770 52.598 3212 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.56 % Allowed : 13.08 % Favored : 85.35 % 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: 0.00 (0.16), residues: 2955 helix: 1.72 (0.21), residues: 672 sheet: -0.61 (0.19), residues: 627 loop : -0.42 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.002 0.001 HIS A1101 PHE 0.022 0.001 PHE B 515 TYR 0.019 0.001 TYR C 369 ARG 0.006 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 1034) hydrogen bonds : angle 5.47763 ( 2808) SS BOND : bond 0.00359 ( 39) SS BOND : angle 1.43518 ( 78) covalent geometry : bond 0.00217 (23964) covalent geometry : angle 0.53241 (32601) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7382 (pttt) cc_final: 0.6663 (pttt) REVERT: A 731 MET cc_start: 0.8407 (ptp) cc_final: 0.8131 (ptp) REVERT: A 902 MET cc_start: 0.8685 (mmm) cc_final: 0.8258 (mmm) REVERT: A 1005 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7683 (tm-30) REVERT: B 104 TRP cc_start: 0.8084 (m-90) cc_final: 0.7757 (m-10) REVERT: B 492 LEU cc_start: 0.8179 (tp) cc_final: 0.7858 (tp) REVERT: C 53 ASP cc_start: 0.8237 (t0) cc_final: 0.7913 (t0) REVERT: C 224 GLU cc_start: 0.8723 (pt0) cc_final: 0.8472 (pm20) REVERT: C 278 LYS cc_start: 0.8726 (tptp) cc_final: 0.8463 (tmtt) REVERT: C 392 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.6728 (m-80) REVERT: C 436 TRP cc_start: 0.8628 (p90) cc_final: 0.8136 (p90) REVERT: C 529 LYS cc_start: 0.8825 (mttt) cc_final: 0.8567 (mmmt) REVERT: C 985 ASP cc_start: 0.7682 (p0) cc_final: 0.7414 (p0) outliers start: 41 outliers final: 33 residues processed: 142 average time/residue: 0.3269 time to fit residues: 77.8681 Evaluate side-chains 129 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 203 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 243 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 158 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 270 optimal weight: 7.9990 chunk 252 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 901 GLN C 544 ASN C 895 GLN ** C1010 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 = 0.3761 r_free = 0.3761 target = 0.069852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.052108 restraints weight = 134929.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.053345 restraints weight = 76069.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.054132 restraints weight = 51535.772| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 24003 Z= 0.174 Angle : 0.591 12.047 32679 Z= 0.307 Chirality : 0.044 0.195 3726 Planarity : 0.004 0.074 4221 Dihedral : 4.872 53.681 3211 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.49 % Allowed : 13.27 % Favored : 85.24 % 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: -0.13 (0.16), residues: 2955 helix: 1.50 (0.20), residues: 680 sheet: -0.55 (0.20), residues: 583 loop : -0.54 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.003 0.001 HIS B 655 PHE 0.039 0.001 PHE C 927 TYR 0.020 0.001 TYR C 369 ARG 0.009 0.001 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 1034) hydrogen bonds : angle 5.65689 ( 2808) SS BOND : bond 0.00395 ( 39) SS BOND : angle 1.64508 ( 78) covalent geometry : bond 0.00376 (23964) covalent geometry : angle 0.58670 (32601) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8412 (ptp) cc_final: 0.8159 (ptp) REVERT: A 902 MET cc_start: 0.8765 (mmm) cc_final: 0.8367 (mmm) REVERT: A 1005 GLN cc_start: 0.8384 (tm-30) cc_final: 0.7761 (tm-30) REVERT: B 104 TRP cc_start: 0.8164 (m-90) cc_final: 0.7838 (m-10) REVERT: B 492 LEU cc_start: 0.8212 (tp) cc_final: 0.7914 (tp) REVERT: C 224 GLU cc_start: 0.8774 (pt0) cc_final: 0.8503 (pm20) REVERT: C 436 TRP cc_start: 0.8693 (p90) cc_final: 0.8168 (p90) REVERT: C 529 LYS cc_start: 0.8853 (mttt) cc_final: 0.8579 (mmmt) REVERT: C 985 ASP cc_start: 0.7871 (p0) cc_final: 0.7625 (p0) outliers start: 39 outliers final: 33 residues processed: 123 average time/residue: 0.3349 time to fit residues: 71.0402 Evaluate side-chains 119 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 38 optimal weight: 20.0000 chunk 292 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 156 optimal weight: 0.6980 chunk 8 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 110 optimal weight: 0.0980 chunk 251 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN C 895 GLN ** C1010 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 = 0.3769 r_free = 0.3769 target = 0.070225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.052427 restraints weight = 134164.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.053670 restraints weight = 75197.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.054487 restraints weight = 50697.337| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24003 Z= 0.129 Angle : 0.566 12.112 32679 Z= 0.292 Chirality : 0.043 0.189 3726 Planarity : 0.004 0.045 4221 Dihedral : 4.714 52.976 3210 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.41 % Allowed : 13.58 % Favored : 85.01 % 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 (0.16), residues: 2955 helix: 1.52 (0.20), residues: 684 sheet: -0.60 (0.20), residues: 614 loop : -0.47 (0.16), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.003 0.001 HIS B 655 PHE 0.040 0.001 PHE C 927 TYR 0.019 0.001 TYR C 369 ARG 0.009 0.000 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 1034) hydrogen bonds : angle 5.55840 ( 2808) SS BOND : bond 0.00357 ( 39) SS BOND : angle 1.58494 ( 78) covalent geometry : bond 0.00284 (23964) covalent geometry : angle 0.56162 (32601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7414.91 seconds wall clock time: 133 minutes 11.07 seconds (7991.07 seconds total)