Starting phenix.real_space_refine on Thu Mar 5 15:58:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8csa_26961/03_2026/8csa_26961.cif Found real_map, /net/cci-nas-00/data/ceres_data/8csa_26961/03_2026/8csa_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 { model { file = "/net/cci-nas-00/data/ceres_data/8csa_26961/03_2026/8csa_26961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8csa_26961/03_2026/8csa_26961.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8csa_26961/03_2026/8csa_26961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8csa_26961/03_2026/8csa_26961.map" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.43, per 1000 atoms: 0.23 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: 1.77 Conformation dependent library (CDL) restraints added in 808.5 milliseconds 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: 0.86 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: 5.26 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 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: 0.03 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: 1.530 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: 0.040 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.380 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.060 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (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 ARG 0.009 0.001 ARG C 273 TYR 0.234 0.027 TYR B 904 PHE 0.069 0.013 PHE C 718 TRP 0.121 0.026 TRP A1102 HIS 0.014 0.004 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.01249 (23964) covalent geometry : angle 1.75012 (32601) SS BOND : bond 0.01282 ( 39) SS BOND : angle 1.69551 ( 78) hydrogen bonds : bond 0.14297 ( 1034) hydrogen bonds : angle 8.63395 ( 2808) *********************** 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 : 0.904 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: symmetry clash REVERT: A 41 LYS cc_start: 0.6550 (mttt) cc_final: 0.6120 (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: 0.8383 (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: 0.7148 (p) REVERT: B 1050 MET cc_start: 0.8360 (ttp) cc_final: 0.8141 (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: 0.9188 (pt) REVERT: C 529 LYS cc_start: 0.8879 (mttt) cc_final: 0.8630 (mmmt) REVERT: C 984 LEU cc_start: 0.8618 (mt) cc_final: 0.8289 (mp) outliers start: 31 outliers final: 15 residues processed: 298 average time/residue: 0.1734 time to fit residues: 78.7125 Evaluate side-chains 133 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 403 ARG 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 9.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- 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 207 HIS B 218 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B1058 HIS B1135 ASN C 613 GLN C 762 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.070443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.052565 restraints weight = 131914.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.053847 restraints weight = 74065.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.054639 restraints weight = 49944.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.055193 restraints weight = 38469.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.055490 restraints weight = 32421.931| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 24003 Z= 0.190 Angle : 0.701 12.432 32679 Z= 0.375 Chirality : 0.047 0.204 3726 Planarity : 0.004 0.052 4221 Dihedral : 7.483 80.704 3238 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.14 % Allowed : 7.70 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.15), residues: 2955 helix: 0.99 (0.20), residues: 673 sheet: -0.45 (0.20), residues: 592 loop : -0.67 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.028 0.002 TYR C 369 PHE 0.025 0.002 PHE A 342 TRP 0.024 0.002 TRP C 436 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00417 (23964) covalent geometry : angle 0.69219 (32601) SS BOND : bond 0.00496 ( 39) SS BOND : angle 2.42535 ( 78) hydrogen bonds : bond 0.04946 ( 1034) hydrogen bonds : angle 6.54143 ( 2808) *********************** 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 208 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 0.960 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: A 902 MET cc_start: 0.8749 (mmm) cc_final: 0.8319 (mmm) REVERT: A 1005 GLN cc_start: 0.8493 (tm-30) cc_final: 0.7841 (tm-30) REVERT: B 455 LEU cc_start: 0.8879 (tp) cc_final: 0.8641 (tt) REVERT: B 492 LEU cc_start: 0.7632 (mt) cc_final: 0.7347 (tp) REVERT: B 988 GLU cc_start: 0.8526 (mp0) cc_final: 0.8303 (pm20) REVERT: C 58 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8696 (m-80) REVERT: C 1014 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7391 (ttm170) outliers start: 56 outliers final: 33 residues processed: 193 average time/residue: 0.1621 time to fit residues: 49.0715 Evaluate side-chains 130 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 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 818 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 270 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 886 TRP Chi-restraints excluded: chain B residue 917 TYR Chi-restraints excluded: chain B residue 997 ILE 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 376 THR 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 217 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 97 optimal weight: 0.0370 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN B 450 ASN B 755 GLN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 544 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.070268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.052591 restraints weight = 133222.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.053861 restraints weight = 73765.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.054682 restraints weight = 49552.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.055209 restraints weight = 38054.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.055490 restraints weight = 32108.466| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24003 Z= 0.146 Angle : 0.607 11.431 32679 Z= 0.323 Chirality : 0.045 0.198 3726 Planarity : 0.004 0.048 4221 Dihedral : 6.480 75.575 3226 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.36 % Allowed : 9.42 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.15), residues: 2955 helix: 1.34 (0.20), residues: 677 sheet: -0.63 (0.20), residues: 624 loop : -0.51 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.024 0.002 TYR C 369 PHE 0.021 0.001 PHE B 392 TRP 0.018 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00315 (23964) covalent geometry : angle 0.60368 (32601) SS BOND : bond 0.00406 ( 39) SS BOND : angle 1.40083 ( 78) hydrogen bonds : bond 0.04311 ( 1034) hydrogen bonds : angle 6.10638 ( 2808) *********************** 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 175 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 113 time to evaluate : 0.822 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: 0.8447 (ptp) cc_final: 0.8197 (ptp) REVERT: A 776 LYS cc_start: 0.8334 (tmtt) cc_final: 0.6833 (tmtt) REVERT: A 780 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7376 (mt-10) REVERT: A 902 MET cc_start: 0.8727 (mmm) cc_final: 0.8342 (mmm) REVERT: A 985 ASP cc_start: 0.9408 (t0) cc_final: 0.9171 (p0) REVERT: A 1005 GLN cc_start: 0.8422 (tm-30) cc_final: 0.7807 (tm-30) REVERT: B 904 TYR cc_start: 0.6986 (OUTLIER) cc_final: 0.5485 (m-10) REVERT: B 988 GLU cc_start: 0.8397 (mp0) cc_final: 0.8046 (mp0) REVERT: C 53 ASP cc_start: 0.8364 (t0) cc_final: 0.7947 (t0) REVERT: C 58 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8617 (m-80) REVERT: C 907 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8013 (m110) outliers start: 62 outliers final: 38 residues processed: 165 average time/residue: 0.1423 time to fit residues: 38.7695 Evaluate side-chains 128 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 818 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 270 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 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 917 TYR 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 585 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 977 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1066 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 218 optimal weight: 10.0000 chunk 251 optimal weight: 0.0000 chunk 274 optimal weight: 10.0000 chunk 271 optimal weight: 0.0370 chunk 7 optimal weight: 30.0000 chunk 186 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 273 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.9666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN B 784 GLN B 856 ASN C 481 ASN C 493 GLN C 655 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.070429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.052748 restraints weight = 132846.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.054028 restraints weight = 74681.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.054823 restraints weight = 50268.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.055338 restraints weight = 38641.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.055619 restraints weight = 32714.347| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24003 Z= 0.135 Angle : 0.580 12.568 32679 Z= 0.306 Chirality : 0.044 0.200 3726 Planarity : 0.004 0.055 4221 Dihedral : 5.718 54.591 3219 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.17 % Allowed : 10.49 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 2955 helix: 1.50 (0.20), residues: 677 sheet: -0.80 (0.20), residues: 591 loop : -0.50 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1014 TYR 0.020 0.001 TYR C 369 PHE 0.015 0.001 PHE B 515 TRP 0.016 0.001 TRP C 436 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00292 (23964) covalent geometry : angle 0.56838 (32601) SS BOND : bond 0.00384 ( 39) SS BOND : angle 2.45594 ( 78) hydrogen bonds : bond 0.03966 ( 1034) hydrogen bonds : angle 5.90521 ( 2808) *********************** 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 159 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 102 time to evaluate : 0.864 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: 0.8511 (ptp) cc_final: 0.8125 (ptp) REVERT: A 776 LYS cc_start: 0.8291 (tmtt) cc_final: 0.6722 (tmtt) REVERT: A 780 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7348 (mt-10) REVERT: A 902 MET cc_start: 0.8741 (mmm) cc_final: 0.8333 (mmm) REVERT: A 1005 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8259 (tm-30) REVERT: B 492 LEU cc_start: 0.7720 (tp) cc_final: 0.7474 (tp) REVERT: B 904 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.5575 (m-10) REVERT: B 988 GLU cc_start: 0.8453 (mp0) cc_final: 0.8141 (mp0) REVERT: B 1010 GLN cc_start: 0.7744 (pp30) cc_final: 0.7240 (pp30) REVERT: C 53 ASP cc_start: 0.8385 (t0) cc_final: 0.7990 (t0) REVERT: C 58 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8665 (m-80) REVERT: C 392 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7110 (m-80) REVERT: C 907 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8003 (m110) outliers start: 57 outliers final: 42 residues processed: 151 average time/residue: 0.1536 time to fit residues: 37.4815 Evaluate side-chains 137 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 91 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 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 760 CYS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1050 MET 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 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 856 ASN Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 916 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 214 ARG Chi-restraints excluded: chain C residue 379 CYS 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 941 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 977 LEU 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 232 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 286 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 203 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS A1106 GLN ** C 955 ASN ** 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 = 0.3731 r_free = 0.3731 target = 0.068726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.050821 restraints weight = 136849.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.052016 restraints weight = 77556.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.052785 restraints weight = 52758.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.053276 restraints weight = 40799.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.053536 restraints weight = 34810.834| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 24003 Z= 0.245 Angle : 0.660 9.542 32679 Z= 0.347 Chirality : 0.045 0.202 3726 Planarity : 0.004 0.071 4221 Dihedral : 5.936 56.496 3219 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.86 % Allowed : 11.02 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 2955 helix: 1.18 (0.20), residues: 678 sheet: -0.89 (0.20), residues: 600 loop : -0.61 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 319 TYR 0.020 0.002 TYR C 369 PHE 0.026 0.002 PHE B1089 TRP 0.015 0.002 TRP C 436 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00521 (23964) covalent geometry : angle 0.65329 (32601) SS BOND : bond 0.00684 ( 39) SS BOND : angle 1.98616 ( 78) hydrogen bonds : bond 0.04343 ( 1034) hydrogen bonds : angle 6.20511 ( 2808) *********************** 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 165 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 90 time to evaluate : 0.919 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: 0.8521 (ptp) cc_final: 0.8268 (ptp) REVERT: A 776 LYS cc_start: 0.8272 (tmtt) cc_final: 0.6542 (tmtt) REVERT: A 780 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7401 (mt-10) REVERT: A 902 MET cc_start: 0.8769 (mmm) cc_final: 0.8391 (mmm) REVERT: A 1005 GLN cc_start: 0.8492 (tm-30) cc_final: 0.7926 (tm-30) REVERT: B 492 LEU cc_start: 0.8070 (tp) cc_final: 0.7785 (tp) REVERT: B 904 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.5905 (m-10) REVERT: B 988 GLU cc_start: 0.8526 (mp0) cc_final: 0.8314 (mp0) REVERT: C 392 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7051 (m-80) REVERT: C 988 GLU cc_start: 0.8128 (tp30) cc_final: 0.7913 (tp30) outliers start: 75 outliers final: 60 residues processed: 155 average time/residue: 0.1372 time to fit residues: 36.1395 Evaluate side-chains 140 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 78 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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 760 CYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 818 ILE 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 1118 ASP Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 270 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 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 917 TYR Chi-restraints excluded: chain B residue 997 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 214 ARG Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS 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 705 VAL Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 907 ASN 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 977 LEU 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 Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1125 ASN B 856 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.069508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.051712 restraints weight = 136727.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.052929 restraints weight = 76388.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.053736 restraints weight = 51609.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.054218 restraints weight = 39832.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.054525 restraints weight = 33934.248| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24003 Z= 0.163 Angle : 0.577 8.361 32679 Z= 0.305 Chirality : 0.044 0.198 3726 Planarity : 0.004 0.047 4221 Dihedral : 5.533 54.533 3217 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.56 % Allowed : 12.13 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 2955 helix: 1.56 (0.20), residues: 664 sheet: -0.79 (0.20), residues: 614 loop : -0.60 (0.16), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.017 0.001 TYR C 369 PHE 0.016 0.001 PHE B1089 TRP 0.014 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00354 (23964) covalent geometry : angle 0.57249 (32601) SS BOND : bond 0.00408 ( 39) SS BOND : angle 1.51729 ( 78) hydrogen bonds : bond 0.03972 ( 1034) hydrogen bonds : angle 5.92978 ( 2808) *********************** 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 156 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 89 time to evaluate : 0.770 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: 0.8421 (ptp) cc_final: 0.8160 (ptp) REVERT: A 776 LYS cc_start: 0.8305 (tmtt) cc_final: 0.6522 (tmtt) REVERT: A 780 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7325 (mt-10) REVERT: A 902 MET cc_start: 0.8778 (mmm) cc_final: 0.8385 (mmm) REVERT: A 1005 GLN cc_start: 0.8474 (tm-30) cc_final: 0.7865 (tm-30) REVERT: B 492 LEU cc_start: 0.8072 (tp) cc_final: 0.7727 (tp) REVERT: B 904 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.5901 (m-10) REVERT: C 392 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.6888 (m-80) REVERT: C 907 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8039 (m110) outliers start: 67 outliers final: 54 residues processed: 150 average time/residue: 0.1421 time to fit residues: 35.5376 Evaluate side-chains 137 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 80 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 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 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 866 THR 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 A residue 1128 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS 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 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 917 TYR 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 136 CYS Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 362 VAL 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 705 VAL Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 907 ASN 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 977 LEU 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 148 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN 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 = 0.069889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.052294 restraints weight = 132707.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.053525 restraints weight = 74620.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.054330 restraints weight = 50640.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.054834 restraints weight = 38921.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.055098 restraints weight = 33004.948| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24003 Z= 0.128 Angle : 0.560 13.547 32679 Z= 0.297 Chirality : 0.043 0.199 3726 Planarity : 0.004 0.046 4221 Dihedral : 5.145 52.791 3214 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.44 % Allowed : 12.70 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.16), residues: 2955 helix: 1.75 (0.21), residues: 656 sheet: -0.72 (0.20), residues: 628 loop : -0.56 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.018 0.001 TYR C 369 PHE 0.017 0.001 PHE B 515 TRP 0.014 0.001 TRP C 436 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00280 (23964) covalent geometry : angle 0.55002 (32601) SS BOND : bond 0.00397 ( 39) SS BOND : angle 2.21610 ( 78) hydrogen bonds : bond 0.03789 ( 1034) hydrogen bonds : angle 5.70519 ( 2808) *********************** 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 164 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 100 time to evaluate : 0.832 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: 0.7217 (pttt) cc_final: 0.6459 (pptt) REVERT: A 731 MET cc_start: 0.8352 (ptp) cc_final: 0.8110 (ptp) REVERT: A 776 LYS cc_start: 0.8312 (tmtt) cc_final: 0.6599 (tmtt) REVERT: A 780 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7317 (mt-10) REVERT: A 902 MET cc_start: 0.8742 (mmm) cc_final: 0.8336 (mmm) REVERT: A 1005 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7788 (tm-30) REVERT: B 104 TRP cc_start: 0.8165 (m-90) cc_final: 0.7949 (m-90) REVERT: B 166 CYS cc_start: 0.5706 (OUTLIER) cc_final: 0.5193 (p) REVERT: B 492 LEU cc_start: 0.8078 (tp) cc_final: 0.7723 (tp) REVERT: B 904 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.5813 (m-10) REVERT: B 1010 GLN cc_start: 0.7850 (pp30) cc_final: 0.7237 (pp30) REVERT: B 1088 HIS cc_start: 0.5762 (OUTLIER) cc_final: 0.5479 (m-70) REVERT: C 53 ASP cc_start: 0.8327 (t0) cc_final: 0.7932 (t0) REVERT: C 392 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.6787 (m-80) REVERT: C 436 TRP cc_start: 0.8613 (p90) cc_final: 0.8097 (p90) REVERT: C 907 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8015 (m110) REVERT: C 1029 MET cc_start: 0.8167 (mmm) cc_final: 0.7885 (tpp) outliers start: 64 outliers final: 50 residues processed: 157 average time/residue: 0.1436 time to fit residues: 37.8064 Evaluate side-chains 138 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 83 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR 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 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 818 ILE 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 A residue 1128 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS 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 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 904 TYR 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 1088 HIS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR 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 767 LEU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 977 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 30 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 278 optimal weight: 7.9990 chunk 286 optimal weight: 0.9980 chunk 205 optimal weight: 8.9990 chunk 279 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 196 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** B1002 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 = 0.3766 r_free = 0.3766 target = 0.070015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.052329 restraints weight = 134392.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.053556 restraints weight = 75449.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.054331 restraints weight = 51095.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.054843 restraints weight = 39513.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.055116 restraints weight = 33575.768| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 24003 Z= 0.127 Angle : 0.568 13.067 32679 Z= 0.297 Chirality : 0.043 0.204 3726 Planarity : 0.004 0.045 4221 Dihedral : 5.033 51.865 3214 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.40 % Allowed : 13.04 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2955 helix: 1.60 (0.20), residues: 674 sheet: -0.68 (0.20), residues: 626 loop : -0.51 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1039 TYR 0.018 0.001 TYR C 369 PHE 0.020 0.001 PHE B 888 TRP 0.013 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00279 (23964) covalent geometry : angle 0.55762 (32601) SS BOND : bond 0.00407 ( 39) SS BOND : angle 2.27925 ( 78) hydrogen bonds : bond 0.03754 ( 1034) hydrogen bonds : angle 5.69751 ( 2808) *********************** 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 155 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 92 time to evaluate : 0.961 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: 0.7290 (pttt) cc_final: 0.6537 (pptt) REVERT: A 731 MET cc_start: 0.8363 (ptp) cc_final: 0.8100 (ptp) REVERT: A 776 LYS cc_start: 0.8290 (tmtt) cc_final: 0.7964 (tmtt) REVERT: A 902 MET cc_start: 0.8745 (mmm) cc_final: 0.8336 (mmm) REVERT: A 1005 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7891 (tm-30) REVERT: B 104 TRP cc_start: 0.8072 (m-90) cc_final: 0.7734 (m-10) REVERT: B 166 CYS cc_start: 0.5934 (OUTLIER) cc_final: 0.5353 (p) REVERT: B 492 LEU cc_start: 0.8124 (tp) cc_final: 0.7760 (tp) REVERT: B 904 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.5813 (m-10) REVERT: B 1010 GLN cc_start: 0.7960 (pp30) cc_final: 0.7422 (pp30) REVERT: B 1088 HIS cc_start: 0.5811 (OUTLIER) cc_final: 0.5502 (m-70) REVERT: C 53 ASP cc_start: 0.8312 (t0) cc_final: 0.7926 (t0) REVERT: C 136 CYS cc_start: 0.7578 (OUTLIER) cc_final: 0.6829 (t) REVERT: C 392 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6691 (m-80) REVERT: C 436 TRP cc_start: 0.8649 (p90) cc_final: 0.8125 (p90) REVERT: C 907 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8058 (m110) outliers start: 63 outliers final: 48 residues processed: 148 average time/residue: 0.1266 time to fit residues: 31.7859 Evaluate side-chains 137 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 83 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR 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 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 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS 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 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR 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 941 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 977 LEU 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 289 optimal weight: 7.9990 chunk 200 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.069298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.051682 restraints weight = 134484.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.052914 restraints weight = 76112.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.053715 restraints weight = 51517.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.054241 restraints weight = 39811.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.054519 restraints weight = 33621.388| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 24003 Z= 0.181 Angle : 0.601 13.432 32679 Z= 0.314 Chirality : 0.044 0.219 3726 Planarity : 0.004 0.044 4221 Dihedral : 5.086 52.496 3212 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.52 % Allowed : 13.04 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2955 helix: 1.48 (0.20), residues: 671 sheet: -0.75 (0.20), residues: 603 loop : -0.56 (0.16), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1039 TYR 0.019 0.001 TYR C 369 PHE 0.018 0.001 PHE B1089 TRP 0.015 0.001 TRP C 436 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00392 (23964) covalent geometry : angle 0.59231 (32601) SS BOND : bond 0.00426 ( 39) SS BOND : angle 2.17295 ( 78) hydrogen bonds : bond 0.03881 ( 1034) hydrogen bonds : angle 5.78409 ( 2808) *********************** 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 147 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 81 time to evaluate : 0.721 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: 0.8361 (ptp) cc_final: 0.8107 (ptp) REVERT: A 776 LYS cc_start: 0.8273 (tmtt) cc_final: 0.6608 (tmtt) REVERT: A 780 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7184 (mt-10) REVERT: A 902 MET cc_start: 0.8785 (mmm) cc_final: 0.8377 (mmm) REVERT: A 1005 GLN cc_start: 0.8430 (tm-30) cc_final: 0.7865 (tm-30) REVERT: B 104 TRP cc_start: 0.8072 (m-90) cc_final: 0.7710 (m-10) REVERT: B 166 CYS cc_start: 0.5792 (OUTLIER) cc_final: 0.5257 (p) REVERT: B 492 LEU cc_start: 0.8227 (tp) cc_final: 0.7851 (tp) REVERT: B 904 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.5855 (m-10) REVERT: B 1010 GLN cc_start: 0.7900 (pp30) cc_final: 0.7352 (pp30) REVERT: B 1088 HIS cc_start: 0.5790 (OUTLIER) cc_final: 0.5468 (m-70) REVERT: C 136 CYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6863 (t) REVERT: C 392 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.6817 (m-80) REVERT: C 436 TRP cc_start: 0.8622 (p90) cc_final: 0.8068 (p90) REVERT: C 1029 MET cc_start: 0.8134 (mmm) cc_final: 0.7714 (tpp) outliers start: 66 outliers final: 55 residues processed: 142 average time/residue: 0.1360 time to fit residues: 32.8118 Evaluate side-chains 139 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 79 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR 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 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 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 866 THR 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 A residue 1128 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS 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 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 917 TYR 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 1088 HIS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 214 ARG 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 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 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 977 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1101 HIS 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 223 optimal weight: 20.0000 chunk 164 optimal weight: 0.5980 chunk 240 optimal weight: 50.0000 chunk 108 optimal weight: 2.9990 chunk 250 optimal weight: 20.0000 chunk 255 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 238 optimal weight: 0.0980 chunk 219 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.069901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.052458 restraints weight = 134125.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.053716 restraints weight = 74919.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.054556 restraints weight = 50475.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.055066 restraints weight = 38405.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.055344 restraints weight = 32480.015| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24003 Z= 0.119 Angle : 0.559 13.918 32679 Z= 0.292 Chirality : 0.043 0.190 3726 Planarity : 0.004 0.045 4221 Dihedral : 4.851 51.177 3212 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.10 % Allowed : 13.54 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.16), residues: 2955 helix: 1.64 (0.21), residues: 672 sheet: -0.63 (0.20), residues: 627 loop : -0.50 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1039 TYR 0.018 0.001 TYR C 369 PHE 0.019 0.001 PHE B 515 TRP 0.013 0.001 TRP C 436 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00261 (23964) covalent geometry : angle 0.55272 (32601) SS BOND : bond 0.00385 ( 39) SS BOND : angle 1.82514 ( 78) hydrogen bonds : bond 0.03653 ( 1034) hydrogen bonds : angle 5.56477 ( 2808) ********************** 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 147 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 92 time to evaluate : 0.663 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: 0.7384 (pttt) cc_final: 0.6664 (pptt) REVERT: A 731 MET cc_start: 0.8328 (ptp) cc_final: 0.8074 (ptp) REVERT: A 780 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7676 (tp30) REVERT: A 902 MET cc_start: 0.8785 (mmm) cc_final: 0.8370 (mmm) REVERT: A 1005 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7832 (tm-30) REVERT: B 104 TRP cc_start: 0.8082 (m-90) cc_final: 0.7798 (m-10) REVERT: B 166 CYS cc_start: 0.5900 (OUTLIER) cc_final: 0.5375 (p) REVERT: B 492 LEU cc_start: 0.8172 (tp) cc_final: 0.7840 (tp) REVERT: B 754 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9049 (pp) REVERT: B 904 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.5724 (m-10) REVERT: B 1010 GLN cc_start: 0.7878 (pp30) cc_final: 0.7382 (pp30) REVERT: B 1088 HIS cc_start: 0.5769 (OUTLIER) cc_final: 0.5467 (m-70) REVERT: C 53 ASP cc_start: 0.8260 (t0) cc_final: 0.7907 (t0) REVERT: C 136 CYS cc_start: 0.7603 (OUTLIER) cc_final: 0.6956 (t) REVERT: C 392 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6644 (m-80) REVERT: C 436 TRP cc_start: 0.8623 (p90) cc_final: 0.8061 (p90) REVERT: C 1029 MET cc_start: 0.8083 (mmm) cc_final: 0.7706 (tpp) outliers start: 55 outliers final: 45 residues processed: 142 average time/residue: 0.1352 time to fit residues: 32.5164 Evaluate side-chains 137 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 86 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR 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 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 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU 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 A residue 1128 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 214 ARG 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 385 THR Chi-restraints excluded: chain C residue 392 PHE 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 1101 HIS 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 293 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 39 optimal weight: 0.0270 chunk 210 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 241 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 285 optimal weight: 0.9980 chunk 198 optimal weight: 8.9990 overall best weight: 4.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.068388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.050922 restraints weight = 135597.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.052102 restraints weight = 77258.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.052877 restraints weight = 52871.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.053349 restraints weight = 40949.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.053654 restraints weight = 34851.195| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 24003 Z= 0.226 Angle : 0.645 13.479 32679 Z= 0.337 Chirality : 0.045 0.191 3726 Planarity : 0.004 0.044 4221 Dihedral : 5.145 53.022 3211 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.21 % Allowed : 13.54 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2955 helix: 1.39 (0.20), residues: 665 sheet: -0.73 (0.21), residues: 575 loop : -0.64 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1039 TYR 0.019 0.002 TYR C 369 PHE 0.033 0.002 PHE C 927 TRP 0.015 0.001 TRP C 436 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00488 (23964) covalent geometry : angle 0.63742 (32601) SS BOND : bond 0.00498 ( 39) SS BOND : angle 2.13872 ( 78) hydrogen bonds : bond 0.04042 ( 1034) hydrogen bonds : angle 5.94279 ( 2808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3716.21 seconds wall clock time: 65 minutes 10.40 seconds (3910.40 seconds total)