Starting phenix.real_space_refine on Thu Mar 5 15:00:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tla_25985/03_2026/7tla_25985.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tla_25985/03_2026/7tla_25985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tla_25985/03_2026/7tla_25985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tla_25985/03_2026/7tla_25985.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tla_25985/03_2026/7tla_25985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tla_25985/03_2026/7tla_25985.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.080 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 14738 2.51 5 N 3827 2.21 5 O 4382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.03s 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: 23052 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "B" Number of atoms: 7757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7757 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 50, 'TRANS': 941} Chain breaks: 10 Chain: "C" Number of atoms: 7693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7693 Classifications: {'peptide': 984} Link IDs: {'PTRANS': 48, 'TRANS': 935} Chain breaks: 11 Time building chain proxies: 5.64, per 1000 atoms: 0.24 Number of scatterers: 23052 At special positions: 0 Unit cell: (131.44, 130.38, 170.66, 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 4382 8.00 N 3827 7.00 C 14738 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS C 383 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.00 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 985 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " 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=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.00 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.00 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 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=2.05 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: 1.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5542 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 49 sheets defined 28.0% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 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 364 through 370 removed outlier: 4.201A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.093A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.781A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.607A 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 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.791A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.613A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.652A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.678A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.753A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.172A 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 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.058A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.108A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.582A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.650A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.604A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.604A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.820A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.688A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.804A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.671A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.530A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.988A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.085A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.626A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) 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 755 removed outlier: 3.937A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.672A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.893A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 838 removed outlier: 4.332A pdb=" N GLN C 836 " --> pdb=" O GLY C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.601A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 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: 3.714A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.164A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.028A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.646A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.431A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.431A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.870A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.643A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.081A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.137A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.137A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.763A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.415A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.726A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.132A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.201A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.669A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.407A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.745A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.765A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.109A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG B 102 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 119 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.724A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.214A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.214A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.899A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD3, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.671A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.551A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.129A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.654A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.468A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.774A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.499A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.298A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.805A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.521A 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 728 removed outlier: 6.803A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.803A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (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: 5.540A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 1062 hydrogen bonds defined for protein. 2877 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.43 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6040 1.33 - 1.45: 4479 1.45 - 1.58: 12917 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 23565 Sorted by residual: bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.540 -0.023 6.70e-03 2.23e+04 1.16e+01 bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.540 -0.023 6.70e-03 2.23e+04 1.15e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.540 -0.023 6.70e-03 2.23e+04 1.14e+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 9.61e+00 bond pdb=" CZ ARG A1039 " pdb=" NH2 ARG A1039 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.11e+00 ... (remaining 23560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 23647 1.94 - 3.88: 7505 3.88 - 5.81: 836 5.81 - 7.75: 66 7.75 - 9.69: 5 Bond angle restraints: 32059 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 118.76 -8.06 1.22e+00 6.72e-01 4.36e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 118.03 -7.33 1.22e+00 6.72e-01 3.61e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.73 -7.03 1.22e+00 6.72e-01 3.32e+01 angle pdb=" CA ASP B 796 " pdb=" CB ASP B 796 " pdb=" CG ASP B 796 " ideal model delta sigma weight residual 112.60 117.99 -5.39 1.00e+00 1.00e+00 2.90e+01 angle pdb=" CB HIS C 519 " pdb=" CG HIS C 519 " pdb=" CD2 HIS C 519 " ideal model delta sigma weight residual 131.20 124.34 6.86 1.30e+00 5.92e-01 2.78e+01 ... (remaining 32054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 13059 18.13 - 36.25: 792 36.25 - 54.38: 127 54.38 - 72.50: 46 72.50 - 90.63: 32 Dihedral angle restraints: 14056 sinusoidal: 5473 harmonic: 8583 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -165.35 79.35 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -160.97 74.97 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 153.55 -60.55 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 14053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2191 0.079 - 0.159: 1231 0.159 - 0.238: 199 0.238 - 0.317: 40 0.317 - 0.397: 10 Chirality restraints: 3671 Sorted by residual: chirality pdb=" CA PRO C 986 " pdb=" N PRO C 986 " pdb=" C PRO C 986 " pdb=" CB PRO C 986 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.94e+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 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA ALA B 123 " pdb=" N ALA B 123 " pdb=" C ALA B 123 " pdb=" CB ALA B 123 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 3668 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 495 " -0.153 2.00e-02 2.50e+03 8.42e-02 1.42e+02 pdb=" CG TYR A 495 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 495 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR A 495 " 0.076 2.00e-02 2.50e+03 pdb=" CE1 TYR A 495 " 0.054 2.00e-02 2.50e+03 pdb=" CE2 TYR A 495 " 0.040 2.00e-02 2.50e+03 pdb=" CZ TYR A 495 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 495 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 707 " -0.113 2.00e-02 2.50e+03 6.81e-02 9.26e+01 pdb=" CG TYR C 707 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 707 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR C 707 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR C 707 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR C 707 " 0.065 2.00e-02 2.50e+03 pdb=" CZ TYR C 707 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 707 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 423 " -0.126 2.00e-02 2.50e+03 6.70e-02 8.97e+01 pdb=" CG TYR B 423 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 423 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR B 423 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR B 423 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR B 423 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR B 423 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 423 " -0.097 2.00e-02 2.50e+03 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 11424 3.00 - 3.47: 22523 3.47 - 3.95: 38851 3.95 - 4.42: 43488 4.42 - 4.90: 74194 Nonbonded interactions: 190480 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.522 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.524 3.040 nonbonded pdb=" OE1 GLU B 516 " pdb=" OH TYR C 200 " model vdw 2.525 3.040 nonbonded pdb=" OE1 GLU A 298 " pdb=" OG SER A 316 " model vdw 2.532 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.543 3.040 ... (remaining 190475 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 620 or resid 641 through 1147)) selection = (chain 'C' and (resid 27 through 827 or resid 854 through 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.030 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 23.630 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 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 0.042 23604 Z= 0.723 Angle : 1.761 9.688 32137 Z= 1.194 Chirality : 0.092 0.397 3671 Planarity : 0.014 0.198 4144 Dihedral : 13.367 90.625 8397 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 0.09 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.01 % Favored : 93.71 % Rotamer: Outliers : 1.12 % Allowed : 2.83 % Favored : 96.05 % 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: -1.09 (0.14), residues: 2878 helix: -0.85 (0.16), residues: 692 sheet: 0.27 (0.21), residues: 581 loop : -1.02 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1019 TYR 0.153 0.020 TYR A 495 PHE 0.073 0.012 PHE B 718 TRP 0.101 0.021 TRP A 104 HIS 0.010 0.003 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.01234 (23565) covalent geometry : angle 1.76018 (32059) SS BOND : bond 0.01479 ( 39) SS BOND : angle 2.15938 ( 78) hydrogen bonds : bond 0.14213 ( 1034) hydrogen bonds : angle 8.33519 ( 2877) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 375 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8017 (p0) cc_final: 0.7654 (p0) REVERT: A 200 TYR cc_start: 0.6918 (m-80) cc_final: 0.6231 (m-80) REVERT: A 237 ARG cc_start: 0.6626 (mtt90) cc_final: 0.6169 (mtp180) REVERT: A 239 GLN cc_start: 0.6163 (tt0) cc_final: 0.5873 (tt0) REVERT: A 269 TYR cc_start: 0.7322 (m-80) cc_final: 0.6925 (m-80) REVERT: A 366 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8870 (p) REVERT: A 442 ASP cc_start: 0.7236 (m-30) cc_final: 0.6983 (m-30) REVERT: A 495 TYR cc_start: 0.6711 (m-80) cc_final: 0.5922 (m-80) REVERT: A 528 LYS cc_start: 0.8254 (tttt) cc_final: 0.8004 (tttm) REVERT: A 529 LYS cc_start: 0.8476 (mttt) cc_final: 0.7640 (mmtt) REVERT: A 558 LYS cc_start: 0.7706 (tttt) cc_final: 0.7117 (mmmt) REVERT: A 614 ASP cc_start: 0.7250 (t70) cc_final: 0.7046 (m-30) REVERT: A 646 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7731 (mtp180) REVERT: A 654 GLU cc_start: 0.6965 (tt0) cc_final: 0.6503 (tp30) REVERT: A 675 GLN cc_start: 0.6524 (mt0) cc_final: 0.5447 (pp30) REVERT: A 776 LYS cc_start: 0.6686 (tttt) cc_final: 0.6437 (tttp) REVERT: A 780 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6660 (mt-10) REVERT: A 786 LYS cc_start: 0.7875 (pttt) cc_final: 0.7473 (pttm) REVERT: A 790 LYS cc_start: 0.7519 (pttt) cc_final: 0.7220 (pttp) REVERT: A 902 MET cc_start: 0.7202 (mmt) cc_final: 0.6846 (mmm) REVERT: A 950 ASP cc_start: 0.6486 (t70) cc_final: 0.6197 (m-30) REVERT: A 957 GLN cc_start: 0.6211 (tp-100) cc_final: 0.5854 (tt0) REVERT: A 995 ARG cc_start: 0.6774 (mtt180) cc_final: 0.6565 (mtp180) REVERT: A 1002 GLN cc_start: 0.6647 (tt0) cc_final: 0.6145 (tp40) REVERT: A 1045 LYS cc_start: 0.7435 (ttpp) cc_final: 0.7229 (mmmt) REVERT: B 29 THR cc_start: 0.7176 (t) cc_final: 0.6930 (t) REVERT: B 81 ASN cc_start: 0.7296 (p0) cc_final: 0.6136 (p0) REVERT: B 118 LEU cc_start: 0.7158 (tp) cc_final: 0.6515 (mt) REVERT: B 128 ILE cc_start: 0.5270 (mt) cc_final: 0.4825 (mt) REVERT: B 198 ASP cc_start: 0.7159 (m-30) cc_final: 0.6777 (p0) REVERT: B 200 TYR cc_start: 0.7156 (m-80) cc_final: 0.6840 (m-80) REVERT: B 231 ILE cc_start: 0.7186 (pt) cc_final: 0.6948 (pt) REVERT: B 307 THR cc_start: 0.8595 (m) cc_final: 0.8153 (t) REVERT: B 309 GLU cc_start: 0.6169 (mp0) cc_final: 0.5905 (mp0) REVERT: B 332 ILE cc_start: 0.5674 (tt) cc_final: 0.5445 (tt) REVERT: B 334 ASN cc_start: 0.6803 (m-40) cc_final: 0.6575 (m110) REVERT: B 335 LEU cc_start: 0.8263 (mt) cc_final: 0.7829 (tt) REVERT: B 351 TYR cc_start: 0.6857 (p90) cc_final: 0.6601 (p90) REVERT: B 518 LEU cc_start: 0.6412 (mt) cc_final: 0.6166 (pp) REVERT: B 529 LYS cc_start: 0.7683 (mttt) cc_final: 0.6927 (mmmm) REVERT: B 556 ASN cc_start: 0.7098 (p0) cc_final: 0.6582 (m110) REVERT: B 661 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7216 (mm-30) REVERT: B 723 THR cc_start: 0.6866 (t) cc_final: 0.6603 (p) REVERT: B 776 LYS cc_start: 0.6495 (tttt) cc_final: 0.5981 (tttm) REVERT: B 786 LYS cc_start: 0.8241 (pttt) cc_final: 0.7979 (pttm) REVERT: B 902 MET cc_start: 0.7492 (mmm) cc_final: 0.6631 (tpt) REVERT: B 950 ASP cc_start: 0.6513 (t70) cc_final: 0.6290 (m-30) REVERT: B 990 GLU cc_start: 0.6482 (mt-10) cc_final: 0.6051 (tt0) REVERT: B 1003 SER cc_start: 0.6932 (t) cc_final: 0.6603 (m) REVERT: B 1045 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7648 (tmtt) REVERT: B 1094 VAL cc_start: 0.7541 (OUTLIER) cc_final: 0.7138 (m) REVERT: B 1114 ILE cc_start: 0.8155 (mm) cc_final: 0.7940 (mm) REVERT: C 32 PHE cc_start: 0.6766 (m-80) cc_final: 0.6478 (m-80) REVERT: C 63 THR cc_start: 0.7142 (m) cc_final: 0.6933 (p) REVERT: C 133 PHE cc_start: 0.6145 (m-80) cc_final: 0.5349 (t80) REVERT: C 239 GLN cc_start: 0.7452 (tt0) cc_final: 0.7102 (tt0) REVERT: C 269 TYR cc_start: 0.7632 (m-80) cc_final: 0.7249 (m-10) REVERT: C 304 LYS cc_start: 0.7556 (mmtm) cc_final: 0.7350 (mmtm) REVERT: C 335 LEU cc_start: 0.7996 (mt) cc_final: 0.7561 (tt) REVERT: C 380 TYR cc_start: 0.6529 (m-80) cc_final: 0.6036 (m-10) REVERT: C 396 TYR cc_start: 0.5062 (m-80) cc_final: 0.4546 (m-10) REVERT: C 558 LYS cc_start: 0.7654 (tttt) cc_final: 0.7363 (mmmt) REVERT: C 568 ASP cc_start: 0.6838 (t0) cc_final: 0.6627 (m-30) REVERT: C 574 ASP cc_start: 0.6281 (t0) cc_final: 0.6080 (t0) REVERT: C 614 ASP cc_start: 0.7515 (t0) cc_final: 0.7180 (m-30) REVERT: C 690 GLN cc_start: 0.7006 (mt0) cc_final: 0.6598 (tp40) REVERT: C 780 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6300 (mm-30) REVERT: C 786 LYS cc_start: 0.8273 (pttt) cc_final: 0.7823 (ptpp) REVERT: C 964 LYS cc_start: 0.7200 (mttt) cc_final: 0.6869 (mmtt) REVERT: C 1005 GLN cc_start: 0.7086 (mt0) cc_final: 0.6635 (mm-40) outliers start: 29 outliers final: 9 residues processed: 402 average time/residue: 0.1605 time to fit residues: 100.0164 Evaluate side-chains 226 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 215 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 751 ASN B 314 GLN B 394 ASN B 540 ASN B 965 GLN C 388 ASN C 613 GLN C 751 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.148914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105076 restraints weight = 33701.715| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.26 r_work: 0.3099 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23604 Z= 0.152 Angle : 0.630 10.752 32137 Z= 0.336 Chirality : 0.046 0.170 3671 Planarity : 0.004 0.041 4144 Dihedral : 6.158 66.174 3151 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.06 % Favored : 96.84 % Rotamer: Outliers : 1.47 % Allowed : 6.32 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.17 (0.15), residues: 2878 helix: 1.22 (0.20), residues: 681 sheet: 0.04 (0.18), residues: 704 loop : -0.79 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 102 TYR 0.019 0.002 TYR A 170 PHE 0.026 0.002 PHE B 168 TRP 0.016 0.002 TRP B 64 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00331 (23565) covalent geometry : angle 0.62622 (32059) SS BOND : bond 0.00345 ( 39) SS BOND : angle 1.56378 ( 78) hydrogen bonds : bond 0.04505 ( 1034) hydrogen bonds : angle 6.16764 ( 2877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 PRO cc_start: 0.8134 (Cg_endo) cc_final: 0.7700 (Cg_exo) REVERT: A 237 ARG cc_start: 0.7615 (mtt90) cc_final: 0.7246 (mtm-85) REVERT: A 269 TYR cc_start: 0.8522 (m-80) cc_final: 0.8278 (m-10) REVERT: A 529 LYS cc_start: 0.8597 (mttt) cc_final: 0.8314 (mmtt) REVERT: A 558 LYS cc_start: 0.8771 (tttt) cc_final: 0.8417 (mmmt) REVERT: A 619 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: A 646 ARG cc_start: 0.8308 (mtm180) cc_final: 0.8100 (mtp180) REVERT: A 654 GLU cc_start: 0.8494 (tt0) cc_final: 0.8010 (tp30) REVERT: A 675 GLN cc_start: 0.7807 (mt0) cc_final: 0.7332 (pp30) REVERT: A 780 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8314 (mm-30) REVERT: A 790 LYS cc_start: 0.8502 (pttt) cc_final: 0.8244 (pttp) REVERT: A 804 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8199 (mp10) REVERT: A 811 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6359 (tmtt) REVERT: A 950 ASP cc_start: 0.8181 (t70) cc_final: 0.7975 (m-30) REVERT: A 957 GLN cc_start: 0.8297 (tp-100) cc_final: 0.8034 (tt0) REVERT: A 1050 MET cc_start: 0.9357 (ptm) cc_final: 0.9043 (ptp) REVERT: A 1107 ARG cc_start: 0.8456 (mtm-85) cc_final: 0.8222 (mtt90) REVERT: B 81 ASN cc_start: 0.7919 (p0) cc_final: 0.7163 (p0) REVERT: B 117 LEU cc_start: 0.7477 (mp) cc_final: 0.7171 (mt) REVERT: B 118 LEU cc_start: 0.7869 (tp) cc_final: 0.7404 (mm) REVERT: B 307 THR cc_start: 0.9274 (m) cc_final: 0.9015 (t) REVERT: B 316 SER cc_start: 0.8900 (t) cc_final: 0.8696 (m) REVERT: B 335 LEU cc_start: 0.8508 (mt) cc_final: 0.8051 (tt) REVERT: B 387 LEU cc_start: 0.7780 (mt) cc_final: 0.7520 (mt) REVERT: B 400 PHE cc_start: 0.8538 (p90) cc_final: 0.8332 (p90) REVERT: B 529 LYS cc_start: 0.8105 (mttt) cc_final: 0.7470 (mmmm) REVERT: B 568 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7341 (m-30) REVERT: B 574 ASP cc_start: 0.7980 (t70) cc_final: 0.7099 (t0) REVERT: B 721 SER cc_start: 0.8957 (t) cc_final: 0.8754 (p) REVERT: B 776 LYS cc_start: 0.8898 (tttt) cc_final: 0.8656 (ttpt) REVERT: B 950 ASP cc_start: 0.8382 (t70) cc_final: 0.8115 (m-30) REVERT: B 990 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7605 (tt0) REVERT: B 1003 SER cc_start: 0.9003 (t) cc_final: 0.8673 (m) REVERT: C 32 PHE cc_start: 0.7430 (m-80) cc_final: 0.7154 (m-80) REVERT: C 133 PHE cc_start: 0.6179 (m-80) cc_final: 0.5406 (t80) REVERT: C 239 GLN cc_start: 0.8147 (tt0) cc_final: 0.7710 (tm-30) REVERT: C 241 LEU cc_start: 0.8084 (mt) cc_final: 0.7656 (mp) REVERT: C 304 LYS cc_start: 0.8816 (mmtm) cc_final: 0.8482 (mmtm) REVERT: C 335 LEU cc_start: 0.8304 (mt) cc_final: 0.7480 (tt) REVERT: C 380 TYR cc_start: 0.7287 (m-80) cc_final: 0.7033 (m-80) REVERT: C 425 LEU cc_start: 0.4259 (OUTLIER) cc_final: 0.3987 (pp) REVERT: C 780 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8111 (mm-30) REVERT: C 964 LYS cc_start: 0.8900 (mttt) cc_final: 0.8569 (mmtt) REVERT: C 990 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7333 (tm-30) outliers start: 38 outliers final: 16 residues processed: 283 average time/residue: 0.1573 time to fit residues: 70.1507 Evaluate side-chains 213 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 119 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 278 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN B 394 ASN B 506 GLN B 540 ASN B 613 GLN B 969 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.144995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.101633 restraints weight = 33562.875| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.28 r_work: 0.3029 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23604 Z= 0.219 Angle : 0.609 7.954 32137 Z= 0.321 Chirality : 0.047 0.170 3671 Planarity : 0.004 0.045 4144 Dihedral : 5.692 63.368 3142 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.74 % Allowed : 8.64 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 2878 helix: 1.24 (0.20), residues: 690 sheet: -0.07 (0.18), residues: 702 loop : -0.83 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 102 TYR 0.020 0.002 TYR B1067 PHE 0.020 0.002 PHE B 400 TRP 0.015 0.002 TRP C 353 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00522 (23565) covalent geometry : angle 0.60517 (32059) SS BOND : bond 0.00396 ( 39) SS BOND : angle 1.49068 ( 78) hydrogen bonds : bond 0.04422 ( 1034) hydrogen bonds : angle 5.94509 ( 2877) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7667 (mtt90) cc_final: 0.7204 (mtm-85) REVERT: A 239 GLN cc_start: 0.7969 (tt0) cc_final: 0.7692 (tt0) REVERT: A 269 TYR cc_start: 0.8576 (m-80) cc_final: 0.8337 (m-10) REVERT: A 529 LYS cc_start: 0.8670 (mttt) cc_final: 0.8344 (mmtt) REVERT: A 546 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7908 (tp) REVERT: A 558 LYS cc_start: 0.8836 (tttt) cc_final: 0.8447 (mmmt) REVERT: A 619 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: A 675 GLN cc_start: 0.7995 (mt0) cc_final: 0.7545 (pp30) REVERT: A 790 LYS cc_start: 0.8608 (pttt) cc_final: 0.8281 (pttp) REVERT: A 804 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8397 (mt0) REVERT: A 811 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.6542 (tmtt) REVERT: A 950 ASP cc_start: 0.8326 (t70) cc_final: 0.8082 (m-30) REVERT: A 957 GLN cc_start: 0.8368 (tp-100) cc_final: 0.8117 (tt0) REVERT: A 1073 LYS cc_start: 0.8928 (tttt) cc_final: 0.8634 (ttmm) REVERT: A 1107 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8253 (mtt90) REVERT: B 81 ASN cc_start: 0.8053 (p0) cc_final: 0.7448 (p0) REVERT: B 101 ILE cc_start: 0.8710 (mt) cc_final: 0.8510 (tp) REVERT: B 118 LEU cc_start: 0.7835 (tp) cc_final: 0.7507 (mm) REVERT: B 140 PHE cc_start: 0.7973 (p90) cc_final: 0.7740 (p90) REVERT: B 307 THR cc_start: 0.9214 (m) cc_final: 0.8924 (t) REVERT: B 400 PHE cc_start: 0.8644 (p90) cc_final: 0.8392 (p90) REVERT: B 568 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.6975 (m-30) REVERT: B 574 ASP cc_start: 0.8166 (t70) cc_final: 0.7439 (t0) REVERT: B 721 SER cc_start: 0.8888 (t) cc_final: 0.8622 (p) REVERT: B 776 LYS cc_start: 0.8937 (tttt) cc_final: 0.8617 (ttpt) REVERT: B 950 ASP cc_start: 0.8581 (t70) cc_final: 0.8265 (m-30) REVERT: B 990 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7609 (tt0) REVERT: B 1003 SER cc_start: 0.9049 (t) cc_final: 0.8746 (m) REVERT: C 32 PHE cc_start: 0.7647 (m-80) cc_final: 0.7398 (m-80) REVERT: C 133 PHE cc_start: 0.6147 (m-80) cc_final: 0.5501 (t80) REVERT: C 239 GLN cc_start: 0.8186 (tt0) cc_final: 0.7728 (tm-30) REVERT: C 241 LEU cc_start: 0.8178 (mt) cc_final: 0.7789 (mp) REVERT: C 304 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8528 (mmtm) REVERT: C 335 LEU cc_start: 0.8111 (mt) cc_final: 0.7564 (tt) REVERT: C 380 TYR cc_start: 0.7330 (m-80) cc_final: 0.7106 (m-80) REVERT: C 425 LEU cc_start: 0.4140 (OUTLIER) cc_final: 0.3840 (pp) REVERT: C 780 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8145 (mm-30) REVERT: C 990 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7422 (tm-30) outliers start: 45 outliers final: 29 residues processed: 237 average time/residue: 0.1446 time to fit residues: 55.5585 Evaluate side-chains 214 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 126 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 293 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 955 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.146325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.102533 restraints weight = 33551.075| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.21 r_work: 0.3057 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23604 Z= 0.157 Angle : 0.551 8.854 32137 Z= 0.290 Chirality : 0.045 0.180 3671 Planarity : 0.004 0.071 4144 Dihedral : 5.373 62.172 3142 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.98 % Allowed : 9.41 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 2878 helix: 1.46 (0.20), residues: 694 sheet: -0.02 (0.18), residues: 664 loop : -0.83 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.019 0.001 TYR B 351 PHE 0.020 0.001 PHE B 400 TRP 0.017 0.001 TRP C 353 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00364 (23565) covalent geometry : angle 0.54649 (32059) SS BOND : bond 0.00642 ( 39) SS BOND : angle 1.56823 ( 78) hydrogen bonds : bond 0.03903 ( 1034) hydrogen bonds : angle 5.64523 ( 2877) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7979 (tt0) cc_final: 0.7669 (tt0) REVERT: A 269 TYR cc_start: 0.8564 (m-80) cc_final: 0.8338 (m-10) REVERT: A 529 LYS cc_start: 0.8596 (mttt) cc_final: 0.8320 (mmtt) REVERT: A 546 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7791 (tp) REVERT: A 558 LYS cc_start: 0.8862 (tttt) cc_final: 0.8451 (mmmt) REVERT: A 675 GLN cc_start: 0.7957 (mt0) cc_final: 0.7461 (pp30) REVERT: A 780 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8407 (mm-30) REVERT: A 790 LYS cc_start: 0.8601 (pttt) cc_final: 0.8297 (pttp) REVERT: A 804 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8166 (mp10) REVERT: A 811 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.6443 (mttt) REVERT: A 957 GLN cc_start: 0.8326 (tp-100) cc_final: 0.8063 (tt0) REVERT: A 1050 MET cc_start: 0.9375 (ptm) cc_final: 0.9000 (ptp) REVERT: A 1073 LYS cc_start: 0.8852 (tttt) cc_final: 0.8556 (ttmm) REVERT: A 1107 ARG cc_start: 0.8400 (mtm-85) cc_final: 0.8157 (mtt180) REVERT: B 81 ASN cc_start: 0.8097 (p0) cc_final: 0.7449 (p0) REVERT: B 118 LEU cc_start: 0.7812 (tp) cc_final: 0.7469 (mm) REVERT: B 307 THR cc_start: 0.9136 (m) cc_final: 0.8825 (t) REVERT: B 364 ASP cc_start: 0.8332 (t0) cc_final: 0.8080 (t0) REVERT: B 400 PHE cc_start: 0.8598 (p90) cc_final: 0.8347 (p90) REVERT: B 508 TYR cc_start: 0.8357 (m-10) cc_final: 0.7941 (m-10) REVERT: B 568 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: B 574 ASP cc_start: 0.8181 (t70) cc_final: 0.7780 (t0) REVERT: B 721 SER cc_start: 0.8833 (t) cc_final: 0.8585 (p) REVERT: B 776 LYS cc_start: 0.8929 (tttt) cc_final: 0.8687 (ttpt) REVERT: B 950 ASP cc_start: 0.8548 (t70) cc_final: 0.8210 (m-30) REVERT: B 990 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7499 (tt0) REVERT: B 1003 SER cc_start: 0.9032 (t) cc_final: 0.8746 (m) REVERT: C 32 PHE cc_start: 0.7584 (m-80) cc_final: 0.7099 (m-80) REVERT: C 133 PHE cc_start: 0.6087 (m-80) cc_final: 0.5453 (t80) REVERT: C 304 LYS cc_start: 0.8830 (mmtm) cc_final: 0.8499 (mmtm) REVERT: C 335 LEU cc_start: 0.8113 (mt) cc_final: 0.7463 (tt) REVERT: C 425 LEU cc_start: 0.4169 (OUTLIER) cc_final: 0.3880 (pp) REVERT: C 427 ASP cc_start: 0.7410 (m-30) cc_final: 0.7089 (t0) REVERT: C 586 ASP cc_start: 0.8184 (m-30) cc_final: 0.7843 (m-30) REVERT: C 643 PHE cc_start: 0.8125 (t80) cc_final: 0.7911 (t80) REVERT: C 780 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8097 (mm-30) REVERT: C 817 PHE cc_start: 0.8465 (t80) cc_final: 0.8178 (t80) REVERT: C 984 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7756 (mt) REVERT: C 990 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7351 (tm-30) outliers start: 51 outliers final: 36 residues processed: 241 average time/residue: 0.1448 time to fit residues: 57.1170 Evaluate side-chains 227 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 115 optimal weight: 0.7980 chunk 191 optimal weight: 0.7980 chunk 290 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 15 optimal weight: 0.0270 chunk 64 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1088 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.149234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099466 restraints weight = 33327.265| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.22 r_work: 0.3101 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23604 Z= 0.103 Angle : 0.503 6.043 32137 Z= 0.265 Chirality : 0.044 0.168 3671 Planarity : 0.004 0.056 4144 Dihedral : 5.008 61.505 3142 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.90 % Allowed : 10.38 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 2878 helix: 1.79 (0.20), residues: 697 sheet: 0.07 (0.18), residues: 653 loop : -0.71 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 577 TYR 0.021 0.001 TYR B 351 PHE 0.023 0.001 PHE C 168 TRP 0.020 0.001 TRP C 436 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00223 (23565) covalent geometry : angle 0.50040 (32059) SS BOND : bond 0.00259 ( 39) SS BOND : angle 1.22765 ( 78) hydrogen bonds : bond 0.03479 ( 1034) hydrogen bonds : angle 5.28160 ( 2877) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8359 (p0) cc_final: 0.8109 (m-40) REVERT: A 237 ARG cc_start: 0.7659 (mtt90) cc_final: 0.7249 (mtm-85) REVERT: A 239 GLN cc_start: 0.8019 (tt0) cc_final: 0.7501 (mm-40) REVERT: A 269 TYR cc_start: 0.8594 (m-80) cc_final: 0.8350 (m-10) REVERT: A 529 LYS cc_start: 0.8616 (mttt) cc_final: 0.8342 (mmtt) REVERT: A 558 LYS cc_start: 0.8911 (tttt) cc_final: 0.8493 (mmmt) REVERT: A 661 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8161 (mm-30) REVERT: A 675 GLN cc_start: 0.7879 (mt0) cc_final: 0.7522 (pp30) REVERT: A 780 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8459 (mm-30) REVERT: A 790 LYS cc_start: 0.8566 (pttt) cc_final: 0.8356 (pttp) REVERT: A 811 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.6725 (mttm) REVERT: A 957 GLN cc_start: 0.8357 (tp-100) cc_final: 0.8114 (tt0) REVERT: A 1050 MET cc_start: 0.9310 (ptm) cc_final: 0.8975 (ptp) REVERT: A 1073 LYS cc_start: 0.8875 (tttt) cc_final: 0.8615 (ttmm) REVERT: B 118 LEU cc_start: 0.7708 (tp) cc_final: 0.7386 (mm) REVERT: B 271 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8604 (mp10) REVERT: B 332 ILE cc_start: 0.6496 (OUTLIER) cc_final: 0.6259 (tt) REVERT: B 364 ASP cc_start: 0.8328 (t0) cc_final: 0.7887 (t0) REVERT: B 400 PHE cc_start: 0.8548 (p90) cc_final: 0.8302 (p90) REVERT: B 492 LEU cc_start: 0.7274 (pt) cc_final: 0.6973 (mt) REVERT: B 528 LYS cc_start: 0.8158 (tppp) cc_final: 0.7896 (mmmm) REVERT: B 568 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: B 574 ASP cc_start: 0.8248 (t70) cc_final: 0.7755 (t0) REVERT: B 950 ASP cc_start: 0.8489 (t70) cc_final: 0.8109 (m-30) REVERT: B 990 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7508 (tt0) REVERT: B 1003 SER cc_start: 0.8956 (t) cc_final: 0.8728 (m) REVERT: C 32 PHE cc_start: 0.7451 (m-80) cc_final: 0.7025 (m-80) REVERT: C 63 THR cc_start: 0.8346 (m) cc_final: 0.8045 (p) REVERT: C 117 LEU cc_start: 0.7875 (tp) cc_final: 0.7233 (mm) REVERT: C 133 PHE cc_start: 0.6020 (m-80) cc_final: 0.5475 (t80) REVERT: C 239 GLN cc_start: 0.8010 (tt0) cc_final: 0.7689 (tt0) REVERT: C 335 LEU cc_start: 0.8204 (mt) cc_final: 0.7465 (tt) REVERT: C 353 TRP cc_start: 0.5271 (p-90) cc_final: 0.4398 (p-90) REVERT: C 387 LEU cc_start: 0.8779 (mp) cc_final: 0.8544 (mt) REVERT: C 425 LEU cc_start: 0.4204 (OUTLIER) cc_final: 0.3971 (pp) REVERT: C 427 ASP cc_start: 0.7343 (m-30) cc_final: 0.7012 (t0) REVERT: C 586 ASP cc_start: 0.8180 (m-30) cc_final: 0.7905 (m-30) REVERT: C 780 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8179 (mm-30) REVERT: C 814 LYS cc_start: 0.8468 (mttt) cc_final: 0.8104 (mmtt) outliers start: 49 outliers final: 30 residues processed: 253 average time/residue: 0.1447 time to fit residues: 60.0750 Evaluate side-chains 224 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 5 optimal weight: 0.7980 chunk 234 optimal weight: 0.0870 chunk 165 optimal weight: 0.0980 chunk 255 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 228 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 overall best weight: 2.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN B 394 ASN B 439 ASN B 506 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.145784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.102422 restraints weight = 33689.794| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.25 r_work: 0.3028 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 23604 Z= 0.233 Angle : 0.583 9.161 32137 Z= 0.304 Chirality : 0.047 0.200 3671 Planarity : 0.004 0.057 4144 Dihedral : 5.232 60.419 3142 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.29 % Allowed : 10.93 % Favored : 86.79 % 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: -0.08 (0.15), residues: 2878 helix: 1.57 (0.20), residues: 691 sheet: 0.02 (0.18), residues: 682 loop : -0.85 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 102 TYR 0.022 0.002 TYR A 904 PHE 0.018 0.002 PHE B1121 TRP 0.015 0.002 TRP C 436 HIS 0.009 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00558 (23565) covalent geometry : angle 0.57761 (32059) SS BOND : bond 0.00395 ( 39) SS BOND : angle 1.66745 ( 78) hydrogen bonds : bond 0.04121 ( 1034) hydrogen bonds : angle 5.58836 ( 2877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 187 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7628 (mtt90) cc_final: 0.7171 (mtm-85) REVERT: A 269 TYR cc_start: 0.8589 (m-80) cc_final: 0.8345 (m-10) REVERT: A 493 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6963 (mm-40) REVERT: A 529 LYS cc_start: 0.8610 (mttt) cc_final: 0.8313 (mmtt) REVERT: A 546 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7836 (tp) REVERT: A 558 LYS cc_start: 0.8900 (tttt) cc_final: 0.8469 (mmmt) REVERT: A 675 GLN cc_start: 0.8073 (mt0) cc_final: 0.7520 (pp30) REVERT: A 790 LYS cc_start: 0.8709 (pttt) cc_final: 0.8396 (pttp) REVERT: A 804 GLN cc_start: 0.8657 (mt0) cc_final: 0.8338 (mt0) REVERT: A 811 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.6553 (mttt) REVERT: A 957 GLN cc_start: 0.8395 (tp-100) cc_final: 0.8103 (tt0) REVERT: A 1073 LYS cc_start: 0.8846 (tttt) cc_final: 0.8586 (ttmm) REVERT: B 118 LEU cc_start: 0.7840 (tp) cc_final: 0.7495 (mm) REVERT: B 271 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8563 (mp10) REVERT: B 307 THR cc_start: 0.9226 (m) cc_final: 0.8950 (t) REVERT: B 321 GLN cc_start: 0.7733 (pt0) cc_final: 0.7502 (mm-40) REVERT: B 332 ILE cc_start: 0.6487 (OUTLIER) cc_final: 0.6269 (tt) REVERT: B 364 ASP cc_start: 0.8367 (t0) cc_final: 0.8124 (t0) REVERT: B 400 PHE cc_start: 0.8560 (p90) cc_final: 0.8319 (p90) REVERT: B 434 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7107 (mt) REVERT: B 492 LEU cc_start: 0.7292 (pt) cc_final: 0.7020 (mt) REVERT: B 554 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7726 (pt0) REVERT: B 574 ASP cc_start: 0.8305 (t70) cc_final: 0.7949 (t0) REVERT: B 950 ASP cc_start: 0.8566 (t70) cc_final: 0.8154 (m-30) REVERT: B 990 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7546 (tt0) REVERT: B 1003 SER cc_start: 0.9077 (t) cc_final: 0.8757 (m) REVERT: C 32 PHE cc_start: 0.7644 (m-80) cc_final: 0.7186 (m-80) REVERT: C 117 LEU cc_start: 0.7859 (tp) cc_final: 0.7214 (mm) REVERT: C 132 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7656 (mt-10) REVERT: C 133 PHE cc_start: 0.6106 (m-80) cc_final: 0.5538 (t80) REVERT: C 192 PHE cc_start: 0.7777 (m-80) cc_final: 0.7385 (m-80) REVERT: C 281 GLU cc_start: 0.6741 (pm20) cc_final: 0.6316 (pm20) REVERT: C 335 LEU cc_start: 0.8264 (mt) cc_final: 0.7485 (tt) REVERT: C 425 LEU cc_start: 0.4336 (OUTLIER) cc_final: 0.4111 (pp) REVERT: C 427 ASP cc_start: 0.7422 (m-30) cc_final: 0.7055 (t0) REVERT: C 586 ASP cc_start: 0.8186 (m-30) cc_final: 0.7791 (m-30) REVERT: C 780 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8089 (mm-30) REVERT: C 814 LYS cc_start: 0.8493 (mttt) cc_final: 0.8138 (mmmt) REVERT: C 817 PHE cc_start: 0.8516 (t80) cc_final: 0.8252 (t80) REVERT: C 990 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7116 (tt0) REVERT: C 1072 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8459 (mp0) outliers start: 59 outliers final: 45 residues processed: 233 average time/residue: 0.1483 time to fit residues: 56.8752 Evaluate side-chains 228 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 191 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 439 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.145776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.102238 restraints weight = 33515.911| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.27 r_work: 0.3023 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23604 Z= 0.195 Angle : 0.551 8.560 32137 Z= 0.288 Chirality : 0.045 0.195 3671 Planarity : 0.004 0.065 4144 Dihedral : 5.149 60.211 3142 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.63 % Allowed : 10.93 % Favored : 86.44 % 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: -0.04 (0.15), residues: 2878 helix: 1.67 (0.20), residues: 686 sheet: 0.03 (0.18), residues: 681 loop : -0.84 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.020 0.001 TYR A 904 PHE 0.016 0.001 PHE A 400 TRP 0.018 0.001 TRP C 353 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00462 (23565) covalent geometry : angle 0.54747 (32059) SS BOND : bond 0.00335 ( 39) SS BOND : angle 1.44514 ( 78) hydrogen bonds : bond 0.03900 ( 1034) hydrogen bonds : angle 5.48646 ( 2877) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 194 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7640 (mtt90) cc_final: 0.7157 (mtm-85) REVERT: A 269 TYR cc_start: 0.8584 (m-80) cc_final: 0.8326 (m-10) REVERT: A 493 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6967 (mm-40) REVERT: A 529 LYS cc_start: 0.8623 (mttt) cc_final: 0.8324 (mmtt) REVERT: A 546 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7861 (tp) REVERT: A 558 LYS cc_start: 0.8896 (tttt) cc_final: 0.8444 (mmmt) REVERT: A 675 GLN cc_start: 0.8036 (mt0) cc_final: 0.7497 (pp30) REVERT: A 790 LYS cc_start: 0.8705 (pttt) cc_final: 0.8356 (pttp) REVERT: A 804 GLN cc_start: 0.8689 (mt0) cc_final: 0.8355 (mt0) REVERT: A 957 GLN cc_start: 0.8368 (tp-100) cc_final: 0.8064 (tt0) REVERT: A 1073 LYS cc_start: 0.8858 (tttt) cc_final: 0.8581 (ttmm) REVERT: B 118 LEU cc_start: 0.7844 (tp) cc_final: 0.7555 (mm) REVERT: B 271 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8579 (mp10) REVERT: B 307 THR cc_start: 0.9228 (m) cc_final: 0.8981 (t) REVERT: B 321 GLN cc_start: 0.7740 (pt0) cc_final: 0.7533 (mm-40) REVERT: B 332 ILE cc_start: 0.6501 (OUTLIER) cc_final: 0.6281 (tt) REVERT: B 364 ASP cc_start: 0.8374 (t0) cc_final: 0.8134 (t0) REVERT: B 400 PHE cc_start: 0.8534 (p90) cc_final: 0.8296 (p90) REVERT: B 434 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7153 (mt) REVERT: B 492 LEU cc_start: 0.7256 (pt) cc_final: 0.7052 (mt) REVERT: B 554 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7735 (pt0) REVERT: B 574 ASP cc_start: 0.8232 (t70) cc_final: 0.7900 (t0) REVERT: B 950 ASP cc_start: 0.8570 (t70) cc_final: 0.8211 (m-30) REVERT: B 990 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7514 (tt0) REVERT: B 1003 SER cc_start: 0.9057 (t) cc_final: 0.8761 (m) REVERT: C 32 PHE cc_start: 0.7623 (m-80) cc_final: 0.7163 (m-80) REVERT: C 117 LEU cc_start: 0.7844 (tp) cc_final: 0.7260 (mp) REVERT: C 118 LEU cc_start: 0.8188 (tp) cc_final: 0.7972 (tt) REVERT: C 132 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7687 (mt-10) REVERT: C 133 PHE cc_start: 0.6108 (m-80) cc_final: 0.5553 (t80) REVERT: C 192 PHE cc_start: 0.7777 (m-80) cc_final: 0.7367 (m-80) REVERT: C 281 GLU cc_start: 0.6783 (pm20) cc_final: 0.6361 (pm20) REVERT: C 335 LEU cc_start: 0.8345 (mt) cc_final: 0.7580 (tt) REVERT: C 427 ASP cc_start: 0.7353 (m-30) cc_final: 0.6987 (t0) REVERT: C 586 ASP cc_start: 0.8154 (m-30) cc_final: 0.7828 (m-30) REVERT: C 780 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8097 (mm-30) REVERT: C 814 LYS cc_start: 0.8465 (mttt) cc_final: 0.8165 (mmmt) REVERT: C 817 PHE cc_start: 0.8402 (t80) cc_final: 0.8141 (t80) outliers start: 68 outliers final: 51 residues processed: 246 average time/residue: 0.1488 time to fit residues: 60.2982 Evaluate side-chains 236 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 288 optimal weight: 1.9990 chunk 246 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 213 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 913 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.147015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103246 restraints weight = 33355.558| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.25 r_work: 0.3058 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23604 Z= 0.139 Angle : 0.531 10.328 32137 Z= 0.276 Chirality : 0.044 0.223 3671 Planarity : 0.004 0.050 4144 Dihedral : 4.989 59.294 3142 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.09 % Allowed : 11.62 % Favored : 86.28 % 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: 0.07 (0.15), residues: 2878 helix: 1.84 (0.20), residues: 686 sheet: 0.08 (0.18), residues: 667 loop : -0.80 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.018 0.001 TYR B1067 PHE 0.016 0.001 PHE B 400 TRP 0.027 0.001 TRP C 436 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00322 (23565) covalent geometry : angle 0.52633 (32059) SS BOND : bond 0.00285 ( 39) SS BOND : angle 1.58864 ( 78) hydrogen bonds : bond 0.03625 ( 1034) hydrogen bonds : angle 5.33358 ( 2877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.6961 (m-80) cc_final: 0.6320 (m-80) REVERT: A 237 ARG cc_start: 0.7685 (mtt90) cc_final: 0.7213 (mtm-85) REVERT: A 269 TYR cc_start: 0.8584 (m-80) cc_final: 0.8352 (m-10) REVERT: A 493 GLN cc_start: 0.7334 (mm-40) cc_final: 0.7104 (mm-40) REVERT: A 529 LYS cc_start: 0.8546 (mttt) cc_final: 0.8275 (mmtt) REVERT: A 558 LYS cc_start: 0.8891 (tttt) cc_final: 0.8372 (mmmt) REVERT: A 675 GLN cc_start: 0.8035 (mt0) cc_final: 0.7823 (mt0) REVERT: A 780 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8409 (mm-30) REVERT: A 790 LYS cc_start: 0.8690 (pttt) cc_final: 0.8369 (pttp) REVERT: A 804 GLN cc_start: 0.8661 (mt0) cc_final: 0.8338 (mt0) REVERT: A 811 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.6585 (mttt) REVERT: A 957 GLN cc_start: 0.8378 (tp-100) cc_final: 0.8075 (tt0) REVERT: A 1050 MET cc_start: 0.9387 (ptm) cc_final: 0.9000 (ptp) REVERT: A 1073 LYS cc_start: 0.8819 (tttt) cc_final: 0.8570 (ttmm) REVERT: B 118 LEU cc_start: 0.7763 (tp) cc_final: 0.7434 (mm) REVERT: B 307 THR cc_start: 0.9225 (m) cc_final: 0.8999 (t) REVERT: B 332 ILE cc_start: 0.6480 (OUTLIER) cc_final: 0.6262 (tt) REVERT: B 364 ASP cc_start: 0.8357 (t0) cc_final: 0.8139 (t0) REVERT: B 400 PHE cc_start: 0.8490 (p90) cc_final: 0.8225 (p90) REVERT: B 434 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7152 (mt) REVERT: B 554 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7730 (pt0) REVERT: B 568 ASP cc_start: 0.8011 (m-30) cc_final: 0.7495 (m-30) REVERT: B 574 ASP cc_start: 0.8217 (t70) cc_final: 0.7751 (t0) REVERT: B 950 ASP cc_start: 0.8529 (t70) cc_final: 0.8173 (m-30) REVERT: B 979 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7805 (t0) REVERT: B 990 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7454 (tt0) REVERT: B 1003 SER cc_start: 0.9011 (t) cc_final: 0.8734 (m) REVERT: C 32 PHE cc_start: 0.7585 (m-80) cc_final: 0.7155 (m-80) REVERT: C 63 THR cc_start: 0.8325 (m) cc_final: 0.8016 (p) REVERT: C 117 LEU cc_start: 0.7875 (tp) cc_final: 0.7313 (mp) REVERT: C 118 LEU cc_start: 0.8177 (tp) cc_final: 0.7966 (tt) REVERT: C 132 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7667 (mt-10) REVERT: C 133 PHE cc_start: 0.6075 (m-80) cc_final: 0.5527 (t80) REVERT: C 192 PHE cc_start: 0.7740 (m-80) cc_final: 0.7392 (m-80) REVERT: C 205 SER cc_start: 0.8781 (p) cc_final: 0.8431 (t) REVERT: C 281 GLU cc_start: 0.6801 (pm20) cc_final: 0.6373 (pm20) REVERT: C 335 LEU cc_start: 0.8343 (mt) cc_final: 0.7634 (tt) REVERT: C 427 ASP cc_start: 0.7306 (m-30) cc_final: 0.6919 (t0) REVERT: C 780 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8098 (mm-30) REVERT: C 814 LYS cc_start: 0.8333 (mttt) cc_final: 0.7974 (mmmt) REVERT: C 990 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7187 (tt0) outliers start: 54 outliers final: 44 residues processed: 239 average time/residue: 0.1495 time to fit residues: 59.2892 Evaluate side-chains 235 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 42 optimal weight: 7.9990 chunk 278 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 271 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 259 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 168 optimal weight: 0.5980 chunk 243 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.148178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.105466 restraints weight = 33549.769| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.53 r_work: 0.3060 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23604 Z= 0.114 Angle : 0.514 10.435 32137 Z= 0.267 Chirality : 0.044 0.215 3671 Planarity : 0.004 0.048 4144 Dihedral : 4.815 58.486 3142 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.90 % Allowed : 11.66 % Favored : 86.44 % 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: 0.19 (0.15), residues: 2878 helix: 1.97 (0.20), residues: 687 sheet: 0.13 (0.19), residues: 653 loop : -0.73 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 577 TYR 0.018 0.001 TYR B1067 PHE 0.016 0.001 PHE B 400 TRP 0.031 0.002 TRP C 436 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00257 (23565) covalent geometry : angle 0.50714 (32059) SS BOND : bond 0.00267 ( 39) SS BOND : angle 1.72727 ( 78) hydrogen bonds : bond 0.03456 ( 1034) hydrogen bonds : angle 5.20398 ( 2877) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.6774 (m-80) cc_final: 0.6183 (m-80) REVERT: A 237 ARG cc_start: 0.7689 (mtt90) cc_final: 0.7211 (mtm-85) REVERT: A 269 TYR cc_start: 0.8555 (m-80) cc_final: 0.8307 (m-10) REVERT: A 493 GLN cc_start: 0.7337 (mm-40) cc_final: 0.7124 (mm-40) REVERT: A 529 LYS cc_start: 0.8519 (mttt) cc_final: 0.8205 (mmtt) REVERT: A 558 LYS cc_start: 0.8904 (tttt) cc_final: 0.8368 (mmmt) REVERT: A 675 GLN cc_start: 0.8072 (mt0) cc_final: 0.7859 (mt0) REVERT: A 780 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8421 (mm-30) REVERT: A 790 LYS cc_start: 0.8686 (pttt) cc_final: 0.8338 (pttp) REVERT: A 804 GLN cc_start: 0.8656 (mt0) cc_final: 0.8339 (mt0) REVERT: A 811 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.6628 (mttt) REVERT: A 957 GLN cc_start: 0.8339 (tp-100) cc_final: 0.8039 (tt0) REVERT: A 1050 MET cc_start: 0.9391 (ptm) cc_final: 0.8990 (ptp) REVERT: A 1073 LYS cc_start: 0.8818 (tttt) cc_final: 0.8557 (ttmm) REVERT: B 118 LEU cc_start: 0.7692 (tp) cc_final: 0.7368 (mm) REVERT: B 271 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8505 (mp10) REVERT: B 307 THR cc_start: 0.9231 (m) cc_final: 0.8993 (t) REVERT: B 332 ILE cc_start: 0.6416 (OUTLIER) cc_final: 0.6201 (tt) REVERT: B 364 ASP cc_start: 0.8340 (t0) cc_final: 0.7948 (t0) REVERT: B 400 PHE cc_start: 0.8431 (p90) cc_final: 0.8154 (p90) REVERT: B 434 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7158 (mt) REVERT: B 554 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7648 (pt0) REVERT: B 568 ASP cc_start: 0.7982 (m-30) cc_final: 0.7474 (m-30) REVERT: B 574 ASP cc_start: 0.8191 (t70) cc_final: 0.7752 (t0) REVERT: B 950 ASP cc_start: 0.8513 (t70) cc_final: 0.8052 (m-30) REVERT: B 990 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7412 (tt0) REVERT: B 1003 SER cc_start: 0.8956 (t) cc_final: 0.8671 (m) REVERT: C 32 PHE cc_start: 0.7493 (m-80) cc_final: 0.7117 (m-80) REVERT: C 63 THR cc_start: 0.8315 (m) cc_final: 0.8024 (p) REVERT: C 117 LEU cc_start: 0.7881 (tp) cc_final: 0.7323 (mp) REVERT: C 118 LEU cc_start: 0.8160 (tp) cc_final: 0.7954 (tt) REVERT: C 132 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7663 (mt-10) REVERT: C 133 PHE cc_start: 0.6066 (m-80) cc_final: 0.5523 (t80) REVERT: C 205 SER cc_start: 0.8748 (p) cc_final: 0.8359 (t) REVERT: C 239 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7773 (tm-30) REVERT: C 281 GLU cc_start: 0.6854 (pm20) cc_final: 0.6421 (pm20) REVERT: C 335 LEU cc_start: 0.8273 (mt) cc_final: 0.7573 (tt) REVERT: C 398 ASP cc_start: 0.8448 (m-30) cc_final: 0.7966 (m-30) REVERT: C 427 ASP cc_start: 0.7302 (m-30) cc_final: 0.6960 (t0) REVERT: C 780 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8128 (mm-30) REVERT: C 814 LYS cc_start: 0.8281 (mttt) cc_final: 0.7946 (mmmt) REVERT: C 990 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7167 (tt0) REVERT: C 1072 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8275 (mp0) outliers start: 49 outliers final: 38 residues processed: 235 average time/residue: 0.1478 time to fit residues: 56.7663 Evaluate side-chains 231 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 184 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 151 optimal weight: 0.0370 chunk 94 optimal weight: 0.7980 chunk 4 optimal weight: 0.0980 chunk 146 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 290 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 439 ASN ** 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 = 0.3916 r_free = 0.3916 target = 0.149094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106712 restraints weight = 33427.117| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.53 r_work: 0.3077 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23604 Z= 0.114 Angle : 0.511 10.617 32137 Z= 0.263 Chirality : 0.043 0.209 3671 Planarity : 0.004 0.057 4144 Dihedral : 4.684 58.936 3141 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.67 % Allowed : 12.17 % Favored : 86.17 % 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: 0.25 (0.15), residues: 2878 helix: 2.05 (0.20), residues: 687 sheet: 0.16 (0.19), residues: 656 loop : -0.70 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 34 TYR 0.020 0.001 TYR A 170 PHE 0.015 0.001 PHE A 400 TRP 0.030 0.002 TRP C 436 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00258 (23565) covalent geometry : angle 0.50526 (32059) SS BOND : bond 0.00279 ( 39) SS BOND : angle 1.57636 ( 78) hydrogen bonds : bond 0.03385 ( 1034) hydrogen bonds : angle 5.13409 ( 2877) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.6790 (m-80) cc_final: 0.6196 (m-80) REVERT: A 237 ARG cc_start: 0.7725 (mtt90) cc_final: 0.7223 (mtm-85) REVERT: A 269 TYR cc_start: 0.8527 (m-80) cc_final: 0.8261 (m-10) REVERT: A 493 GLN cc_start: 0.7345 (mm-40) cc_final: 0.7128 (mm-40) REVERT: A 529 LYS cc_start: 0.8515 (mttt) cc_final: 0.8205 (mmtt) REVERT: A 558 LYS cc_start: 0.8890 (tttt) cc_final: 0.8344 (mmmt) REVERT: A 675 GLN cc_start: 0.8017 (mt0) cc_final: 0.7778 (mt0) REVERT: A 780 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8421 (mm-30) REVERT: A 790 LYS cc_start: 0.8690 (pttt) cc_final: 0.8367 (pttp) REVERT: A 804 GLN cc_start: 0.8639 (mt0) cc_final: 0.8342 (mt0) REVERT: A 811 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.6614 (mttt) REVERT: A 957 GLN cc_start: 0.8347 (tp-100) cc_final: 0.8059 (tt0) REVERT: A 1050 MET cc_start: 0.9394 (ptm) cc_final: 0.8996 (ptp) REVERT: A 1073 LYS cc_start: 0.8825 (tttt) cc_final: 0.8558 (ttmm) REVERT: A 1094 VAL cc_start: 0.8618 (m) cc_final: 0.8269 (p) REVERT: B 118 LEU cc_start: 0.7660 (tp) cc_final: 0.7356 (mm) REVERT: B 271 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8546 (mp10) REVERT: B 307 THR cc_start: 0.9222 (m) cc_final: 0.8993 (t) REVERT: B 332 ILE cc_start: 0.6334 (OUTLIER) cc_final: 0.6109 (tt) REVERT: B 364 ASP cc_start: 0.8338 (t0) cc_final: 0.7972 (t0) REVERT: B 400 PHE cc_start: 0.8443 (p90) cc_final: 0.8169 (p90) REVERT: B 568 ASP cc_start: 0.7970 (m-30) cc_final: 0.7460 (m-30) REVERT: B 574 ASP cc_start: 0.8190 (t70) cc_final: 0.7741 (t0) REVERT: B 950 ASP cc_start: 0.8522 (t70) cc_final: 0.8107 (m-30) REVERT: B 990 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7421 (tt0) REVERT: B 1003 SER cc_start: 0.8961 (t) cc_final: 0.8669 (m) REVERT: C 32 PHE cc_start: 0.7440 (m-80) cc_final: 0.7105 (m-80) REVERT: C 63 THR cc_start: 0.8344 (m) cc_final: 0.8052 (p) REVERT: C 117 LEU cc_start: 0.7893 (tp) cc_final: 0.7320 (mp) REVERT: C 118 LEU cc_start: 0.8167 (tp) cc_final: 0.7960 (tt) REVERT: C 132 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7656 (mt-10) REVERT: C 205 SER cc_start: 0.8727 (p) cc_final: 0.8375 (t) REVERT: C 239 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7837 (tm-30) REVERT: C 281 GLU cc_start: 0.6899 (pm20) cc_final: 0.6488 (pm20) REVERT: C 335 LEU cc_start: 0.8264 (mt) cc_final: 0.7529 (tt) REVERT: C 398 ASP cc_start: 0.8462 (m-30) cc_final: 0.8006 (m-30) REVERT: C 427 ASP cc_start: 0.7343 (m-30) cc_final: 0.6956 (t0) REVERT: C 690 GLN cc_start: 0.7693 (mt0) cc_final: 0.7390 (mm-40) REVERT: C 780 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8140 (mm-30) REVERT: C 814 LYS cc_start: 0.8253 (mttt) cc_final: 0.7951 (mmmt) REVERT: C 990 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7152 (tt0) REVERT: C 1072 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8266 (mp0) outliers start: 43 outliers final: 38 residues processed: 231 average time/residue: 0.1457 time to fit residues: 55.6073 Evaluate side-chains 229 residues out of total 2581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 8 optimal weight: 9.9990 chunk 255 optimal weight: 0.7980 chunk 250 optimal weight: 6.9990 chunk 172 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 264 optimal weight: 4.9990 chunk 280 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.150012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100849 restraints weight = 33495.439| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.42 r_work: 0.3087 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 23604 Z= 0.106 Angle : 0.496 10.795 32137 Z= 0.257 Chirality : 0.043 0.208 3671 Planarity : 0.004 0.049 4144 Dihedral : 4.595 59.373 3141 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.82 % Allowed : 12.24 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 2878 helix: 2.12 (0.20), residues: 692 sheet: 0.21 (0.19), residues: 656 loop : -0.65 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.018 0.001 TYR B1067 PHE 0.015 0.001 PHE B 400 TRP 0.027 0.002 TRP C 436 HIS 0.011 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00238 (23565) covalent geometry : angle 0.49165 (32059) SS BOND : bond 0.00262 ( 39) SS BOND : angle 1.34795 ( 78) hydrogen bonds : bond 0.03293 ( 1034) hydrogen bonds : angle 5.04342 ( 2877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6496.65 seconds wall clock time: 111 minutes 44.39 seconds (6704.39 seconds total)