Starting phenix.real_space_refine on Mon Sep 14 12:20:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wrf_32725/09_2026/7wrf_32725.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrf_32725/09_2026/7wrf_32725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wrf_32725/09_2026/7wrf_32725.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wrf_32725/09_2026/7wrf_32725.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wrf_32725/09_2026/7wrf_32725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrf_32725/09_2026/7wrf_32725.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wrf_32725/09_2026/7wrf_32725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrf_32725/09_2026/7wrf_32725.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 S 140 5.16 5 Na 1 4.78 5 C 19820 2.51 5 N 5052 2.21 5 O 5452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30469 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "B" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "C" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "D" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' CA': 1, ' NA': 1, 'KX7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.88, per 1000 atoms: 0.23 Number of scatterers: 30469 At special positions: 0 Unit cell: (151.086, 151.086, 156.156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 140 16.00 Na 1 11.00 O 5452 8.00 N 5052 7.00 C 19820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.03 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.02 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.02 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.02 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: 2.83 Conformation dependent library (CDL) restraints added in 1.5 seconds 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7080 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 4 sheets defined 70.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 125 through 136 removed outlier: 3.860A pdb=" N LEU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 204 removed outlier: 3.735A pdb=" N TYR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.695A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.830A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 removed outlier: 3.576A pdb=" N LEU A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 385 removed outlier: 4.102A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.787A pdb=" N TYR A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.728A pdb=" N ALA A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 502 through 516 removed outlier: 3.680A pdb=" N TYR A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 532 Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.586A pdb=" N ALA A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 582 removed outlier: 3.718A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 602 Processing helix chain 'A' and resid 607 through 636 removed outlier: 3.773A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 636 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.766A pdb=" N ILE A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 removed outlier: 3.635A pdb=" N GLY A 684 " --> pdb=" O LYS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.692A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.603A pdb=" N VAL A 705 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 702 through 706' Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 759 removed outlier: 3.540A pdb=" N ASP A 759 " --> pdb=" O VAL A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 790 Processing helix chain 'A' and resid 791 through 795 Processing helix chain 'A' and resid 796 through 817 removed outlier: 3.523A pdb=" N VAL A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 847 removed outlier: 4.187A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 853 through 860 Processing helix chain 'A' and resid 863 through 890 Processing helix chain 'A' and resid 895 through 901 Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 925 through 929 removed outlier: 3.955A pdb=" N HIS A 928 " --> pdb=" O ASP A 925 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS A 929 " --> pdb=" O PHE A 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 925 through 929' Processing helix chain 'A' and resid 952 through 969 Proline residue: A 958 - end of helix Processing helix chain 'A' and resid 969 through 1006 removed outlier: 3.620A pdb=" N LEU A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1014 No H-bonds generated for 'chain 'A' and resid 1012 through 1014' Processing helix chain 'A' and resid 1015 through 1030 removed outlier: 3.631A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1071 removed outlier: 3.859A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A1071 " --> pdb=" O ILE A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1104 removed outlier: 3.635A pdb=" N MET A1078 " --> pdb=" O ASN A1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 136 removed outlier: 3.860A pdb=" N LEU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 204 removed outlier: 3.734A pdb=" N TYR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.695A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.829A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 removed outlier: 3.576A pdb=" N LEU B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 370 through 385 removed outlier: 4.102A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.786A pdb=" N TYR B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.728A pdb=" N ALA B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 468 Processing helix chain 'B' and resid 470 through 481 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 502 through 516 removed outlier: 3.680A pdb=" N TYR B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 532 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.585A pdb=" N ALA B 563 " --> pdb=" O HIS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 582 removed outlier: 3.719A pdb=" N VAL B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 607 through 636 removed outlier: 3.774A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 636 " --> pdb=" O CYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.766A pdb=" N ILE B 669 " --> pdb=" O ASP B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 removed outlier: 3.635A pdb=" N GLY B 684 " --> pdb=" O LYS B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.693A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.603A pdb=" N VAL B 705 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 706 " --> pdb=" O PRO B 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 702 through 706' Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 759 removed outlier: 3.541A pdb=" N ASP B 759 " --> pdb=" O VAL B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 790 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 796 through 817 removed outlier: 3.523A pdb=" N VAL B 800 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 847 removed outlier: 4.186A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 853 through 860 Processing helix chain 'B' and resid 863 through 890 Processing helix chain 'B' and resid 895 through 901 Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 925 through 929 removed outlier: 3.955A pdb=" N HIS B 928 " --> pdb=" O ASP B 925 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS B 929 " --> pdb=" O PHE B 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 925 through 929' Processing helix chain 'B' and resid 952 through 969 Proline residue: B 958 - end of helix Processing helix chain 'B' and resid 969 through 1006 removed outlier: 3.620A pdb=" N LEU B 975 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1014 No H-bonds generated for 'chain 'B' and resid 1012 through 1014' Processing helix chain 'B' and resid 1015 through 1030 removed outlier: 3.631A pdb=" N ALA B1019 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1071 removed outlier: 3.859A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET B1059 " --> pdb=" O TRP B1055 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA B1071 " --> pdb=" O ILE B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1104 removed outlier: 3.635A pdb=" N MET B1078 " --> pdb=" O ASN B1074 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 136 removed outlier: 3.860A pdb=" N LEU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 204 removed outlier: 3.736A pdb=" N TYR C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.695A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 341 removed outlier: 3.829A pdb=" N VAL C 338 " --> pdb=" O GLN C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 removed outlier: 3.575A pdb=" N LEU C 362 " --> pdb=" O LEU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 370 through 385 removed outlier: 4.103A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 402 through 418 removed outlier: 3.786A pdb=" N TYR C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.728A pdb=" N ALA C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 468 Processing helix chain 'C' and resid 470 through 481 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 502 through 516 removed outlier: 3.681A pdb=" N TYR C 506 " --> pdb=" O SER C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 532 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.585A pdb=" N ALA C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 582 removed outlier: 3.718A pdb=" N VAL C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 602 Processing helix chain 'C' and resid 607 through 636 removed outlier: 3.774A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 636 " --> pdb=" O CYS C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 644 Processing helix chain 'C' and resid 655 through 663 Processing helix chain 'C' and resid 665 through 670 removed outlier: 3.766A pdb=" N ILE C 669 " --> pdb=" O ASP C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 684 removed outlier: 3.635A pdb=" N GLY C 684 " --> pdb=" O LYS C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 701 removed outlier: 3.694A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 706 removed outlier: 3.604A pdb=" N VAL C 705 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY C 706 " --> pdb=" O PRO C 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 702 through 706' Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 759 removed outlier: 3.540A pdb=" N ASP C 759 " --> pdb=" O VAL C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 765 through 790 Processing helix chain 'C' and resid 791 through 795 Processing helix chain 'C' and resid 796 through 817 removed outlier: 3.523A pdb=" N VAL C 800 " --> pdb=" O ASP C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 847 removed outlier: 4.186A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 850 No H-bonds generated for 'chain 'C' and resid 848 through 850' Processing helix chain 'C' and resid 853 through 860 Processing helix chain 'C' and resid 863 through 890 Processing helix chain 'C' and resid 895 through 901 Processing helix chain 'C' and resid 904 through 910 Processing helix chain 'C' and resid 925 through 929 removed outlier: 3.955A pdb=" N HIS C 928 " --> pdb=" O ASP C 925 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS C 929 " --> pdb=" O PHE C 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 925 through 929' Processing helix chain 'C' and resid 952 through 969 Proline residue: C 958 - end of helix Processing helix chain 'C' and resid 969 through 1006 removed outlier: 3.620A pdb=" N LEU C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1014 No H-bonds generated for 'chain 'C' and resid 1012 through 1014' Processing helix chain 'C' and resid 1015 through 1030 removed outlier: 3.631A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1071 removed outlier: 3.859A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET C1059 " --> pdb=" O TRP C1055 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C1071 " --> pdb=" O ILE C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1104 removed outlier: 3.634A pdb=" N MET C1078 " --> pdb=" O ASN C1074 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 136 removed outlier: 3.860A pdb=" N LEU D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 204 removed outlier: 3.736A pdb=" N TYR D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 309 through 322 removed outlier: 3.695A pdb=" N LEU D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 341 removed outlier: 3.829A pdb=" N VAL D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 removed outlier: 3.575A pdb=" N LEU D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 369 Processing helix chain 'D' and resid 370 through 385 removed outlier: 4.102A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 402 through 418 removed outlier: 3.786A pdb=" N TYR D 410 " --> pdb=" O ASN D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.728A pdb=" N ALA D 442 " --> pdb=" O GLN D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 468 Processing helix chain 'D' and resid 470 through 481 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'D' and resid 502 through 516 removed outlier: 3.680A pdb=" N TYR D 506 " --> pdb=" O SER D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 532 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.585A pdb=" N ALA D 563 " --> pdb=" O HIS D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 582 removed outlier: 3.718A pdb=" N VAL D 579 " --> pdb=" O GLU D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 602 Processing helix chain 'D' and resid 607 through 636 removed outlier: 3.774A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP D 636 " --> pdb=" O CYS D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 644 Processing helix chain 'D' and resid 655 through 663 Processing helix chain 'D' and resid 665 through 670 removed outlier: 3.765A pdb=" N ILE D 669 " --> pdb=" O ASP D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 684 removed outlier: 3.635A pdb=" N GLY D 684 " --> pdb=" O LYS D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 701 removed outlier: 3.694A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 706 removed outlier: 3.603A pdb=" N VAL D 705 " --> pdb=" O ILE D 702 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY D 706 " --> pdb=" O PRO D 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 702 through 706' Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'D' and resid 733 through 759 removed outlier: 3.540A pdb=" N ASP D 759 " --> pdb=" O VAL D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 790 Processing helix chain 'D' and resid 791 through 795 Processing helix chain 'D' and resid 796 through 817 removed outlier: 3.522A pdb=" N VAL D 800 " --> pdb=" O ASP D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 847 removed outlier: 4.186A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 850 No H-bonds generated for 'chain 'D' and resid 848 through 850' Processing helix chain 'D' and resid 853 through 860 Processing helix chain 'D' and resid 863 through 890 Processing helix chain 'D' and resid 895 through 901 Processing helix chain 'D' and resid 904 through 910 Processing helix chain 'D' and resid 925 through 929 removed outlier: 3.955A pdb=" N HIS D 928 " --> pdb=" O ASP D 925 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS D 929 " --> pdb=" O PHE D 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 925 through 929' Processing helix chain 'D' and resid 952 through 969 Proline residue: D 958 - end of helix Processing helix chain 'D' and resid 969 through 1006 removed outlier: 3.620A pdb=" N LEU D 975 " --> pdb=" O LEU D 971 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1014 No H-bonds generated for 'chain 'D' and resid 1012 through 1014' Processing helix chain 'D' and resid 1015 through 1030 removed outlier: 3.631A pdb=" N ALA D1019 " --> pdb=" O PHE D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1046 through 1071 removed outlier: 3.859A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET D1059 " --> pdb=" O TRP D1055 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA D1071 " --> pdb=" O ILE D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1074 through 1104 removed outlier: 3.636A pdb=" N MET D1078 " --> pdb=" O ASN D1074 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121 removed outlier: 6.922A pdb=" N LEU A 120 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 179 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE A 214 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR A 181 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL A 328 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS A 303 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 119 through 121 removed outlier: 6.923A pdb=" N LEU B 120 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE B 179 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE B 214 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR B 181 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL B 328 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS B 303 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 119 through 121 removed outlier: 6.922A pdb=" N LEU C 120 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE C 179 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE C 214 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR C 181 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL C 328 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS C 303 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 119 through 121 removed outlier: 6.921A pdb=" N LEU D 120 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE D 179 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE D 214 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR D 181 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL D 328 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS D 303 " --> pdb=" O VAL D 328 " (cutoff:3.500A) 1768 hydrogen bonds defined for protein. 5244 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: 6.46 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4884 1.31 - 1.44: 8856 1.44 - 1.57: 17236 1.57 - 1.70: 0 1.70 - 1.83: 212 Bond restraints: 31188 Sorted by residual: bond pdb=" N21 KX7 D1202 " pdb=" O23 KX7 D1202 " ideal model delta sigma weight residual 1.208 1.402 -0.194 2.00e-02 2.50e+03 9.36e+01 bond pdb=" N21 KX7 B1202 " pdb=" O23 KX7 B1202 " ideal model delta sigma weight residual 1.208 1.401 -0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" N21 KX7 A1203 " pdb=" O23 KX7 A1203 " ideal model delta sigma weight residual 1.208 1.401 -0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" N21 KX7 C1202 " pdb=" O23 KX7 C1202 " ideal model delta sigma weight residual 1.208 1.401 -0.193 2.00e-02 2.50e+03 9.28e+01 bond pdb=" C05 KX7 D1202 " pdb=" N07 KX7 D1202 " ideal model delta sigma weight residual 1.355 1.495 -0.140 2.00e-02 2.50e+03 4.89e+01 ... (remaining 31183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 39939 1.94 - 3.88: 1912 3.88 - 5.82: 297 5.82 - 7.76: 76 7.76 - 9.71: 28 Bond angle restraints: 42252 Sorted by residual: angle pdb=" N VAL B 791 " pdb=" CA VAL B 791 " pdb=" C VAL B 791 " ideal model delta sigma weight residual 112.96 108.21 4.75 1.00e+00 1.00e+00 2.26e+01 angle pdb=" N VAL A 791 " pdb=" CA VAL A 791 " pdb=" C VAL A 791 " ideal model delta sigma weight residual 112.96 108.25 4.71 1.00e+00 1.00e+00 2.22e+01 angle pdb=" N VAL C 791 " pdb=" CA VAL C 791 " pdb=" C VAL C 791 " ideal model delta sigma weight residual 112.96 108.26 4.70 1.00e+00 1.00e+00 2.21e+01 angle pdb=" N VAL D 791 " pdb=" CA VAL D 791 " pdb=" C VAL D 791 " ideal model delta sigma weight residual 112.96 108.28 4.68 1.00e+00 1.00e+00 2.19e+01 angle pdb=" C ILE A 701 " pdb=" N ILE A 702 " pdb=" CA ILE A 702 " ideal model delta sigma weight residual 120.33 123.78 -3.45 8.00e-01 1.56e+00 1.86e+01 ... (remaining 42247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.57: 17104 14.57 - 29.14: 884 29.14 - 43.71: 272 43.71 - 58.28: 16 58.28 - 72.85: 28 Dihedral angle restraints: 18304 sinusoidal: 7392 harmonic: 10912 Sorted by residual: dihedral pdb=" CA PRO B1012 " pdb=" C PRO B1012 " pdb=" N PHE B1013 " pdb=" CA PHE B1013 " ideal model delta harmonic sigma weight residual -180.00 -150.09 -29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA PRO D1012 " pdb=" C PRO D1012 " pdb=" N PHE D1013 " pdb=" CA PHE D1013 " ideal model delta harmonic sigma weight residual -180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA PRO A1012 " pdb=" C PRO A1012 " pdb=" N PHE A1013 " pdb=" CA PHE A1013 " ideal model delta harmonic sigma weight residual -180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2875 0.045 - 0.090: 1358 0.090 - 0.134: 352 0.134 - 0.179: 99 0.179 - 0.224: 24 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CG LEU A 521 " pdb=" CB LEU A 521 " pdb=" CD1 LEU A 521 " pdb=" CD2 LEU A 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU B 521 " pdb=" CB LEU B 521 " pdb=" CD1 LEU B 521 " pdb=" CD2 LEU B 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU D 521 " pdb=" CB LEU D 521 " pdb=" CD1 LEU D 521 " pdb=" CD2 LEU D 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 4705 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 141 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO D 142 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 142 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 142 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 141 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO A 142 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 141 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO B 142 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 142 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 142 " 0.034 5.00e-02 4.00e+02 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 8661 2.82 - 3.34: 28118 3.34 - 3.86: 48975 3.86 - 4.38: 56324 4.38 - 4.90: 96780 Nonbonded interactions: 238858 Sorted by model distance: nonbonded pdb=" O VAL A1065 " pdb=" OG1 THR A1069 " model vdw 2.294 3.040 nonbonded pdb=" O VAL C1065 " pdb=" OG1 THR C1069 " model vdw 2.295 3.040 nonbonded pdb=" O VAL B1065 " pdb=" OG1 THR B1069 " model vdw 2.295 3.040 nonbonded pdb=" O VAL D1065 " pdb=" OG1 THR D1069 " model vdw 2.295 3.040 nonbonded pdb=" O VAL D 728 " pdb=" OG1 THR D 732 " model vdw 2.324 3.040 ... (remaining 238853 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' and resid 102 through 1201) selection = (chain 'B' and resid 102 through 1201) selection = (chain 'C' and resid 102 through 1201) selection = (chain 'D' and resid 102 through 1201) } 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 29.040 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 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:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.008 0.194 31192 Z= 0.352 Angle : 0.989 9.705 42260 Z= 0.544 Chirality : 0.056 0.224 4708 Planarity : 0.007 0.062 5280 Dihedral : 10.460 72.845 11212 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.12 % Allowed : 1.80 % Favored : 98.08 % 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: -3.74 (0.11), residues: 3656 helix: -2.03 (0.08), residues: 2412 sheet: -1.90 (0.32), residues: 208 loop : -3.28 (0.15), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1008 TYR 0.038 0.003 TYR A 772 PHE 0.031 0.003 PHE B 304 TRP 0.026 0.003 TRP B 377 HIS 0.007 0.002 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00808 / 0.35 (31188) covalent geometry : angle 0.98652 / 0.54 (42252) SS BOND : bond 0.00636 / 0.29 ( 4) SS BOND : angle 4.83437 / 2.79 ( 8) hydrogen bonds : bond 0.14823 / 9.91 ( 1768) hydrogen bonds : angle 6.41497 / 4.41 ( 5244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 827 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.8176 (ttt180) cc_final: 0.7920 (ttp-110) REVERT: A 280 GLN cc_start: 0.8309 (tt0) cc_final: 0.8104 (tm-30) REVERT: A 569 ILE cc_start: 0.9136 (tp) cc_final: 0.8904 (tp) REVERT: A 702 ILE cc_start: 0.8413 (mt) cc_final: 0.8152 (tt) REVERT: A 787 TYR cc_start: 0.7393 (t80) cc_final: 0.7114 (t80) REVERT: A 868 PHE cc_start: 0.8203 (m-10) cc_final: 0.7610 (t80) REVERT: A 1023 MET cc_start: 0.7034 (mmm) cc_final: 0.5993 (mtp) REVERT: B 162 ARG cc_start: 0.8118 (ttt180) cc_final: 0.7887 (ttp-110) REVERT: B 191 TYR cc_start: 0.7537 (t80) cc_final: 0.7231 (t80) REVERT: B 627 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7843 (mt-10) REVERT: B 691 LYS cc_start: 0.7529 (mtpt) cc_final: 0.7271 (mtpt) REVERT: B 702 ILE cc_start: 0.8410 (mt) cc_final: 0.8163 (tt) REVERT: B 787 TYR cc_start: 0.7387 (t80) cc_final: 0.7102 (t80) REVERT: B 868 PHE cc_start: 0.8192 (m-10) cc_final: 0.7601 (t80) REVERT: B 1023 MET cc_start: 0.6992 (mmm) cc_final: 0.5936 (mtp) REVERT: C 191 TYR cc_start: 0.7627 (t80) cc_final: 0.7354 (t80) REVERT: C 280 GLN cc_start: 0.8276 (tt0) cc_final: 0.8063 (tm-30) REVERT: C 569 ILE cc_start: 0.9143 (tp) cc_final: 0.8922 (tp) REVERT: C 627 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7856 (mt-10) REVERT: C 702 ILE cc_start: 0.8404 (mt) cc_final: 0.8160 (tt) REVERT: C 787 TYR cc_start: 0.7411 (t80) cc_final: 0.7151 (t80) REVERT: C 868 PHE cc_start: 0.8177 (m-10) cc_final: 0.7612 (t80) REVERT: C 1023 MET cc_start: 0.6850 (mmm) cc_final: 0.5837 (mtp) REVERT: C 1047 ASN cc_start: 0.7790 (m-40) cc_final: 0.7583 (m110) REVERT: D 191 TYR cc_start: 0.7609 (t80) cc_final: 0.7317 (t80) REVERT: D 280 GLN cc_start: 0.8337 (tt0) cc_final: 0.8136 (tm-30) REVERT: D 569 ILE cc_start: 0.9109 (tp) cc_final: 0.8899 (tp) REVERT: D 702 ILE cc_start: 0.8403 (mt) cc_final: 0.8141 (tt) REVERT: D 787 TYR cc_start: 0.7408 (t80) cc_final: 0.7139 (t80) REVERT: D 868 PHE cc_start: 0.8181 (m-10) cc_final: 0.7621 (t80) REVERT: D 1023 MET cc_start: 0.6889 (mmm) cc_final: 0.5893 (mtp) outliers start: 4 outliers final: 0 residues processed: 827 average time/residue: 0.2135 time to fit residues: 270.5036 Evaluate side-chains 427 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 HIS A 257 HIS A 259 HIS A 438 GLN A 572 ASN A 675 GLN A 987 GLN B 136 HIS B 256 ASN B 257 HIS B 259 HIS B 438 GLN B 572 ASN B 675 GLN B 741 ASN C 136 HIS C 257 HIS C 259 HIS C 294 ASN C 438 GLN C 572 ASN C 675 GLN C 741 ASN D 136 HIS D 257 HIS D 259 HIS D 438 GLN D 572 ASN D 675 GLN D 987 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.159862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.107802 restraints weight = 48820.082| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.42 r_work: 0.3220 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 31192 Z= 0.234 Angle : 0.703 8.924 42260 Z= 0.369 Chirality : 0.044 0.147 4708 Planarity : 0.005 0.054 5280 Dihedral : 6.087 50.303 4024 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.16 % Allowed : 8.26 % Favored : 89.57 % 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: -1.74 (0.13), residues: 3656 helix: -0.19 (0.10), residues: 2440 sheet: -1.89 (0.32), residues: 192 loop : -3.26 (0.15), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 278 TYR 0.016 0.002 TYR B1005 PHE 0.032 0.002 PHE A 752 TRP 0.022 0.002 TRP A 898 HIS 0.005 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.23 (31188) covalent geometry : angle 0.70204 / 0.37 (42252) SS BOND : bond 0.00853 / 0.39 ( 4) SS BOND : angle 2.67642 / 1.55 ( 8) hydrogen bonds : bond 0.05750 / 3.92 ( 1768) hydrogen bonds : angle 4.58802 / 3.16 ( 5244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 458 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8109 (t80) cc_final: 0.7755 (t80) REVERT: A 280 GLN cc_start: 0.8533 (tt0) cc_final: 0.8220 (tp40) REVERT: A 491 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7923 (tp30) REVERT: A 702 ILE cc_start: 0.8508 (mt) cc_final: 0.8272 (tt) REVERT: A 787 TYR cc_start: 0.7927 (t80) cc_final: 0.7467 (t80) REVERT: A 800 VAL cc_start: 0.9312 (t) cc_final: 0.9100 (p) REVERT: A 868 PHE cc_start: 0.8863 (m-10) cc_final: 0.7693 (t80) REVERT: A 914 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8351 (mm-40) REVERT: A 1005 TYR cc_start: 0.6938 (m-10) cc_final: 0.5669 (m-80) REVERT: A 1021 PHE cc_start: 0.7528 (m-80) cc_final: 0.7286 (m-80) REVERT: A 1023 MET cc_start: 0.7040 (mmm) cc_final: 0.5978 (mtp) REVERT: B 491 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7859 (tp30) REVERT: B 569 ILE cc_start: 0.9172 (tp) cc_final: 0.8971 (tp) REVERT: B 702 ILE cc_start: 0.8512 (mt) cc_final: 0.8298 (tt) REVERT: B 787 TYR cc_start: 0.7907 (t80) cc_final: 0.7461 (t80) REVERT: B 801 MET cc_start: 0.8255 (ptm) cc_final: 0.8012 (ptt) REVERT: B 868 PHE cc_start: 0.8845 (m-10) cc_final: 0.7661 (t80) REVERT: B 1005 TYR cc_start: 0.6856 (m-10) cc_final: 0.5647 (m-80) REVERT: B 1021 PHE cc_start: 0.7556 (m-80) cc_final: 0.7312 (m-80) REVERT: B 1023 MET cc_start: 0.6981 (mmm) cc_final: 0.5904 (mtp) REVERT: C 191 TYR cc_start: 0.8126 (t80) cc_final: 0.7823 (t80) REVERT: C 280 GLN cc_start: 0.8520 (tt0) cc_final: 0.8209 (tp40) REVERT: C 353 MET cc_start: 0.6291 (mpp) cc_final: 0.5897 (ptp) REVERT: C 491 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7879 (tp30) REVERT: C 702 ILE cc_start: 0.8498 (mt) cc_final: 0.8297 (tt) REVERT: C 741 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8679 (m-40) REVERT: C 787 TYR cc_start: 0.7909 (t80) cc_final: 0.7460 (t80) REVERT: C 800 VAL cc_start: 0.9308 (t) cc_final: 0.9101 (p) REVERT: C 801 MET cc_start: 0.8419 (ptm) cc_final: 0.8187 (ptt) REVERT: C 864 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8658 (mp) REVERT: C 868 PHE cc_start: 0.8840 (m-10) cc_final: 0.7665 (t80) REVERT: C 1005 TYR cc_start: 0.6855 (m-10) cc_final: 0.5634 (m-80) REVERT: C 1021 PHE cc_start: 0.7564 (m-80) cc_final: 0.7320 (m-80) REVERT: C 1023 MET cc_start: 0.6948 (mmm) cc_final: 0.5876 (mtp) REVERT: D 280 GLN cc_start: 0.8559 (tt0) cc_final: 0.8252 (tp40) REVERT: D 353 MET cc_start: 0.6356 (mpp) cc_final: 0.5974 (ptp) REVERT: D 491 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7921 (tp30) REVERT: D 702 ILE cc_start: 0.8510 (mt) cc_final: 0.8275 (tt) REVERT: D 787 TYR cc_start: 0.7919 (t80) cc_final: 0.7463 (t80) REVERT: D 800 VAL cc_start: 0.9332 (t) cc_final: 0.9103 (p) REVERT: D 868 PHE cc_start: 0.8847 (m-10) cc_final: 0.7688 (t80) REVERT: D 1005 TYR cc_start: 0.6929 (m-10) cc_final: 0.5732 (m-80) REVERT: D 1023 MET cc_start: 0.7059 (mmm) cc_final: 0.5999 (mtp) REVERT: D 1066 LYS cc_start: 0.9007 (mtpp) cc_final: 0.8805 (mmtp) outliers start: 72 outliers final: 38 residues processed: 505 average time/residue: 0.1897 time to fit residues: 152.2618 Evaluate side-chains 435 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 395 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 741 ASN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 63 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 278 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 311 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 294 ASN ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN B 294 ASN ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 571 GLN D 741 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.161761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110448 restraints weight = 48555.480| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.37 r_work: 0.3256 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31192 Z= 0.146 Angle : 0.595 7.856 42260 Z= 0.311 Chirality : 0.040 0.145 4708 Planarity : 0.004 0.048 5280 Dihedral : 5.713 50.284 4024 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.19 % Allowed : 10.28 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.14), residues: 3656 helix: 0.63 (0.10), residues: 2472 sheet: -1.70 (0.34), residues: 192 loop : -2.94 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 160 TYR 0.014 0.002 TYR C1005 PHE 0.015 0.001 PHE B 779 TRP 0.019 0.002 TRP B 898 HIS 0.004 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (31188) covalent geometry : angle 0.59316 / 0.31 (42252) SS BOND : bond 0.01137 / 0.52 ( 4) SS BOND : angle 3.30435 / 1.91 ( 8) hydrogen bonds : bond 0.04546 / 3.08 ( 1768) hydrogen bonds : angle 4.17729 / 2.87 ( 5244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 443 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8479 (tt0) cc_final: 0.8166 (tp40) REVERT: A 353 MET cc_start: 0.6478 (mpp) cc_final: 0.5943 (ptp) REVERT: A 396 MET cc_start: 0.7034 (mmp) cc_final: 0.6168 (mmp) REVERT: A 491 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7847 (tp30) REVERT: A 787 TYR cc_start: 0.7891 (t80) cc_final: 0.7433 (t80) REVERT: A 868 PHE cc_start: 0.8797 (m-10) cc_final: 0.7588 (t80) REVERT: A 1005 TYR cc_start: 0.6884 (m-10) cc_final: 0.5538 (m-80) REVERT: A 1023 MET cc_start: 0.6952 (mmm) cc_final: 0.5867 (mtp) REVERT: A 1068 ASN cc_start: 0.8428 (m-40) cc_final: 0.8206 (m-40) REVERT: B 191 TYR cc_start: 0.7869 (t80) cc_final: 0.7524 (t80) REVERT: B 353 MET cc_start: 0.6412 (mpp) cc_final: 0.5862 (ptp) REVERT: B 396 MET cc_start: 0.7039 (mmp) cc_final: 0.6180 (mmp) REVERT: B 491 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7860 (tp30) REVERT: B 689 ASP cc_start: 0.8366 (t0) cc_final: 0.8122 (t0) REVERT: B 787 TYR cc_start: 0.7927 (t80) cc_final: 0.7479 (t80) REVERT: B 868 PHE cc_start: 0.8764 (m-10) cc_final: 0.7560 (t80) REVERT: B 1005 TYR cc_start: 0.6834 (m-10) cc_final: 0.5413 (m-80) REVERT: B 1023 MET cc_start: 0.6870 (mmm) cc_final: 0.5760 (mtp) REVERT: B 1068 ASN cc_start: 0.8386 (m-40) cc_final: 0.8155 (m-40) REVERT: C 280 GLN cc_start: 0.8502 (tt0) cc_final: 0.8163 (tp40) REVERT: C 353 MET cc_start: 0.6414 (mpp) cc_final: 0.5905 (ptp) REVERT: C 396 MET cc_start: 0.6976 (mmp) cc_final: 0.6136 (mmp) REVERT: C 491 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7882 (tp30) REVERT: C 787 TYR cc_start: 0.7921 (t80) cc_final: 0.7463 (t80) REVERT: C 868 PHE cc_start: 0.8787 (m-10) cc_final: 0.7568 (t80) REVERT: C 1005 TYR cc_start: 0.6880 (m-10) cc_final: 0.5461 (m-80) REVERT: C 1023 MET cc_start: 0.6861 (mmm) cc_final: 0.5755 (mtp) REVERT: C 1068 ASN cc_start: 0.8345 (m-40) cc_final: 0.8106 (m-40) REVERT: D 280 GLN cc_start: 0.8492 (tt0) cc_final: 0.8177 (tp40) REVERT: D 353 MET cc_start: 0.6568 (mpp) cc_final: 0.5992 (ptp) REVERT: D 396 MET cc_start: 0.6968 (mmp) cc_final: 0.6274 (mmp) REVERT: D 689 ASP cc_start: 0.8361 (t0) cc_final: 0.8157 (t0) REVERT: D 787 TYR cc_start: 0.7896 (t80) cc_final: 0.7437 (t80) REVERT: D 868 PHE cc_start: 0.8792 (m-10) cc_final: 0.7581 (t80) REVERT: D 1005 TYR cc_start: 0.6905 (m-10) cc_final: 0.5536 (m-80) REVERT: D 1023 MET cc_start: 0.6951 (mmm) cc_final: 0.5874 (mtp) REVERT: D 1066 LYS cc_start: 0.9005 (mtpp) cc_final: 0.8792 (mmtp) REVERT: D 1068 ASN cc_start: 0.8367 (m-40) cc_final: 0.8141 (m-40) outliers start: 73 outliers final: 43 residues processed: 492 average time/residue: 0.1814 time to fit residues: 144.7696 Evaluate side-chains 424 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 381 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 40 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 51 optimal weight: 0.5980 chunk 134 optimal weight: 8.9990 chunk 333 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 311 optimal weight: 0.0980 chunk 284 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 571 GLN B 990 ASN C 571 GLN C 609 ASN C 990 ASN D 294 ASN D 609 ASN D 635 ASN D 990 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.159154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107481 restraints weight = 48649.259| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.38 r_work: 0.3211 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31192 Z= 0.195 Angle : 0.620 6.398 42260 Z= 0.322 Chirality : 0.042 0.184 4708 Planarity : 0.004 0.045 5280 Dihedral : 5.485 48.488 4024 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.31 % Allowed : 11.93 % Favored : 84.77 % 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: -0.29 (0.14), residues: 3656 helix: 0.91 (0.10), residues: 2476 sheet: -1.47 (0.35), residues: 192 loop : -2.80 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 278 TYR 0.027 0.002 TYR C 191 PHE 0.018 0.002 PHE C 752 TRP 0.020 0.002 TRP A 898 HIS 0.005 0.001 HIS C 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 (31188) covalent geometry : angle 0.61835 / 0.32 (42252) SS BOND : bond 0.00842 / 0.38 ( 4) SS BOND : angle 2.88576 / 1.67 ( 8) hydrogen bonds : bond 0.04907 / 3.33 ( 1768) hydrogen bonds : angle 4.11731 / 2.83 ( 5244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 406 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8536 (tt0) cc_final: 0.8233 (tp40) REVERT: A 304 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.6739 (m-80) REVERT: A 396 MET cc_start: 0.7444 (mmp) cc_final: 0.6750 (mmp) REVERT: A 488 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8055 (tt) REVERT: A 732 THR cc_start: 0.8796 (m) cc_final: 0.8519 (p) REVERT: A 788 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7837 (mmp) REVERT: A 868 PHE cc_start: 0.8833 (m-10) cc_final: 0.7656 (t80) REVERT: A 914 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8288 (mm-40) REVERT: A 1023 MET cc_start: 0.6851 (mmm) cc_final: 0.5792 (mtp) REVERT: A 1068 ASN cc_start: 0.8439 (m-40) cc_final: 0.8180 (m-40) REVERT: B 304 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.6656 (m-80) REVERT: B 396 MET cc_start: 0.7421 (mmp) cc_final: 0.7207 (mmp) REVERT: B 488 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7992 (tt) REVERT: B 491 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7869 (tp30) REVERT: B 702 ILE cc_start: 0.8487 (mp) cc_final: 0.8027 (tt) REVERT: B 732 THR cc_start: 0.8763 (m) cc_final: 0.8443 (p) REVERT: B 788 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7829 (mmp) REVERT: B 801 MET cc_start: 0.8323 (ptt) cc_final: 0.8084 (ptt) REVERT: B 868 PHE cc_start: 0.8811 (m-10) cc_final: 0.7636 (t80) REVERT: B 1023 MET cc_start: 0.6780 (mmm) cc_final: 0.5722 (mtp) REVERT: B 1068 ASN cc_start: 0.8411 (m-40) cc_final: 0.8149 (m-40) REVERT: C 280 GLN cc_start: 0.8539 (tt0) cc_final: 0.8229 (tp40) REVERT: C 396 MET cc_start: 0.7058 (mmp) cc_final: 0.6393 (mmp) REVERT: C 488 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7990 (tt) REVERT: C 491 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7898 (tp30) REVERT: C 732 THR cc_start: 0.8738 (m) cc_final: 0.8446 (p) REVERT: C 788 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7863 (mmp) REVERT: C 868 PHE cc_start: 0.8799 (m-10) cc_final: 0.7625 (t80) REVERT: C 1023 MET cc_start: 0.6760 (mmm) cc_final: 0.5691 (mtp) REVERT: C 1068 ASN cc_start: 0.8408 (m-40) cc_final: 0.8137 (m-40) REVERT: D 280 GLN cc_start: 0.8538 (tt0) cc_final: 0.8241 (tp40) REVERT: D 304 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: D 395 LYS cc_start: 0.8608 (mmmm) cc_final: 0.8364 (mmmm) REVERT: D 396 MET cc_start: 0.7305 (mmp) cc_final: 0.6776 (mmp) REVERT: D 488 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7981 (tt) REVERT: D 702 ILE cc_start: 0.8507 (mp) cc_final: 0.8022 (tt) REVERT: D 732 THR cc_start: 0.8817 (m) cc_final: 0.8487 (p) REVERT: D 788 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7857 (mmp) REVERT: D 868 PHE cc_start: 0.8841 (m-10) cc_final: 0.7658 (t80) REVERT: D 914 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8212 (mm-40) REVERT: D 1023 MET cc_start: 0.6950 (mmm) cc_final: 0.5865 (mtp) REVERT: D 1066 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8819 (mmtp) REVERT: D 1068 ASN cc_start: 0.8430 (m-40) cc_final: 0.8167 (m-40) outliers start: 110 outliers final: 58 residues processed: 483 average time/residue: 0.1811 time to fit residues: 141.6949 Evaluate side-chains 452 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 383 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 788 MET Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 54 optimal weight: 6.9990 chunk 348 optimal weight: 1.9990 chunk 340 optimal weight: 4.9990 chunk 252 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 336 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 280 optimal weight: 2.9990 chunk 274 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN D 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.160424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107621 restraints weight = 49412.757| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.47 r_work: 0.3222 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31192 Z= 0.157 Angle : 0.585 6.614 42260 Z= 0.303 Chirality : 0.040 0.185 4708 Planarity : 0.004 0.044 5280 Dihedral : 5.414 51.678 4024 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.85 % Allowed : 13.67 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3656 helix: 1.15 (0.11), residues: 2476 sheet: -1.45 (0.35), residues: 192 loop : -2.73 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1046 TYR 0.030 0.002 TYR C 191 PHE 0.025 0.001 PHE B1021 TRP 0.020 0.001 TRP A 898 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (31188) covalent geometry : angle 0.58249 / 0.30 (42252) SS BOND : bond 0.00992 / 0.45 ( 4) SS BOND : angle 3.69354 / 2.12 ( 8) hydrogen bonds : bond 0.04426 / 3.01 ( 1768) hydrogen bonds : angle 3.99231 / 2.75 ( 5244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 390 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8521 (tt0) cc_final: 0.8197 (tp40) REVERT: A 304 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.6822 (m-80) REVERT: A 488 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7898 (tt) REVERT: A 689 ASP cc_start: 0.8331 (t0) cc_final: 0.8022 (m-30) REVERT: A 732 THR cc_start: 0.8852 (m) cc_final: 0.8598 (p) REVERT: A 868 PHE cc_start: 0.8823 (m-10) cc_final: 0.7660 (t80) REVERT: A 1021 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7299 (t80) REVERT: A 1023 MET cc_start: 0.6760 (mmm) cc_final: 0.5742 (mtp) REVERT: A 1068 ASN cc_start: 0.8343 (m-40) cc_final: 0.8067 (m-40) REVERT: B 304 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.6719 (m-80) REVERT: B 488 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7875 (tt) REVERT: B 491 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7837 (tp30) REVERT: B 689 ASP cc_start: 0.8375 (t0) cc_final: 0.8055 (m-30) REVERT: B 702 ILE cc_start: 0.8485 (mp) cc_final: 0.8043 (tt) REVERT: B 732 THR cc_start: 0.8803 (m) cc_final: 0.8578 (p) REVERT: B 788 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7834 (mmp) REVERT: B 801 MET cc_start: 0.8400 (ptt) cc_final: 0.8187 (ptt) REVERT: B 868 PHE cc_start: 0.8814 (m-10) cc_final: 0.7631 (t80) REVERT: B 1023 MET cc_start: 0.6755 (mmm) cc_final: 0.5731 (mtp) REVERT: B 1068 ASN cc_start: 0.8261 (m-40) cc_final: 0.7970 (m-40) REVERT: C 280 GLN cc_start: 0.8532 (tt0) cc_final: 0.8219 (tp40) REVERT: C 396 MET cc_start: 0.7306 (mmp) cc_final: 0.6813 (mmp) REVERT: C 488 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7948 (tt) REVERT: C 491 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7858 (tp30) REVERT: C 689 ASP cc_start: 0.8317 (t0) cc_final: 0.7994 (m-30) REVERT: C 732 THR cc_start: 0.8792 (m) cc_final: 0.8578 (p) REVERT: C 788 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7834 (mmp) REVERT: C 801 MET cc_start: 0.8359 (ptt) cc_final: 0.8040 (ptt) REVERT: C 868 PHE cc_start: 0.8803 (m-10) cc_final: 0.7627 (t80) REVERT: C 1023 MET cc_start: 0.6760 (mmm) cc_final: 0.5738 (mtp) REVERT: C 1068 ASN cc_start: 0.8288 (m-40) cc_final: 0.8006 (m-40) REVERT: D 280 GLN cc_start: 0.8532 (tt0) cc_final: 0.8201 (tp40) REVERT: D 294 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7517 (p0) REVERT: D 304 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.6800 (m-80) REVERT: D 396 MET cc_start: 0.7252 (mmp) cc_final: 0.6941 (mmp) REVERT: D 488 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8016 (tt) REVERT: D 689 ASP cc_start: 0.8331 (t0) cc_final: 0.7997 (m-30) REVERT: D 702 ILE cc_start: 0.8441 (mp) cc_final: 0.7966 (tt) REVERT: D 732 THR cc_start: 0.8853 (m) cc_final: 0.8609 (p) REVERT: D 868 PHE cc_start: 0.8843 (m-10) cc_final: 0.7661 (t80) REVERT: D 1021 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.6627 (t80) REVERT: D 1023 MET cc_start: 0.6825 (mmm) cc_final: 0.5794 (mtp) REVERT: D 1049 ASP cc_start: 0.7280 (m-30) cc_final: 0.6925 (m-30) REVERT: D 1068 ASN cc_start: 0.8304 (m-40) cc_final: 0.8028 (m-40) outliers start: 95 outliers final: 47 residues processed: 450 average time/residue: 0.1815 time to fit residues: 132.3424 Evaluate side-chains 429 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 370 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain B residue 1078 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 788 MET Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1045 PHE Chi-restraints excluded: chain D residue 1078 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 117 optimal weight: 20.0000 chunk 303 optimal weight: 20.0000 chunk 360 optimal weight: 0.7980 chunk 187 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 337 optimal weight: 5.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 ASN B 635 ASN C 635 ASN C 990 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.155680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102434 restraints weight = 49502.611| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.52 r_work: 0.3148 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 31192 Z= 0.324 Angle : 0.717 7.336 42260 Z= 0.371 Chirality : 0.046 0.205 4708 Planarity : 0.005 0.046 5280 Dihedral : 5.705 56.785 4024 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.49 % Allowed : 13.58 % Favored : 82.93 % 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 (0.14), residues: 3656 helix: 0.91 (0.10), residues: 2468 sheet: -1.81 (0.33), residues: 192 loop : -2.79 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 901 TYR 0.027 0.002 TYR C 191 PHE 0.022 0.002 PHE D1013 TRP 0.024 0.002 TRP A 898 HIS 0.008 0.001 HIS B 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00785 / 0.32 (31188) covalent geometry : angle 0.71518 / 0.37 (42252) SS BOND : bond 0.00940 / 0.43 ( 4) SS BOND : angle 4.14767 / 2.39 ( 8) hydrogen bonds : bond 0.05810 / 3.95 ( 1768) hydrogen bonds : angle 4.32757 / 2.99 ( 5244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 379 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8628 (tt0) cc_final: 0.8307 (tp40) REVERT: A 304 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.6717 (m-80) REVERT: A 353 MET cc_start: 0.6768 (mpp) cc_final: 0.6092 (pmm) REVERT: A 395 LYS cc_start: 0.8623 (mmmm) cc_final: 0.8294 (mmmm) REVERT: A 488 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7939 (tt) REVERT: A 613 GLU cc_start: 0.8590 (mp0) cc_final: 0.8224 (mp0) REVERT: A 689 ASP cc_start: 0.8451 (t0) cc_final: 0.8147 (m-30) REVERT: A 732 THR cc_start: 0.8912 (m) cc_final: 0.8619 (p) REVERT: A 868 PHE cc_start: 0.8875 (m-10) cc_final: 0.7725 (t80) REVERT: A 1021 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7419 (t80) REVERT: A 1023 MET cc_start: 0.7061 (mmm) cc_final: 0.5941 (mtp) REVERT: A 1059 MET cc_start: 0.7522 (mpp) cc_final: 0.7147 (mmm) REVERT: B 141 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7885 (p) REVERT: B 304 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: B 353 MET cc_start: 0.6704 (mpp) cc_final: 0.6223 (pmm) REVERT: B 401 ASP cc_start: 0.8329 (t70) cc_final: 0.8012 (m-30) REVERT: B 402 GLU cc_start: 0.7957 (tt0) cc_final: 0.7690 (tt0) REVERT: B 488 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7851 (tt) REVERT: B 689 ASP cc_start: 0.8430 (t0) cc_final: 0.8080 (m-30) REVERT: B 702 ILE cc_start: 0.8468 (mp) cc_final: 0.8051 (tt) REVERT: B 732 THR cc_start: 0.8868 (m) cc_final: 0.8623 (p) REVERT: B 1023 MET cc_start: 0.6995 (mmm) cc_final: 0.5892 (mtp) REVERT: B 1046 ARG cc_start: 0.7309 (ttm170) cc_final: 0.7019 (ttm110) REVERT: B 1059 MET cc_start: 0.7471 (mpp) cc_final: 0.7103 (mmm) REVERT: C 280 GLN cc_start: 0.8612 (tt0) cc_final: 0.8288 (tp40) REVERT: C 353 MET cc_start: 0.6738 (mpp) cc_final: 0.6090 (pmm) REVERT: C 395 LYS cc_start: 0.8460 (mmmm) cc_final: 0.8234 (mmmm) REVERT: C 401 ASP cc_start: 0.8278 (t70) cc_final: 0.7947 (m-30) REVERT: C 402 GLU cc_start: 0.7989 (tt0) cc_final: 0.7721 (tt0) REVERT: C 488 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7866 (tt) REVERT: C 491 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7947 (tp30) REVERT: C 627 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8603 (mp0) REVERT: C 646 TYR cc_start: 0.6096 (t80) cc_final: 0.5754 (t80) REVERT: C 689 ASP cc_start: 0.8406 (t0) cc_final: 0.8065 (m-30) REVERT: C 732 THR cc_start: 0.8817 (m) cc_final: 0.8572 (p) REVERT: C 801 MET cc_start: 0.8445 (ptt) cc_final: 0.8178 (ptt) REVERT: C 868 PHE cc_start: 0.8882 (m-10) cc_final: 0.7738 (t80) REVERT: C 1023 MET cc_start: 0.6969 (mmm) cc_final: 0.5829 (mtp) REVERT: C 1059 MET cc_start: 0.7501 (mpp) cc_final: 0.7151 (mmm) REVERT: D 280 GLN cc_start: 0.8612 (tt0) cc_final: 0.8305 (tp40) REVERT: D 304 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.6703 (m-80) REVERT: D 353 MET cc_start: 0.6731 (mpp) cc_final: 0.6096 (pmm) REVERT: D 395 LYS cc_start: 0.8521 (mmmm) cc_final: 0.8268 (mmmm) REVERT: D 488 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7992 (tt) REVERT: D 689 ASP cc_start: 0.8382 (t0) cc_final: 0.8074 (m-30) REVERT: D 702 ILE cc_start: 0.8497 (mp) cc_final: 0.8057 (tt) REVERT: D 732 THR cc_start: 0.8886 (m) cc_final: 0.8604 (p) REVERT: D 868 PHE cc_start: 0.8884 (m-10) cc_final: 0.7731 (t80) REVERT: D 1021 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6670 (t80) REVERT: D 1023 MET cc_start: 0.7059 (mmm) cc_final: 0.5920 (mtp) REVERT: D 1049 ASP cc_start: 0.7232 (m-30) cc_final: 0.6865 (m-30) REVERT: D 1059 MET cc_start: 0.7564 (mpp) cc_final: 0.7161 (mmm) outliers start: 116 outliers final: 64 residues processed: 468 average time/residue: 0.1804 time to fit residues: 137.4782 Evaluate side-chains 430 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 356 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain B residue 1078 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain C residue 1078 MET Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1045 PHE Chi-restraints excluded: chain D residue 1078 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 246 optimal weight: 3.9990 chunk 341 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 51 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.6881 > 50:) chunk 11 optimal weight: 20.0000 chunk 242 optimal weight: 7.9990 chunk 295 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN A 571 GLN A 609 ASN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 ASN D 306 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.157491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104462 restraints weight = 49578.859| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.46 r_work: 0.3180 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31192 Z= 0.211 Angle : 0.639 8.055 42260 Z= 0.331 Chirality : 0.042 0.201 4708 Planarity : 0.004 0.049 5280 Dihedral : 5.537 51.236 4024 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.64 % Allowed : 15.32 % Favored : 82.03 % 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 (0.14), residues: 3656 helix: 1.12 (0.10), residues: 2468 sheet: -1.82 (0.33), residues: 192 loop : -2.70 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1046 TYR 0.030 0.002 TYR D 191 PHE 0.034 0.002 PHE B1021 TRP 0.024 0.002 TRP A 898 HIS 0.004 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.21 (31188) covalent geometry : angle 0.63820 / 0.33 (42252) SS BOND : bond 0.00771 / 0.35 ( 4) SS BOND : angle 2.97318 / 1.71 ( 8) hydrogen bonds : bond 0.04999 / 3.40 ( 1768) hydrogen bonds : angle 4.16101 / 2.88 ( 5244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 365 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8588 (tt0) cc_final: 0.8230 (tp40) REVERT: A 304 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.6778 (m-80) REVERT: A 353 MET cc_start: 0.6781 (mpp) cc_final: 0.6316 (pmm) REVERT: A 395 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8312 (mmmm) REVERT: A 488 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7883 (tt) REVERT: A 613 GLU cc_start: 0.8484 (mp0) cc_final: 0.8096 (mp0) REVERT: A 627 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8520 (mp0) REVERT: A 689 ASP cc_start: 0.8407 (t0) cc_final: 0.8085 (m-30) REVERT: A 732 THR cc_start: 0.8875 (m) cc_final: 0.8603 (p) REVERT: A 868 PHE cc_start: 0.8849 (m-10) cc_final: 0.7604 (t80) REVERT: A 1023 MET cc_start: 0.6988 (mmm) cc_final: 0.5895 (mtp) REVERT: A 1059 MET cc_start: 0.7731 (mpp) cc_final: 0.7468 (mmm) REVERT: B 304 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.6712 (m-80) REVERT: B 353 MET cc_start: 0.6661 (mpp) cc_final: 0.6185 (pmm) REVERT: B 396 MET cc_start: 0.7036 (mmp) cc_final: 0.6105 (mmp) REVERT: B 401 ASP cc_start: 0.8246 (t70) cc_final: 0.7968 (m-30) REVERT: B 402 GLU cc_start: 0.7984 (tt0) cc_final: 0.7704 (tt0) REVERT: B 488 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7728 (tt) REVERT: B 689 ASP cc_start: 0.8407 (t0) cc_final: 0.8001 (m-30) REVERT: B 702 ILE cc_start: 0.8433 (mp) cc_final: 0.8040 (tt) REVERT: B 732 THR cc_start: 0.8847 (m) cc_final: 0.8604 (p) REVERT: B 801 MET cc_start: 0.8431 (ptt) cc_final: 0.8142 (ptt) REVERT: B 868 PHE cc_start: 0.8835 (m-10) cc_final: 0.7636 (t80) REVERT: B 1023 MET cc_start: 0.6942 (mmm) cc_final: 0.5825 (mtp) REVERT: B 1046 ARG cc_start: 0.7554 (ttm170) cc_final: 0.7301 (ttm110) REVERT: B 1059 MET cc_start: 0.7719 (mpp) cc_final: 0.7473 (mmm) REVERT: C 280 GLN cc_start: 0.8599 (tt0) cc_final: 0.8267 (tp40) REVERT: C 353 MET cc_start: 0.6803 (mpp) cc_final: 0.6163 (pmm) REVERT: C 401 ASP cc_start: 0.8233 (t70) cc_final: 0.7929 (m-30) REVERT: C 402 GLU cc_start: 0.8012 (tt0) cc_final: 0.7731 (tt0) REVERT: C 488 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7872 (tt) REVERT: C 491 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7860 (tp30) REVERT: C 646 TYR cc_start: 0.6057 (t80) cc_final: 0.5761 (t80) REVERT: C 689 ASP cc_start: 0.8362 (t0) cc_final: 0.8028 (m-30) REVERT: C 732 THR cc_start: 0.8819 (m) cc_final: 0.8588 (p) REVERT: C 801 MET cc_start: 0.8456 (ptt) cc_final: 0.8213 (ptt) REVERT: C 868 PHE cc_start: 0.8836 (m-10) cc_final: 0.7647 (t80) REVERT: C 1023 MET cc_start: 0.6979 (mmm) cc_final: 0.5856 (mtp) REVERT: C 1059 MET cc_start: 0.7709 (mpp) cc_final: 0.7463 (mmm) REVERT: D 280 GLN cc_start: 0.8610 (tt0) cc_final: 0.8283 (tp40) REVERT: D 304 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.6748 (m-80) REVERT: D 306 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.7122 (pp30) REVERT: D 353 MET cc_start: 0.6779 (mpp) cc_final: 0.6338 (pmm) REVERT: D 488 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7982 (tt) REVERT: D 689 ASP cc_start: 0.8379 (t0) cc_final: 0.8034 (m-30) REVERT: D 702 ILE cc_start: 0.8482 (mp) cc_final: 0.8069 (tt) REVERT: D 732 THR cc_start: 0.8878 (m) cc_final: 0.8613 (p) REVERT: D 868 PHE cc_start: 0.8851 (m-10) cc_final: 0.7627 (t80) REVERT: D 1021 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6758 (t80) REVERT: D 1023 MET cc_start: 0.7006 (mmm) cc_final: 0.5881 (mtp) REVERT: D 1059 MET cc_start: 0.7672 (mpp) cc_final: 0.7372 (mmm) outliers start: 88 outliers final: 52 residues processed: 430 average time/residue: 0.1805 time to fit residues: 127.5481 Evaluate side-chains 417 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 356 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain B residue 1078 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain C residue 1078 MET Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1045 PHE Chi-restraints excluded: chain D residue 1078 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 78 optimal weight: 0.5980 chunk 28 optimal weight: 9.9990 chunk 265 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 295 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 261 optimal weight: 0.0060 chunk 182 optimal weight: 0.0170 chunk 366 optimal weight: 8.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 HIS ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 HIS D 306 GLN D 500 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.161203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110533 restraints weight = 48842.916| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.39 r_work: 0.3263 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31192 Z= 0.115 Angle : 0.578 9.865 42260 Z= 0.296 Chirality : 0.039 0.175 4708 Planarity : 0.004 0.046 5280 Dihedral : 5.159 44.762 4024 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.59 % Allowed : 16.53 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.41 (0.14), residues: 3656 helix: 1.48 (0.11), residues: 2468 sheet: -1.17 (0.36), residues: 184 loop : -2.60 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1046 TYR 0.032 0.002 TYR C 191 PHE 0.026 0.001 PHE B 779 TRP 0.021 0.001 TRP B 898 HIS 0.004 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (31188) covalent geometry : angle 0.57779 / 0.30 (42252) SS BOND : bond 0.00543 / 0.25 ( 4) SS BOND : angle 1.87826 / 1.08 ( 8) hydrogen bonds : bond 0.03800 / 2.57 ( 1768) hydrogen bonds : angle 3.87858 / 2.67 ( 5244) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 394 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8554 (tt0) cc_final: 0.8209 (tp40) REVERT: A 353 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6364 (pmm) REVERT: A 396 MET cc_start: 0.6906 (mmp) cc_final: 0.5828 (mmp) REVERT: A 445 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8243 (mm-30) REVERT: A 488 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7857 (tt) REVERT: A 627 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8439 (mp0) REVERT: A 689 ASP cc_start: 0.8345 (t0) cc_final: 0.8141 (m-30) REVERT: A 731 PHE cc_start: 0.7391 (m-80) cc_final: 0.7019 (t80) REVERT: A 732 THR cc_start: 0.8644 (m) cc_final: 0.8424 (p) REVERT: A 868 PHE cc_start: 0.8748 (m-10) cc_final: 0.7535 (t80) REVERT: A 989 ASN cc_start: 0.7359 (t0) cc_final: 0.7135 (t0) REVERT: A 1023 MET cc_start: 0.6944 (mmm) cc_final: 0.5883 (mtp) REVERT: B 304 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.6723 (m-80) REVERT: B 353 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.6281 (pmm) REVERT: B 396 MET cc_start: 0.7095 (mmp) cc_final: 0.6231 (mmp) REVERT: B 402 GLU cc_start: 0.7925 (tt0) cc_final: 0.7674 (tt0) REVERT: B 434 LEU cc_start: 0.8467 (tt) cc_final: 0.8219 (tp) REVERT: B 689 ASP cc_start: 0.8373 (t0) cc_final: 0.8124 (m-30) REVERT: B 702 ILE cc_start: 0.8439 (mp) cc_final: 0.8068 (tt) REVERT: B 731 PHE cc_start: 0.7559 (m-80) cc_final: 0.7066 (t80) REVERT: B 732 THR cc_start: 0.8813 (m) cc_final: 0.8599 (p) REVERT: B 801 MET cc_start: 0.8304 (ptt) cc_final: 0.8035 (ptt) REVERT: B 868 PHE cc_start: 0.8754 (m-10) cc_final: 0.7544 (t80) REVERT: B 989 ASN cc_start: 0.7243 (t0) cc_final: 0.7034 (t0) REVERT: B 1023 MET cc_start: 0.6895 (mmm) cc_final: 0.5802 (mtp) REVERT: B 1046 ARG cc_start: 0.7537 (ttm170) cc_final: 0.7227 (ttm110) REVERT: C 198 ASP cc_start: 0.8090 (m-30) cc_final: 0.7885 (m-30) REVERT: C 280 GLN cc_start: 0.8542 (tt0) cc_final: 0.8246 (tp40) REVERT: C 353 MET cc_start: 0.6651 (mpp) cc_final: 0.6239 (pmm) REVERT: C 396 MET cc_start: 0.6940 (mmp) cc_final: 0.5900 (mmp) REVERT: C 488 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7817 (tt) REVERT: C 731 PHE cc_start: 0.7465 (m-80) cc_final: 0.7007 (t80) REVERT: C 732 THR cc_start: 0.8782 (m) cc_final: 0.8578 (p) REVERT: C 801 MET cc_start: 0.8299 (ptt) cc_final: 0.8063 (ptt) REVERT: C 868 PHE cc_start: 0.8744 (m-10) cc_final: 0.7534 (t80) REVERT: C 989 ASN cc_start: 0.7256 (t0) cc_final: 0.7034 (t0) REVERT: C 1023 MET cc_start: 0.6915 (mmm) cc_final: 0.5825 (mtp) REVERT: D 280 GLN cc_start: 0.8541 (tt0) cc_final: 0.8248 (tp40) REVERT: D 304 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.6753 (m-80) REVERT: D 353 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.6310 (pmm) REVERT: D 396 MET cc_start: 0.6730 (mmp) cc_final: 0.5675 (mmp) REVERT: D 566 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8803 (mp) REVERT: D 605 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7987 (mmtm) REVERT: D 702 ILE cc_start: 0.8457 (mp) cc_final: 0.8083 (tt) REVERT: D 731 PHE cc_start: 0.7533 (m-80) cc_final: 0.7015 (t80) REVERT: D 732 THR cc_start: 0.8797 (m) cc_final: 0.8588 (p) REVERT: D 868 PHE cc_start: 0.8761 (m-10) cc_final: 0.7541 (t80) REVERT: D 989 ASN cc_start: 0.7316 (t0) cc_final: 0.7099 (t0) REVERT: D 1021 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6752 (t80) REVERT: D 1023 MET cc_start: 0.6889 (mmm) cc_final: 0.5770 (mtp) outliers start: 53 outliers final: 17 residues processed: 429 average time/residue: 0.1819 time to fit residues: 127.7982 Evaluate side-chains 393 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 367 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 613 GLU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 1021 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 227 optimal weight: 0.7980 chunk 131 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 264 optimal weight: 5.9990 chunk 366 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 500 HIS D 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.157577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106217 restraints weight = 48809.743| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.38 r_work: 0.3195 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 31192 Z= 0.209 Angle : 0.653 8.924 42260 Z= 0.332 Chirality : 0.042 0.183 4708 Planarity : 0.004 0.046 5280 Dihedral : 5.195 51.637 4024 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.53 % Allowed : 16.83 % Favored : 81.64 % 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: 0.27 (0.14), residues: 3656 helix: 1.35 (0.11), residues: 2484 sheet: -1.23 (0.35), residues: 184 loop : -2.63 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 842 TYR 0.025 0.002 TYR C 191 PHE 0.034 0.002 PHE C1021 TRP 0.020 0.002 TRP C 453 HIS 0.005 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (31188) covalent geometry : angle 0.65164 / 0.33 (42252) SS BOND : bond 0.00696 / 0.32 ( 4) SS BOND : angle 2.68942 / 1.55 ( 8) hydrogen bonds : bond 0.04840 / 3.29 ( 1768) hydrogen bonds : angle 4.04824 / 2.79 ( 5244) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 364 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8592 (tt0) cc_final: 0.8251 (tp40) REVERT: A 304 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.6759 (m-80) REVERT: A 353 MET cc_start: 0.6822 (mpp) cc_final: 0.6374 (pmm) REVERT: A 395 LYS cc_start: 0.8600 (mmtm) cc_final: 0.8339 (mmtm) REVERT: A 396 MET cc_start: 0.7005 (mmp) cc_final: 0.5857 (mmp) REVERT: A 488 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7932 (tt) REVERT: A 613 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: A 627 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8505 (mp0) REVERT: A 689 ASP cc_start: 0.8462 (t0) cc_final: 0.8170 (m-30) REVERT: A 732 THR cc_start: 0.8693 (m) cc_final: 0.8429 (p) REVERT: A 868 PHE cc_start: 0.8812 (m-10) cc_final: 0.7630 (t80) REVERT: A 1023 MET cc_start: 0.7006 (mmm) cc_final: 0.5929 (mtp) REVERT: B 141 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7934 (p) REVERT: B 304 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.6746 (m-80) REVERT: B 353 MET cc_start: 0.6706 (mpp) cc_final: 0.6267 (pmm) REVERT: B 445 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8255 (mm-30) REVERT: B 627 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8525 (mp0) REVERT: B 646 TYR cc_start: 0.6252 (t80) cc_final: 0.5964 (t80) REVERT: B 689 ASP cc_start: 0.8489 (t0) cc_final: 0.8141 (m-30) REVERT: B 732 THR cc_start: 0.8684 (m) cc_final: 0.8448 (p) REVERT: B 801 MET cc_start: 0.8437 (ptt) cc_final: 0.8162 (ptt) REVERT: B 868 PHE cc_start: 0.8834 (m-10) cc_final: 0.7663 (t80) REVERT: B 989 ASN cc_start: 0.7579 (t0) cc_final: 0.7310 (t0) REVERT: B 1023 MET cc_start: 0.6971 (mmm) cc_final: 0.5859 (mtp) REVERT: C 198 ASP cc_start: 0.8135 (m-30) cc_final: 0.7782 (m-30) REVERT: C 280 GLN cc_start: 0.8577 (tt0) cc_final: 0.8268 (tp40) REVERT: C 353 MET cc_start: 0.6687 (mpp) cc_final: 0.6258 (pmm) REVERT: C 401 ASP cc_start: 0.8297 (t70) cc_final: 0.8061 (m-30) REVERT: C 402 GLU cc_start: 0.7966 (tt0) cc_final: 0.7674 (tt0) REVERT: C 488 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7878 (tt) REVERT: C 566 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8728 (mp) REVERT: C 627 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8553 (mp0) REVERT: C 732 THR cc_start: 0.8650 (m) cc_final: 0.8428 (p) REVERT: C 801 MET cc_start: 0.8369 (ptt) cc_final: 0.8152 (ptt) REVERT: C 868 PHE cc_start: 0.8821 (m-10) cc_final: 0.7661 (t80) REVERT: C 989 ASN cc_start: 0.7572 (t0) cc_final: 0.7299 (t0) REVERT: C 1023 MET cc_start: 0.6953 (mmm) cc_final: 0.5845 (mtp) REVERT: D 198 ASP cc_start: 0.8116 (m-30) cc_final: 0.7868 (m-30) REVERT: D 280 GLN cc_start: 0.8583 (tt0) cc_final: 0.8284 (tp40) REVERT: D 304 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.6714 (m-80) REVERT: D 353 MET cc_start: 0.6675 (mpp) cc_final: 0.6252 (pmm) REVERT: D 395 LYS cc_start: 0.8544 (mmtm) cc_final: 0.8285 (mmtm) REVERT: D 396 MET cc_start: 0.6955 (mmp) cc_final: 0.5969 (mmp) REVERT: D 605 LYS cc_start: 0.8297 (mmtp) cc_final: 0.8061 (mmtm) REVERT: D 732 THR cc_start: 0.8684 (m) cc_final: 0.8438 (p) REVERT: D 868 PHE cc_start: 0.8817 (m-10) cc_final: 0.7633 (t80) REVERT: D 1021 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6766 (t80) REVERT: D 1023 MET cc_start: 0.7017 (mmm) cc_final: 0.5875 (mtp) outliers start: 51 outliers final: 29 residues processed: 399 average time/residue: 0.1788 time to fit residues: 117.0615 Evaluate side-chains 393 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 355 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 1078 MET Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 613 GLU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 1021 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 1 optimal weight: 20.0000 chunk 176 optimal weight: 2.9990 chunk 338 optimal weight: 3.9990 chunk 212 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 265 optimal weight: 0.7980 chunk 312 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.159895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109061 restraints weight = 48585.922| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.38 r_work: 0.3238 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31192 Z= 0.135 Angle : 0.614 12.433 42260 Z= 0.310 Chirality : 0.040 0.196 4708 Planarity : 0.004 0.045 5280 Dihedral : 5.099 48.292 4024 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.44 % Allowed : 16.95 % Favored : 81.61 % 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: 0.49 (0.14), residues: 3656 helix: 1.53 (0.11), residues: 2468 sheet: -1.06 (0.36), residues: 184 loop : -2.56 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1046 TYR 0.028 0.001 TYR C 191 PHE 0.014 0.001 PHE C 165 TRP 0.020 0.001 TRP B 898 HIS 0.004 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (31188) covalent geometry : angle 0.61196 / 0.31 (42252) SS BOND : bond 0.00811 / 0.37 ( 4) SS BOND : angle 3.48895 / 2.00 ( 8) hydrogen bonds : bond 0.04127 / 2.80 ( 1768) hydrogen bonds : angle 3.90229 / 2.69 ( 5244) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 366 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8567 (tt0) cc_final: 0.8215 (tp40) REVERT: A 353 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.6256 (pmm) REVERT: A 396 MET cc_start: 0.6956 (mmp) cc_final: 0.6217 (mmp) REVERT: A 445 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8232 (mm-30) REVERT: A 488 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7887 (tt) REVERT: A 605 LYS cc_start: 0.8238 (mmtp) cc_final: 0.7881 (mmtm) REVERT: A 689 ASP cc_start: 0.8379 (t0) cc_final: 0.8080 (m-30) REVERT: A 731 PHE cc_start: 0.7474 (m-80) cc_final: 0.7049 (t80) REVERT: A 732 THR cc_start: 0.8672 (m) cc_final: 0.8446 (p) REVERT: A 868 PHE cc_start: 0.8797 (m-10) cc_final: 0.7597 (t80) REVERT: A 989 ASN cc_start: 0.7342 (t0) cc_final: 0.7114 (t0) REVERT: A 1023 MET cc_start: 0.6992 (mmm) cc_final: 0.5891 (mtp) REVERT: B 141 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7887 (p) REVERT: B 304 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: B 353 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6170 (pmm) REVERT: B 445 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8253 (mm-30) REVERT: B 566 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8800 (mp) REVERT: B 646 TYR cc_start: 0.6269 (t80) cc_final: 0.6068 (t80) REVERT: B 689 ASP cc_start: 0.8377 (t0) cc_final: 0.8047 (m-30) REVERT: B 702 ILE cc_start: 0.8438 (mp) cc_final: 0.8021 (tt) REVERT: B 731 PHE cc_start: 0.7576 (m-80) cc_final: 0.7113 (t80) REVERT: B 732 THR cc_start: 0.8598 (m) cc_final: 0.8379 (p) REVERT: B 801 MET cc_start: 0.8402 (ptt) cc_final: 0.8124 (ptt) REVERT: B 868 PHE cc_start: 0.8779 (m-10) cc_final: 0.7595 (t80) REVERT: B 989 ASN cc_start: 0.7380 (t0) cc_final: 0.7151 (t0) REVERT: B 1023 MET cc_start: 0.6897 (mmm) cc_final: 0.5810 (mtp) REVERT: C 198 ASP cc_start: 0.8107 (m-30) cc_final: 0.7888 (m-30) REVERT: C 280 GLN cc_start: 0.8536 (tt0) cc_final: 0.8251 (tp40) REVERT: C 353 MET cc_start: 0.6577 (mpp) cc_final: 0.6181 (pmm) REVERT: C 402 GLU cc_start: 0.8024 (tt0) cc_final: 0.7779 (tt0) REVERT: C 488 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7769 (tt) REVERT: C 566 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8712 (mp) REVERT: C 627 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8503 (mp0) REVERT: C 731 PHE cc_start: 0.7503 (m-80) cc_final: 0.7031 (t80) REVERT: C 732 THR cc_start: 0.8546 (m) cc_final: 0.8335 (p) REVERT: C 801 MET cc_start: 0.8294 (ptt) cc_final: 0.8072 (ptt) REVERT: C 868 PHE cc_start: 0.8767 (m-10) cc_final: 0.7583 (t80) REVERT: C 989 ASN cc_start: 0.7429 (t0) cc_final: 0.7177 (t0) REVERT: C 1023 MET cc_start: 0.6945 (mmm) cc_final: 0.5832 (mtp) REVERT: D 198 ASP cc_start: 0.8080 (m-30) cc_final: 0.7866 (m-30) REVERT: D 280 GLN cc_start: 0.8579 (tt0) cc_final: 0.8284 (tp40) REVERT: D 304 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.6711 (m-80) REVERT: D 353 MET cc_start: 0.6639 (OUTLIER) cc_final: 0.6245 (pmm) REVERT: D 395 LYS cc_start: 0.8596 (mmtm) cc_final: 0.8395 (mmtm) REVERT: D 396 MET cc_start: 0.6954 (mmp) cc_final: 0.6079 (mmp) REVERT: D 605 LYS cc_start: 0.8256 (mmtp) cc_final: 0.8018 (mmtm) REVERT: D 627 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8475 (mp0) REVERT: D 702 ILE cc_start: 0.8404 (mp) cc_final: 0.7999 (tt) REVERT: D 731 PHE cc_start: 0.7499 (m-80) cc_final: 0.7045 (t80) REVERT: D 732 THR cc_start: 0.8650 (m) cc_final: 0.8432 (p) REVERT: D 868 PHE cc_start: 0.8766 (m-10) cc_final: 0.7588 (t80) REVERT: D 989 ASN cc_start: 0.7358 (t0) cc_final: 0.7124 (t0) REVERT: D 1021 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6740 (t80) REVERT: D 1023 MET cc_start: 0.6960 (mmm) cc_final: 0.5842 (mtp) outliers start: 48 outliers final: 27 residues processed: 395 average time/residue: 0.1793 time to fit residues: 116.1564 Evaluate side-chains 397 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 359 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 1078 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 613 GLU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 1021 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 364 optimal weight: 0.7980 chunk 174 optimal weight: 0.7980 chunk 144 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 282 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.158863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107689 restraints weight = 48688.367| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.38 r_work: 0.3218 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31192 Z= 0.166 Angle : 0.634 12.150 42260 Z= 0.319 Chirality : 0.041 0.194 4708 Planarity : 0.004 0.044 5280 Dihedral : 5.103 47.216 4024 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.56 % Allowed : 17.13 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3656 helix: 1.51 (0.11), residues: 2476 sheet: -1.26 (0.35), residues: 192 loop : -2.51 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1046 TYR 0.025 0.002 TYR C 191 PHE 0.043 0.001 PHE A1021 TRP 0.019 0.002 TRP A 898 HIS 0.003 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (31188) covalent geometry : angle 0.63275 / 0.32 (42252) SS BOND : bond 0.00742 / 0.34 ( 4) SS BOND : angle 3.31236 / 1.90 ( 8) hydrogen bonds : bond 0.04425 / 3.01 ( 1768) hydrogen bonds : angle 3.94679 / 2.72 ( 5244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10767.13 seconds wall clock time: 184 minutes 4.94 seconds (11044.94 seconds total)