Starting phenix.real_space_refine on Thu Jun 26 08:09:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrf_32725/06_2025/7wrf_32725.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrf_32725/06_2025/7wrf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wrf_32725/06_2025/7wrf_32725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrf_32725/06_2025/7wrf_32725.map" model { file = "/net/cci-nas-00/data/ceres_data/7wrf_32725/06_2025/7wrf_32725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrf_32725/06_2025/7wrf_32725.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.54s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.37, per 1000 atoms: 0.57 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: 7.92 Conformation dependent library (CDL) restraints added in 3.8 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: 3.55 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: 11.48 Time building geometry restraints manager: 9.42 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 1104 or resid 1201)) selection = (chain 'B' and (resid 102 through 1104 or resid 1201)) selection = (chain 'C' and (resid 102 through 1104 or resid 1201)) selection = (chain 'D' and (resid 102 through 1104 or resid 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 68.380 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.003 TRP B 377 HIS 0.007 0.002 HIS A 138 PHE 0.031 0.003 PHE B 304 TYR 0.038 0.003 TYR A 772 ARG 0.009 0.001 ARG C1008 Details of bonding type rmsd hydrogen bonds : bond 0.14823 ( 1768) hydrogen bonds : angle 6.41497 ( 5244) SS BOND : bond 0.00636 ( 4) SS BOND : angle 4.83437 ( 8) covalent geometry : bond 0.00808 (31188) covalent geometry : angle 0.98652 (42252) *********************** 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 : 3.355 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: 0.8151 (tt) REVERT: A 787 TYR cc_start: 0.7393 (t80) cc_final: 0.7115 (t80) REVERT: A 868 PHE cc_start: 0.8203 (m-10) cc_final: 0.7609 (t80) REVERT: A 1023 MET cc_start: 0.7034 (mmm) cc_final: 0.5995 (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: 0.7230 (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: 0.7103 (t80) REVERT: B 868 PHE cc_start: 0.8192 (m-10) cc_final: 0.7598 (t80) REVERT: B 1023 MET cc_start: 0.6992 (mmm) cc_final: 0.5939 (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: 0.8060 (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: 0.7152 (t80) REVERT: C 868 PHE cc_start: 0.8177 (m-10) cc_final: 0.7611 (t80) REVERT: C 1023 MET cc_start: 0.6850 (mmm) cc_final: 0.5838 (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: 0.8898 (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: 0.7140 (t80) REVERT: D 868 PHE cc_start: 0.8181 (m-10) cc_final: 0.7622 (t80) REVERT: D 1023 MET cc_start: 0.6889 (mmm) cc_final: 0.5892 (mtp) outliers start: 4 outliers final: 0 residues processed: 827 average time/residue: 0.4744 time to fit residues: 594.5735 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 : 3.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 9.9990 chunk 281 optimal weight: 9.9990 chunk 156 optimal weight: 0.0000 chunk 96 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 291 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 337 optimal weight: 0.8980 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS A 259 HIS A 438 GLN A 572 ASN A 675 GLN A 987 GLN B 256 ASN B 257 HIS B 259 HIS B 438 GLN B 675 GLN B 741 ASN 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.162238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.110661 restraints weight = 48416.915| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.38 r_work: 0.3260 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31192 Z= 0.175 Angle : 0.655 7.252 42260 Z= 0.344 Chirality : 0.042 0.146 4708 Planarity : 0.005 0.052 5280 Dihedral : 5.996 48.999 4024 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.83 % Allowed : 8.26 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.13), residues: 3656 helix: -0.16 (0.10), residues: 2464 sheet: -1.80 (0.32), residues: 192 loop : -3.18 (0.16), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 898 HIS 0.005 0.001 HIS B 138 PHE 0.025 0.002 PHE B 752 TYR 0.016 0.002 TYR A 191 ARG 0.003 0.000 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.05246 ( 1768) hydrogen bonds : angle 4.49184 ( 5244) SS BOND : bond 0.00831 ( 4) SS BOND : angle 2.36808 ( 8) covalent geometry : bond 0.00409 (31188) covalent geometry : angle 0.65394 (42252) *********************** 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 541 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 480 time to evaluate : 3.405 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: A 191 TYR cc_start: 0.8069 (t80) cc_final: 0.7743 (t80) REVERT: A 280 GLN cc_start: 0.8484 (tt0) cc_final: 0.8181 (tp40) REVERT: A 491 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7885 (tp30) REVERT: A 700 PHE cc_start: 0.6948 (m-80) cc_final: 0.6662 (m-80) REVERT: A 702 ILE cc_start: 0.8449 (mt) cc_final: 0.8225 (tt) REVERT: A 787 TYR cc_start: 0.7892 (t80) cc_final: 0.7446 (t80) REVERT: A 800 VAL cc_start: 0.9311 (t) cc_final: 0.9099 (p) REVERT: A 868 PHE cc_start: 0.8840 (m-10) cc_final: 0.7658 (t80) REVERT: A 1005 TYR cc_start: 0.6803 (m-10) cc_final: 0.5595 (m-80) REVERT: A 1023 MET cc_start: 0.7059 (mmm) cc_final: 0.6053 (mtp) REVERT: A 1066 LYS cc_start: 0.8961 (mtpp) cc_final: 0.8760 (mmtp) REVERT: B 191 TYR cc_start: 0.7996 (t80) cc_final: 0.7563 (t80) REVERT: B 491 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7832 (tp30) REVERT: B 787 TYR cc_start: 0.7868 (t80) cc_final: 0.7429 (t80) REVERT: B 801 MET cc_start: 0.8207 (ptm) cc_final: 0.7958 (ptt) REVERT: B 868 PHE cc_start: 0.8819 (m-10) cc_final: 0.7624 (t80) REVERT: B 1005 TYR cc_start: 0.6751 (m-10) cc_final: 0.5593 (m-80) REVERT: B 1021 PHE cc_start: 0.7554 (m-80) cc_final: 0.7315 (m-80) REVERT: B 1023 MET cc_start: 0.6936 (mmm) cc_final: 0.5886 (mtp) REVERT: B 1066 LYS cc_start: 0.8958 (mtpp) cc_final: 0.8751 (mmtp) REVERT: C 191 TYR cc_start: 0.8076 (t80) cc_final: 0.7783 (t80) REVERT: C 280 GLN cc_start: 0.8488 (tt0) cc_final: 0.8124 (tp40) REVERT: C 491 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7885 (tp30) REVERT: C 700 PHE cc_start: 0.7007 (m-80) cc_final: 0.6747 (m-80) REVERT: C 741 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8649 (m-40) REVERT: C 787 TYR cc_start: 0.7890 (t80) cc_final: 0.7450 (t80) REVERT: C 801 MET cc_start: 0.8345 (ptm) cc_final: 0.8087 (ptt) REVERT: C 868 PHE cc_start: 0.8821 (m-10) cc_final: 0.7622 (t80) REVERT: C 1005 TYR cc_start: 0.6739 (m-10) cc_final: 0.5567 (m-80) REVERT: C 1023 MET cc_start: 0.7061 (mmm) cc_final: 0.6044 (mtp) REVERT: C 1066 LYS cc_start: 0.8909 (mtpp) cc_final: 0.8702 (mmtp) REVERT: D 191 TYR cc_start: 0.8091 (t80) cc_final: 0.7651 (t80) REVERT: D 280 GLN cc_start: 0.8503 (tt0) cc_final: 0.8202 (tp40) REVERT: D 491 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7906 (tp30) REVERT: D 700 PHE cc_start: 0.7023 (m-80) cc_final: 0.6732 (m-80) REVERT: D 702 ILE cc_start: 0.8463 (mt) cc_final: 0.8232 (tt) REVERT: D 787 TYR cc_start: 0.7903 (t80) cc_final: 0.7461 (t80) REVERT: D 800 VAL cc_start: 0.9307 (t) cc_final: 0.9080 (p) REVERT: D 868 PHE cc_start: 0.8822 (m-10) cc_final: 0.7644 (t80) REVERT: D 1005 TYR cc_start: 0.6788 (m-10) cc_final: 0.5658 (m-80) REVERT: D 1023 MET cc_start: 0.7111 (mmm) cc_final: 0.6106 (mtp) REVERT: D 1066 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8740 (mmtp) outliers start: 61 outliers final: 31 residues processed: 520 average time/residue: 0.4427 time to fit residues: 364.6876 Evaluate side-chains 419 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 387 time to evaluate : 3.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 391 LEU 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 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 955 ILE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 440 ASP 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 955 ILE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 132 LEU 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 209 optimal weight: 9.9990 chunk 263 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 328 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 129 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 chunk 239 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 256 ASN A 294 ASN B 136 HIS B 294 ASN B 990 ASN C 136 HIS C 256 ASN C 990 ASN D 256 ASN D 741 ASN D 990 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.162717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111276 restraints weight = 48645.441| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.37 r_work: 0.3271 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31192 Z= 0.140 Angle : 0.593 11.964 42260 Z= 0.308 Chirality : 0.040 0.169 4708 Planarity : 0.004 0.048 5280 Dihedral : 5.591 51.471 4024 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.28 % Allowed : 10.79 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3656 helix: 0.64 (0.10), residues: 2484 sheet: -1.54 (0.35), residues: 192 loop : -2.92 (0.17), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 898 HIS 0.004 0.001 HIS C 138 PHE 0.016 0.001 PHE B 779 TYR 0.015 0.001 TYR D 621 ARG 0.002 0.000 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 1768) hydrogen bonds : angle 4.12965 ( 5244) SS BOND : bond 0.01034 ( 4) SS BOND : angle 3.34312 ( 8) covalent geometry : bond 0.00330 (31188) covalent geometry : angle 0.59166 (42252) *********************** 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 497 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 421 time to evaluate : 3.126 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: 0.8493 (tt0) cc_final: 0.8187 (tp40) REVERT: A 353 MET cc_start: 0.6522 (mpp) cc_final: 0.5926 (ptp) REVERT: A 396 MET cc_start: 0.7027 (mmp) cc_final: 0.6157 (mmp) REVERT: A 491 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7834 (tp30) REVERT: A 521 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7149 (tp) REVERT: A 787 TYR cc_start: 0.7920 (t80) cc_final: 0.7467 (t80) REVERT: A 868 PHE cc_start: 0.8788 (m-10) cc_final: 0.7624 (t80) REVERT: A 1023 MET cc_start: 0.7015 (mmm) cc_final: 0.5950 (mtp) REVERT: B 353 MET cc_start: 0.6472 (mpp) cc_final: 0.5850 (ptp) REVERT: B 396 MET cc_start: 0.7028 (mmp) cc_final: 0.6167 (mmp) REVERT: B 491 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7841 (tp30) REVERT: B 521 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7092 (tp) REVERT: B 787 TYR cc_start: 0.7900 (t80) cc_final: 0.7465 (t80) REVERT: B 868 PHE cc_start: 0.8787 (m-10) cc_final: 0.7613 (t80) REVERT: B 1023 MET cc_start: 0.6923 (mmm) cc_final: 0.5837 (mtp) REVERT: B 1066 LYS cc_start: 0.8966 (mtpp) cc_final: 0.8743 (mmtp) REVERT: C 280 GLN cc_start: 0.8452 (tt0) cc_final: 0.8150 (tp40) REVERT: C 353 MET cc_start: 0.6475 (mpp) cc_final: 0.5891 (ptp) REVERT: C 396 MET cc_start: 0.6985 (mmp) cc_final: 0.6140 (mmp) REVERT: C 491 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7873 (tp30) REVERT: C 521 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7102 (tp) REVERT: C 787 TYR cc_start: 0.7918 (t80) cc_final: 0.7480 (t80) REVERT: C 868 PHE cc_start: 0.8778 (m-10) cc_final: 0.7607 (t80) REVERT: C 1023 MET cc_start: 0.6908 (mmm) cc_final: 0.5833 (mtp) REVERT: C 1066 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8758 (mmtp) REVERT: D 191 TYR cc_start: 0.8147 (t80) cc_final: 0.7885 (t80) REVERT: D 280 GLN cc_start: 0.8477 (tt0) cc_final: 0.8178 (tp40) REVERT: D 353 MET cc_start: 0.6523 (mpp) cc_final: 0.5964 (ptp) REVERT: D 396 MET cc_start: 0.6956 (mmp) cc_final: 0.6139 (mmp) REVERT: D 521 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7138 (tp) REVERT: D 787 TYR cc_start: 0.7901 (t80) cc_final: 0.7456 (t80) REVERT: D 868 PHE cc_start: 0.8785 (m-10) cc_final: 0.7621 (t80) REVERT: D 1023 MET cc_start: 0.7030 (mmm) cc_final: 0.5965 (mtp) outliers start: 76 outliers final: 40 residues processed: 480 average time/residue: 0.4081 time to fit residues: 314.3542 Evaluate side-chains 419 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 375 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 521 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 942 GLU 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 521 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1045 PHE 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 521 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 942 GLU 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 338 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 521 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 804 LEU 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 1045 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 250 optimal weight: 6.9990 chunk 334 optimal weight: 0.0370 chunk 259 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 347 optimal weight: 0.0980 chunk 110 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 254 optimal weight: 0.8980 chunk 253 optimal weight: 0.7980 chunk 183 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 990 ASN C 483 ASN C 741 ASN D 483 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.165467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115078 restraints weight = 48808.230| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.39 r_work: 0.3328 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31192 Z= 0.108 Angle : 0.539 9.340 42260 Z= 0.278 Chirality : 0.038 0.150 4708 Planarity : 0.004 0.039 5280 Dihedral : 5.081 42.856 4024 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.34 % Allowed : 12.14 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3656 helix: 1.13 (0.11), residues: 2492 sheet: -1.27 (0.36), residues: 192 loop : -2.63 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 453 HIS 0.004 0.001 HIS D 138 PHE 0.021 0.001 PHE A 779 TYR 0.025 0.001 TYR C 191 ARG 0.003 0.000 ARG B 160 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 1768) hydrogen bonds : angle 3.82655 ( 5244) SS BOND : bond 0.00689 ( 4) SS BOND : angle 1.84384 ( 8) covalent geometry : bond 0.00233 (31188) covalent geometry : angle 0.53842 (42252) *********************** 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 526 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 448 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8427 (tt0) cc_final: 0.8136 (tp40) REVERT: A 396 MET cc_start: 0.6902 (mmp) cc_final: 0.6156 (mmp) REVERT: A 521 LEU cc_start: 0.7363 (mp) cc_final: 0.7074 (tp) REVERT: A 605 LYS cc_start: 0.8282 (mmtp) cc_final: 0.8011 (mmtm) REVERT: A 732 THR cc_start: 0.8760 (m) cc_final: 0.8507 (p) REVERT: A 788 MET cc_start: 0.8008 (ttm) cc_final: 0.7795 (mmp) REVERT: A 864 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8539 (mp) REVERT: A 868 PHE cc_start: 0.8740 (m-10) cc_final: 0.7537 (t80) REVERT: A 989 ASN cc_start: 0.7243 (t0) cc_final: 0.7002 (t0) REVERT: A 992 GLN cc_start: 0.8795 (mt0) cc_final: 0.8392 (tt0) REVERT: A 1023 MET cc_start: 0.7029 (mmm) cc_final: 0.6033 (mtp) REVERT: B 396 MET cc_start: 0.6892 (mmp) cc_final: 0.6118 (mmp) REVERT: B 491 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7758 (tp30) REVERT: B 521 LEU cc_start: 0.7319 (mp) cc_final: 0.7026 (tp) REVERT: B 605 LYS cc_start: 0.8294 (mmtp) cc_final: 0.8050 (mmtm) REVERT: B 732 THR cc_start: 0.8706 (m) cc_final: 0.8467 (p) REVERT: B 868 PHE cc_start: 0.8685 (m-10) cc_final: 0.7528 (t80) REVERT: B 1023 MET cc_start: 0.6911 (mmm) cc_final: 0.5932 (mtp) REVERT: C 191 TYR cc_start: 0.8164 (t80) cc_final: 0.7876 (t80) REVERT: C 280 GLN cc_start: 0.8421 (tt0) cc_final: 0.8141 (tp40) REVERT: C 396 MET cc_start: 0.6719 (mmp) cc_final: 0.6004 (mmp) REVERT: C 491 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7820 (tp30) REVERT: C 521 LEU cc_start: 0.7300 (mp) cc_final: 0.7022 (tp) REVERT: C 732 THR cc_start: 0.8728 (m) cc_final: 0.8500 (p) REVERT: C 787 TYR cc_start: 0.7852 (t80) cc_final: 0.7400 (t80) REVERT: C 868 PHE cc_start: 0.8686 (m-10) cc_final: 0.7506 (t80) REVERT: C 1023 MET cc_start: 0.6965 (mmm) cc_final: 0.5960 (mtp) REVERT: D 280 GLN cc_start: 0.8440 (tt0) cc_final: 0.8162 (tp40) REVERT: D 396 MET cc_start: 0.6845 (mmp) cc_final: 0.6152 (mmp) REVERT: D 521 LEU cc_start: 0.7297 (mp) cc_final: 0.7023 (tp) REVERT: D 605 LYS cc_start: 0.8305 (mmtp) cc_final: 0.8041 (mmtm) REVERT: D 732 THR cc_start: 0.8769 (m) cc_final: 0.8516 (p) REVERT: D 788 MET cc_start: 0.8052 (ttm) cc_final: 0.7817 (mmp) REVERT: D 868 PHE cc_start: 0.8715 (m-10) cc_final: 0.7517 (t80) REVERT: D 1023 MET cc_start: 0.7041 (mmm) cc_final: 0.6009 (mtp) outliers start: 78 outliers final: 34 residues processed: 500 average time/residue: 0.4092 time to fit residues: 328.5859 Evaluate side-chains 425 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 390 time to evaluate : 3.589 ------------------------------------------------------------------------------- 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 338 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 985 ILE 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 645 VAL Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 645 VAL 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 851 ARG Chi-restraints excluded: chain D residue 955 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 294 optimal weight: 8.9990 chunk 272 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 355 optimal weight: 1.9990 chunk 321 optimal weight: 7.9990 chunk 249 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 300 optimal weight: 7.9990 chunk 196 optimal weight: 0.4980 chunk 208 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 741 ASN B 572 ASN D 635 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.161836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108858 restraints weight = 49270.761| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.48 r_work: 0.3242 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31192 Z= 0.173 Angle : 0.595 10.018 42260 Z= 0.306 Chirality : 0.041 0.163 4708 Planarity : 0.004 0.039 5280 Dihedral : 5.130 51.328 4024 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.25 % Allowed : 12.56 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3656 helix: 1.27 (0.11), residues: 2488 sheet: -1.26 (0.36), residues: 192 loop : -2.55 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 898 HIS 0.004 0.001 HIS B 765 PHE 0.026 0.002 PHE C1021 TYR 0.025 0.002 TYR A 191 ARG 0.006 0.000 ARG D1046 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 1768) hydrogen bonds : angle 3.91549 ( 5244) SS BOND : bond 0.01396 ( 4) SS BOND : angle 4.42479 ( 8) covalent geometry : bond 0.00419 (31188) covalent geometry : angle 0.59237 (42252) *********************** 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 512 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 404 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8498 (tt0) cc_final: 0.8185 (tp40) REVERT: A 396 MET cc_start: 0.7022 (mmp) cc_final: 0.6289 (mmp) REVERT: A 488 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7945 (tt) REVERT: A 521 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7098 (tp) REVERT: A 605 LYS cc_start: 0.8184 (mmtp) cc_final: 0.7880 (mmtm) REVERT: A 689 ASP cc_start: 0.8337 (t0) cc_final: 0.8042 (m-30) REVERT: A 732 THR cc_start: 0.8844 (m) cc_final: 0.8569 (p) REVERT: A 868 PHE cc_start: 0.8808 (m-10) cc_final: 0.7622 (t80) REVERT: A 1021 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6775 (t80) REVERT: A 1023 MET cc_start: 0.6921 (mmm) cc_final: 0.5811 (mtp) REVERT: B 280 GLN cc_start: 0.8222 (tm-30) cc_final: 0.8002 (tm-30) REVERT: B 396 MET cc_start: 0.7053 (mmp) cc_final: 0.6317 (mmp) REVERT: B 488 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7963 (tt) REVERT: B 491 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7861 (tp30) REVERT: B 521 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7103 (tp) REVERT: B 605 LYS cc_start: 0.8180 (mmtp) cc_final: 0.7872 (mmtm) REVERT: B 627 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8444 (mp0) REVERT: B 689 ASP cc_start: 0.8356 (t0) cc_final: 0.8058 (m-30) REVERT: B 732 THR cc_start: 0.8798 (m) cc_final: 0.8556 (p) REVERT: B 787 TYR cc_start: 0.7916 (t80) cc_final: 0.7714 (t80) REVERT: B 868 PHE cc_start: 0.8782 (m-10) cc_final: 0.7593 (t80) REVERT: B 1023 MET cc_start: 0.6692 (mmm) cc_final: 0.5640 (mtp) REVERT: C 191 TYR cc_start: 0.8249 (t80) cc_final: 0.8049 (t80) REVERT: C 280 GLN cc_start: 0.8484 (tt0) cc_final: 0.8194 (tp40) REVERT: C 396 MET cc_start: 0.6843 (mmp) cc_final: 0.6237 (mmp) REVERT: C 488 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7968 (tt) REVERT: C 491 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7900 (tp30) REVERT: C 521 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7063 (tp) REVERT: C 627 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8453 (mp0) REVERT: C 689 ASP cc_start: 0.8320 (t0) cc_final: 0.8008 (m-30) REVERT: C 732 THR cc_start: 0.8814 (m) cc_final: 0.8581 (p) REVERT: C 868 PHE cc_start: 0.8770 (m-10) cc_final: 0.7579 (t80) REVERT: C 989 ASN cc_start: 0.7354 (t0) cc_final: 0.7105 (t0) REVERT: C 1023 MET cc_start: 0.6805 (mmm) cc_final: 0.5739 (mtp) REVERT: D 189 MET cc_start: 0.7879 (mtm) cc_final: 0.7415 (mtm) REVERT: D 280 GLN cc_start: 0.8488 (tt0) cc_final: 0.8213 (tp40) REVERT: D 396 MET cc_start: 0.6978 (mmp) cc_final: 0.6395 (mmp) REVERT: D 488 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7910 (tt) REVERT: D 521 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7100 (tp) REVERT: D 702 ILE cc_start: 0.8479 (mp) cc_final: 0.8011 (tt) REVERT: D 732 THR cc_start: 0.8852 (m) cc_final: 0.8588 (p) REVERT: D 868 PHE cc_start: 0.8786 (m-10) cc_final: 0.7622 (t80) REVERT: D 1023 MET cc_start: 0.6876 (mmm) cc_final: 0.5784 (mtp) outliers start: 108 outliers final: 52 residues processed: 476 average time/residue: 0.4344 time to fit residues: 335.1014 Evaluate side-chains 449 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 388 time to evaluate : 3.291 ------------------------------------------------------------------------------- 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 338 VAL Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 521 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 804 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 302 VAL 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 521 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain C residue 148 VAL 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 521 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1078 MET 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 355 LYS Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 521 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 804 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 955 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 83 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 238 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 290 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN B 609 ASN C 609 ASN D 609 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.159148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107433 restraints weight = 48753.281| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.37 r_work: 0.3215 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31192 Z= 0.204 Angle : 0.631 10.043 42260 Z= 0.325 Chirality : 0.042 0.192 4708 Planarity : 0.004 0.041 5280 Dihedral : 5.289 52.713 4024 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.91 % Allowed : 13.73 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3656 helix: 1.31 (0.10), residues: 2476 sheet: -1.43 (0.35), residues: 192 loop : -2.56 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 898 HIS 0.006 0.001 HIS C 765 PHE 0.024 0.002 PHE D1021 TYR 0.025 0.002 TYR A 191 ARG 0.004 0.000 ARG D1046 Details of bonding type rmsd hydrogen bonds : bond 0.04724 ( 1768) hydrogen bonds : angle 3.99500 ( 5244) SS BOND : bond 0.00962 ( 4) SS BOND : angle 3.73960 ( 8) covalent geometry : bond 0.00493 (31188) covalent geometry : angle 0.62892 (42252) *********************** 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 481 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 384 time to evaluate : 3.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8570 (tt0) cc_final: 0.8247 (tp40) REVERT: A 304 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.6807 (m-80) REVERT: A 353 MET cc_start: 0.6729 (mpp) cc_final: 0.6072 (pmm) REVERT: A 396 MET cc_start: 0.7404 (mmp) cc_final: 0.6833 (mmp) REVERT: A 488 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7982 (tt) REVERT: A 521 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7181 (tp) REVERT: A 605 LYS cc_start: 0.8262 (mmtp) cc_final: 0.7975 (mmtm) REVERT: A 689 ASP cc_start: 0.8305 (t0) cc_final: 0.8018 (m-30) REVERT: A 702 ILE cc_start: 0.8521 (mp) cc_final: 0.8063 (tt) REVERT: A 732 THR cc_start: 0.8875 (m) cc_final: 0.8595 (p) REVERT: A 868 PHE cc_start: 0.8843 (m-10) cc_final: 0.7667 (t80) REVERT: A 1021 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6730 (t80) REVERT: A 1023 MET cc_start: 0.6785 (mmm) cc_final: 0.5721 (mtp) REVERT: A 1059 MET cc_start: 0.7633 (mpp) cc_final: 0.7331 (mmm) REVERT: B 353 MET cc_start: 0.6556 (mpp) cc_final: 0.6070 (pmm) REVERT: B 488 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7959 (tt) REVERT: B 491 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7843 (tp30) REVERT: B 605 LYS cc_start: 0.8273 (mmtp) cc_final: 0.7979 (mmtm) REVERT: B 689 ASP cc_start: 0.8409 (t0) cc_final: 0.8090 (m-30) REVERT: B 732 THR cc_start: 0.8852 (m) cc_final: 0.8599 (p) REVERT: B 788 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7787 (mmp) REVERT: B 868 PHE cc_start: 0.8843 (m-10) cc_final: 0.7628 (t80) REVERT: B 1023 MET cc_start: 0.6745 (mmm) cc_final: 0.5694 (mtp) REVERT: B 1046 ARG cc_start: 0.7267 (ttm170) cc_final: 0.6971 (ttm110) REVERT: B 1059 MET cc_start: 0.7643 (mpp) cc_final: 0.7368 (mmm) REVERT: C 189 MET cc_start: 0.7838 (mtm) cc_final: 0.7393 (mtm) REVERT: C 280 GLN cc_start: 0.8545 (tt0) cc_final: 0.8219 (tp40) REVERT: C 353 MET cc_start: 0.6668 (mpp) cc_final: 0.6035 (pmm) REVERT: C 396 MET cc_start: 0.7355 (mmp) cc_final: 0.6870 (mmp) REVERT: C 488 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7980 (tt) REVERT: C 491 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7879 (tp30) REVERT: C 689 ASP cc_start: 0.8309 (t0) cc_final: 0.7968 (m-30) REVERT: C 732 THR cc_start: 0.8815 (m) cc_final: 0.8576 (p) REVERT: C 868 PHE cc_start: 0.8796 (m-10) cc_final: 0.7610 (t80) REVERT: C 914 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8318 (mm-40) REVERT: C 989 ASN cc_start: 0.7453 (t0) cc_final: 0.7155 (t0) REVERT: C 1023 MET cc_start: 0.6728 (mmm) cc_final: 0.5667 (mtp) REVERT: C 1059 MET cc_start: 0.7663 (mpp) cc_final: 0.7397 (mmm) REVERT: C 1068 ASN cc_start: 0.8186 (m-40) cc_final: 0.7929 (m-40) REVERT: D 189 MET cc_start: 0.7893 (mtm) cc_final: 0.7454 (mtm) REVERT: D 280 GLN cc_start: 0.8561 (tt0) cc_final: 0.8238 (tp40) REVERT: D 353 MET cc_start: 0.6777 (mpp) cc_final: 0.6160 (pmm) REVERT: D 396 MET cc_start: 0.7268 (mmp) cc_final: 0.6882 (mmp) REVERT: D 488 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7966 (tt) REVERT: D 521 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7141 (tp) REVERT: D 689 ASP cc_start: 0.8432 (t0) cc_final: 0.8115 (m-30) REVERT: D 702 ILE cc_start: 0.8513 (mp) cc_final: 0.8065 (tt) REVERT: D 732 THR cc_start: 0.8898 (m) cc_final: 0.8627 (p) REVERT: D 868 PHE cc_start: 0.8823 (m-10) cc_final: 0.7633 (t80) REVERT: D 1023 MET cc_start: 0.6868 (mmm) cc_final: 0.5801 (mtp) REVERT: D 1059 MET cc_start: 0.7586 (mpp) cc_final: 0.7247 (mmm) REVERT: D 1068 ASN cc_start: 0.8184 (m-40) cc_final: 0.7959 (m-40) outliers start: 97 outliers final: 52 residues processed: 451 average time/residue: 0.4641 time to fit residues: 338.0731 Evaluate side-chains 430 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 369 time to evaluate : 3.142 ------------------------------------------------------------------------------- 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 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 521 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 851 ARG 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 148 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 302 VAL 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 676 ASN 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 1009 LEU 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 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 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 1078 MET Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL 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 521 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 851 ARG 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 293 optimal weight: 6.9990 chunk 334 optimal weight: 10.0000 chunk 286 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 351 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.160550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107873 restraints weight = 49069.954| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.46 r_work: 0.3228 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31192 Z= 0.158 Angle : 0.594 8.997 42260 Z= 0.305 Chirality : 0.041 0.182 4708 Planarity : 0.004 0.042 5280 Dihedral : 5.124 48.434 4024 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.34 % Allowed : 15.14 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3656 helix: 1.44 (0.11), residues: 2480 sheet: -1.32 (0.35), residues: 192 loop : -2.48 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 898 HIS 0.004 0.001 HIS C 138 PHE 0.036 0.001 PHE C1021 TYR 0.032 0.002 TYR C 191 ARG 0.006 0.000 ARG A1046 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 1768) hydrogen bonds : angle 3.89714 ( 5244) SS BOND : bond 0.00740 ( 4) SS BOND : angle 2.86261 ( 8) covalent geometry : bond 0.00381 (31188) covalent geometry : angle 0.59301 (42252) *********************** 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 459 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 381 time to evaluate : 7.266 Fit side-chains revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8570 (tt0) cc_final: 0.8249 (tp40) REVERT: A 304 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.6858 (m-80) REVERT: A 353 MET cc_start: 0.6710 (mpp) cc_final: 0.6043 (pmm) REVERT: A 396 MET cc_start: 0.7480 (mmp) cc_final: 0.6925 (mmp) REVERT: A 488 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7944 (tt) REVERT: A 605 LYS cc_start: 0.8256 (mmtp) cc_final: 0.7990 (mmtm) REVERT: A 613 GLU cc_start: 0.8614 (mp0) cc_final: 0.8391 (mp0) REVERT: A 731 PHE cc_start: 0.7442 (m-80) cc_final: 0.7001 (t80) REVERT: A 732 THR cc_start: 0.8875 (m) cc_final: 0.8630 (p) REVERT: A 868 PHE cc_start: 0.8836 (m-10) cc_final: 0.7659 (t80) REVERT: A 1021 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6747 (t80) REVERT: A 1023 MET cc_start: 0.6954 (mmm) cc_final: 0.5879 (mtp) REVERT: A 1059 MET cc_start: 0.7661 (mpp) cc_final: 0.7451 (mmm) REVERT: B 353 MET cc_start: 0.6581 (mpp) cc_final: 0.6100 (pmm) REVERT: B 488 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7866 (tt) REVERT: B 605 LYS cc_start: 0.8263 (mmtp) cc_final: 0.7993 (mmtm) REVERT: B 613 GLU cc_start: 0.8567 (mp0) cc_final: 0.8361 (mp0) REVERT: B 627 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8494 (mp0) REVERT: B 689 ASP cc_start: 0.8344 (t0) cc_final: 0.8082 (m-30) REVERT: B 732 THR cc_start: 0.8828 (m) cc_final: 0.8588 (p) REVERT: B 868 PHE cc_start: 0.8817 (m-10) cc_final: 0.7628 (t80) REVERT: B 1023 MET cc_start: 0.6804 (mmm) cc_final: 0.5725 (mtp) REVERT: B 1046 ARG cc_start: 0.7581 (ttm170) cc_final: 0.7372 (ttm110) REVERT: B 1059 MET cc_start: 0.7526 (mpp) cc_final: 0.7324 (mmm) REVERT: C 189 MET cc_start: 0.7831 (mtm) cc_final: 0.7470 (mtm) REVERT: C 280 GLN cc_start: 0.8542 (tt0) cc_final: 0.8210 (tp40) REVERT: C 353 MET cc_start: 0.6675 (mpp) cc_final: 0.6048 (pmm) REVERT: C 396 MET cc_start: 0.7489 (mmp) cc_final: 0.7090 (mmp) REVERT: C 488 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7975 (tt) REVERT: C 491 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7837 (tp30) REVERT: C 627 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8515 (mp0) REVERT: C 689 ASP cc_start: 0.8284 (t0) cc_final: 0.8051 (m-30) REVERT: C 732 THR cc_start: 0.8825 (m) cc_final: 0.8585 (p) REVERT: C 868 PHE cc_start: 0.8773 (m-10) cc_final: 0.7609 (t80) REVERT: C 1023 MET cc_start: 0.6851 (mmm) cc_final: 0.5756 (mtp) REVERT: D 189 MET cc_start: 0.7844 (mtm) cc_final: 0.7477 (mtm) REVERT: D 280 GLN cc_start: 0.8560 (tt0) cc_final: 0.8232 (tp40) REVERT: D 353 MET cc_start: 0.6747 (mpp) cc_final: 0.6142 (pmm) REVERT: D 396 MET cc_start: 0.7176 (mmp) cc_final: 0.6725 (mmp) REVERT: D 488 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7950 (tt) REVERT: D 521 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7135 (tp) REVERT: D 689 ASP cc_start: 0.8274 (t0) cc_final: 0.8035 (m-30) REVERT: D 702 ILE cc_start: 0.8521 (mp) cc_final: 0.8069 (tt) REVERT: D 732 THR cc_start: 0.8835 (m) cc_final: 0.8584 (p) REVERT: D 868 PHE cc_start: 0.8833 (m-10) cc_final: 0.7649 (t80) REVERT: D 989 ASN cc_start: 0.7318 (t0) cc_final: 0.7040 (t0) REVERT: D 1023 MET cc_start: 0.6834 (mmm) cc_final: 0.5795 (mtp) REVERT: D 1059 MET cc_start: 0.7653 (mpp) cc_final: 0.7416 (mmm) REVERT: D 1068 ASN cc_start: 0.8213 (m-40) cc_final: 0.7998 (m-40) outliers start: 78 outliers final: 49 residues processed: 431 average time/residue: 0.6949 time to fit residues: 499.6628 Evaluate side-chains 426 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 370 time to evaluate : 7.500 ------------------------------------------------------------------------------- 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 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 484 LEU 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 851 ARG Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 179 ILE 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 645 VAL Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1078 MET 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 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 851 ARG 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 148 VAL Chi-restraints excluded: chain D residue 179 ILE 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 521 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 851 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 103 optimal weight: 9.9990 chunk 185 optimal weight: 0.0050 chunk 286 optimal weight: 7.9990 chunk 201 optimal weight: 0.8980 chunk 271 optimal weight: 0.2980 chunk 126 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 326 optimal weight: 6.9990 chunk 281 optimal weight: 8.9990 chunk 238 optimal weight: 4.9990 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 HIS B 500 HIS C 635 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.162414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110115 restraints weight = 49243.501| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.47 r_work: 0.3261 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31192 Z= 0.121 Angle : 0.570 9.902 42260 Z= 0.293 Chirality : 0.039 0.178 4708 Planarity : 0.003 0.041 5280 Dihedral : 4.945 44.849 4024 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.04 % Allowed : 15.53 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3656 helix: 1.55 (0.11), residues: 2484 sheet: -1.17 (0.35), residues: 192 loop : -2.33 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 898 HIS 0.004 0.001 HIS A 138 PHE 0.023 0.001 PHE D1021 TYR 0.032 0.001 TYR C 191 ARG 0.005 0.000 ARG A1046 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 1768) hydrogen bonds : angle 3.82916 ( 5244) SS BOND : bond 0.00644 ( 4) SS BOND : angle 2.28686 ( 8) covalent geometry : bond 0.00278 (31188) covalent geometry : angle 0.56899 (42252) *********************** 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 450 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 382 time to evaluate : 3.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8571 (tt0) cc_final: 0.8267 (tp40) REVERT: A 304 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.6863 (m-80) REVERT: A 353 MET cc_start: 0.6626 (mpp) cc_final: 0.5987 (pmm) REVERT: A 396 MET cc_start: 0.7490 (mmp) cc_final: 0.6993 (mmp) REVERT: A 488 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7892 (tt) REVERT: A 605 LYS cc_start: 0.8231 (mmtp) cc_final: 0.7953 (mmtm) REVERT: A 613 GLU cc_start: 0.8553 (mp0) cc_final: 0.8127 (mp0) REVERT: A 731 PHE cc_start: 0.7382 (m-80) cc_final: 0.7034 (t80) REVERT: A 732 THR cc_start: 0.8665 (m) cc_final: 0.8440 (p) REVERT: A 868 PHE cc_start: 0.8765 (m-10) cc_final: 0.7604 (t80) REVERT: A 989 ASN cc_start: 0.7271 (t0) cc_final: 0.7044 (t0) REVERT: A 1021 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6746 (t80) REVERT: A 1023 MET cc_start: 0.6981 (mmm) cc_final: 0.5847 (mtp) REVERT: B 304 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.7285 (m-80) REVERT: B 353 MET cc_start: 0.6553 (mpp) cc_final: 0.6118 (pmm) REVERT: B 396 MET cc_start: 0.6603 (mmp) cc_final: 0.5683 (mmp) REVERT: B 488 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7651 (tt) REVERT: B 605 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7952 (mmtm) REVERT: B 613 GLU cc_start: 0.8540 (mp0) cc_final: 0.8130 (mp0) REVERT: B 731 PHE cc_start: 0.7408 (m-80) cc_final: 0.7019 (t80) REVERT: B 732 THR cc_start: 0.8614 (m) cc_final: 0.8401 (p) REVERT: B 868 PHE cc_start: 0.8785 (m-10) cc_final: 0.7606 (t80) REVERT: B 1023 MET cc_start: 0.6871 (mmm) cc_final: 0.5783 (mtp) REVERT: B 1046 ARG cc_start: 0.7586 (ttm170) cc_final: 0.7307 (ttm110) REVERT: C 189 MET cc_start: 0.7691 (mtm) cc_final: 0.7335 (mtm) REVERT: C 280 GLN cc_start: 0.8537 (tt0) cc_final: 0.8194 (tp40) REVERT: C 304 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.7376 (m-80) REVERT: C 353 MET cc_start: 0.6543 (mpp) cc_final: 0.6088 (pmm) REVERT: C 356 GLU cc_start: 0.8483 (pt0) cc_final: 0.8210 (tp30) REVERT: C 396 MET cc_start: 0.7363 (mmp) cc_final: 0.6931 (mmp) REVERT: C 491 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7760 (tp30) REVERT: C 627 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8519 (mp0) REVERT: C 731 PHE cc_start: 0.7400 (m-80) cc_final: 0.7001 (t80) REVERT: C 732 THR cc_start: 0.8791 (m) cc_final: 0.8573 (p) REVERT: C 868 PHE cc_start: 0.8756 (m-10) cc_final: 0.7588 (t80) REVERT: C 1023 MET cc_start: 0.6866 (mmm) cc_final: 0.5773 (mtp) REVERT: D 189 MET cc_start: 0.7828 (mtm) cc_final: 0.7492 (mtm) REVERT: D 280 GLN cc_start: 0.8551 (tt0) cc_final: 0.8232 (tp40) REVERT: D 353 MET cc_start: 0.6716 (mpp) cc_final: 0.6027 (pmm) REVERT: D 356 GLU cc_start: 0.8505 (pt0) cc_final: 0.8237 (tp30) REVERT: D 396 MET cc_start: 0.7380 (mmp) cc_final: 0.7062 (mmp) REVERT: D 488 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7914 (tt) REVERT: D 521 LEU cc_start: 0.7313 (mp) cc_final: 0.7080 (tp) REVERT: D 627 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8473 (mp0) REVERT: D 731 PHE cc_start: 0.7428 (m-80) cc_final: 0.7016 (t80) REVERT: D 732 THR cc_start: 0.8691 (m) cc_final: 0.8465 (p) REVERT: D 868 PHE cc_start: 0.8799 (m-10) cc_final: 0.7604 (t80) REVERT: D 1023 MET cc_start: 0.7034 (mmm) cc_final: 0.6017 (mtp) outliers start: 68 outliers final: 34 residues processed: 427 average time/residue: 0.4912 time to fit residues: 342.6559 Evaluate side-chains 404 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 363 time to evaluate : 3.800 ------------------------------------------------------------------------------- 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 469 ASP Chi-restraints excluded: chain A residue 484 LEU 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 851 ARG Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain B residue 121 SER 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 355 LYS Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL 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 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 851 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 327 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN B 635 ASN C 500 HIS D 500 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.158303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105549 restraints weight = 49422.651| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.51 r_work: 0.3194 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 31192 Z= 0.229 Angle : 0.658 10.468 42260 Z= 0.337 Chirality : 0.043 0.187 4708 Planarity : 0.004 0.042 5280 Dihedral : 5.207 51.305 4024 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.16 % Allowed : 15.72 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3656 helix: 1.42 (0.11), residues: 2472 sheet: -1.32 (0.34), residues: 192 loop : -2.48 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 898 HIS 0.005 0.001 HIS C 765 PHE 0.033 0.002 PHE B1021 TYR 0.028 0.002 TYR D 191 ARG 0.009 0.001 ARG C1046 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 1768) hydrogen bonds : angle 4.04447 ( 5244) SS BOND : bond 0.00762 ( 4) SS BOND : angle 3.11766 ( 8) covalent geometry : bond 0.00558 (31188) covalent geometry : angle 0.65639 (42252) *********************** 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 450 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 378 time to evaluate : 5.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8596 (tt0) cc_final: 0.8292 (tp40) REVERT: A 304 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.6958 (m-80) REVERT: A 353 MET cc_start: 0.6732 (mpp) cc_final: 0.6064 (pmm) REVERT: A 488 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7950 (tt) REVERT: A 613 GLU cc_start: 0.8546 (mp0) cc_final: 0.8120 (mp0) REVERT: A 616 GLU cc_start: 0.7971 (mp0) cc_final: 0.7650 (mp0) REVERT: A 627 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8688 (mt-10) REVERT: A 702 ILE cc_start: 0.8468 (mp) cc_final: 0.8020 (tt) REVERT: A 731 PHE cc_start: 0.7424 (m-80) cc_final: 0.7007 (t80) REVERT: A 732 THR cc_start: 0.8717 (m) cc_final: 0.8457 (p) REVERT: A 868 PHE cc_start: 0.8856 (m-10) cc_final: 0.7682 (t80) REVERT: A 1021 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6818 (t80) REVERT: A 1023 MET cc_start: 0.6984 (mmm) cc_final: 0.5852 (mtp) REVERT: B 198 ASP cc_start: 0.8084 (m-30) cc_final: 0.7823 (m-30) REVERT: B 353 MET cc_start: 0.6659 (mpp) cc_final: 0.5979 (pmm) REVERT: B 396 MET cc_start: 0.6654 (mmp) cc_final: 0.5615 (mmp) REVERT: B 402 GLU cc_start: 0.8035 (tt0) cc_final: 0.7810 (tt0) REVERT: B 488 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7758 (tt) REVERT: B 613 GLU cc_start: 0.8542 (mp0) cc_final: 0.8137 (mp0) REVERT: B 616 GLU cc_start: 0.7946 (mp0) cc_final: 0.7617 (mp0) REVERT: B 731 PHE cc_start: 0.7426 (m-80) cc_final: 0.7005 (t80) REVERT: B 732 THR cc_start: 0.8650 (m) cc_final: 0.8395 (p) REVERT: B 788 MET cc_start: 0.7817 (mmt) cc_final: 0.7569 (mmp) REVERT: B 868 PHE cc_start: 0.8830 (m-10) cc_final: 0.7680 (t80) REVERT: B 1023 MET cc_start: 0.6983 (mmm) cc_final: 0.5855 (mtp) REVERT: C 189 MET cc_start: 0.7725 (mtm) cc_final: 0.7332 (mtm) REVERT: C 280 GLN cc_start: 0.8580 (tt0) cc_final: 0.8246 (tp40) REVERT: C 353 MET cc_start: 0.6735 (mpp) cc_final: 0.6107 (pmm) REVERT: C 396 MET cc_start: 0.7400 (mmp) cc_final: 0.7031 (mmp) REVERT: C 488 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8055 (tt) REVERT: C 491 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7883 (tp30) REVERT: C 627 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8575 (mp0) REVERT: C 646 TYR cc_start: 0.6324 (t80) cc_final: 0.5998 (t80) REVERT: C 731 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6981 (t80) REVERT: C 732 THR cc_start: 0.8648 (m) cc_final: 0.8393 (p) REVERT: C 788 MET cc_start: 0.7794 (mmt) cc_final: 0.7548 (mmp) REVERT: C 868 PHE cc_start: 0.8823 (m-10) cc_final: 0.7681 (t80) REVERT: C 1023 MET cc_start: 0.6997 (mmm) cc_final: 0.5872 (mtp) REVERT: C 1049 ASP cc_start: 0.7399 (m-30) cc_final: 0.6917 (m-30) REVERT: D 189 MET cc_start: 0.7865 (mtm) cc_final: 0.7505 (mtm) REVERT: D 280 GLN cc_start: 0.8583 (tt0) cc_final: 0.8238 (tp40) REVERT: D 353 MET cc_start: 0.6741 (mpp) cc_final: 0.6129 (pmm) REVERT: D 488 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7971 (tt) REVERT: D 521 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7230 (tp) REVERT: D 627 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8533 (mp0) REVERT: D 731 PHE cc_start: 0.7468 (m-80) cc_final: 0.7016 (t80) REVERT: D 732 THR cc_start: 0.8722 (m) cc_final: 0.8466 (p) REVERT: D 868 PHE cc_start: 0.8848 (m-10) cc_final: 0.7660 (t80) REVERT: D 1023 MET cc_start: 0.6991 (mmm) cc_final: 0.5910 (mtp) outliers start: 72 outliers final: 52 residues processed: 425 average time/residue: 0.6663 time to fit residues: 465.2717 Evaluate side-chains 424 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 364 time to evaluate : 5.894 ------------------------------------------------------------------------------- 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 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 484 LEU 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 851 ARG Chi-restraints excluded: chain A residue 1021 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 179 ILE Chi-restraints excluded: chain B residue 209 ILE 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 645 VAL Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 1009 LEU 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 209 ILE 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 731 PHE Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL 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 521 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 804 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 1078 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 194 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 279 optimal weight: 20.0000 chunk 213 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 356 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN D 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.160717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108145 restraints weight = 49392.938| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.49 r_work: 0.3232 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.003 0.047 31192 Z= 0.145 Angle : 0.611 11.881 42260 Z= 0.311 Chirality : 0.040 0.178 4708 Planarity : 0.004 0.040 5280 Dihedral : 5.044 46.240 4024 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.86 % Allowed : 16.41 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3656 helix: 1.53 (0.11), residues: 2476 sheet: -1.20 (0.35), residues: 192 loop : -2.43 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 898 HIS 0.004 0.001 HIS A 138 PHE 0.022 0.001 PHE D1021 TYR 0.032 0.001 TYR D 191 ARG 0.008 0.000 ARG C1046 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 1768) hydrogen bonds : angle 3.92243 ( 5244) SS BOND : bond 0.00690 ( 4) SS BOND : angle 2.51257 ( 8) covalent geometry : bond 0.00345 (31188) covalent geometry : angle 0.61055 (42252) ********************** 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 431 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 369 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8580 (tt0) cc_final: 0.8288 (tp40) REVERT: A 304 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.6911 (m-80) REVERT: A 353 MET cc_start: 0.6675 (mpp) cc_final: 0.6229 (pmm) REVERT: A 396 MET cc_start: 0.7418 (mmp) cc_final: 0.6864 (mmp) REVERT: A 488 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7903 (tt) REVERT: A 566 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8799 (mp) REVERT: A 613 GLU cc_start: 0.8483 (mp0) cc_final: 0.8160 (mp0) REVERT: A 627 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8664 (mt-10) REVERT: A 702 ILE cc_start: 0.8447 (mp) cc_final: 0.8010 (tt) REVERT: A 731 PHE cc_start: 0.7414 (m-80) cc_final: 0.6997 (t80) REVERT: A 732 THR cc_start: 0.8653 (m) cc_final: 0.8416 (p) REVERT: A 788 MET cc_start: 0.7812 (mmt) cc_final: 0.7558 (mmp) REVERT: A 868 PHE cc_start: 0.8820 (m-10) cc_final: 0.7644 (t80) REVERT: A 989 ASN cc_start: 0.7395 (t0) cc_final: 0.7136 (t0) REVERT: A 1021 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.6815 (t80) REVERT: A 1023 MET cc_start: 0.6975 (mmm) cc_final: 0.5836 (mtp) REVERT: B 198 ASP cc_start: 0.8078 (m-30) cc_final: 0.7837 (m-30) REVERT: B 353 MET cc_start: 0.6630 (mpp) cc_final: 0.6201 (pmm) REVERT: B 396 MET cc_start: 0.6611 (mmp) cc_final: 0.5611 (mmp) REVERT: B 488 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7720 (tt) REVERT: B 613 GLU cc_start: 0.8477 (mp0) cc_final: 0.8168 (mp0) REVERT: B 731 PHE cc_start: 0.7405 (m-80) cc_final: 0.7007 (t80) REVERT: B 732 THR cc_start: 0.8602 (m) cc_final: 0.8379 (p) REVERT: B 788 MET cc_start: 0.7761 (mmt) cc_final: 0.7512 (mmp) REVERT: B 868 PHE cc_start: 0.8796 (m-10) cc_final: 0.7641 (t80) REVERT: B 1023 MET cc_start: 0.6887 (mmm) cc_final: 0.5797 (mtp) REVERT: B 1046 ARG cc_start: 0.7523 (ttm170) cc_final: 0.7202 (ttm110) REVERT: C 189 MET cc_start: 0.7702 (mtm) cc_final: 0.7332 (mtm) REVERT: C 280 GLN cc_start: 0.8556 (tt0) cc_final: 0.8196 (tp40) REVERT: C 353 MET cc_start: 0.6594 (mpp) cc_final: 0.6131 (pmm) REVERT: C 356 GLU cc_start: 0.8530 (pt0) cc_final: 0.8276 (tp30) REVERT: C 396 MET cc_start: 0.7373 (mmp) cc_final: 0.6980 (mmp) REVERT: C 488 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7931 (tt) REVERT: C 491 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7776 (tp30) REVERT: C 646 TYR cc_start: 0.6368 (t80) cc_final: 0.6028 (t80) REVERT: C 731 PHE cc_start: 0.7396 (m-80) cc_final: 0.6971 (t80) REVERT: C 732 THR cc_start: 0.8595 (m) cc_final: 0.8365 (p) REVERT: C 788 MET cc_start: 0.7749 (mmt) cc_final: 0.7495 (mmp) REVERT: C 868 PHE cc_start: 0.8768 (m-10) cc_final: 0.7608 (t80) REVERT: C 1023 MET cc_start: 0.6922 (mmm) cc_final: 0.5803 (mtp) REVERT: C 1059 MET cc_start: 0.8224 (mmm) cc_final: 0.7976 (mmm) REVERT: D 189 MET cc_start: 0.7854 (mtm) cc_final: 0.7496 (mtm) REVERT: D 198 ASP cc_start: 0.8088 (m-30) cc_final: 0.7835 (m-30) REVERT: D 280 GLN cc_start: 0.8564 (tt0) cc_final: 0.8214 (tp40) REVERT: D 353 MET cc_start: 0.6678 (mpp) cc_final: 0.6274 (pmm) REVERT: D 445 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8203 (mm-30) REVERT: D 488 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7914 (tt) REVERT: D 521 LEU cc_start: 0.7381 (mp) cc_final: 0.7116 (tp) REVERT: D 566 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8791 (mp) REVERT: D 627 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8502 (mp0) REVERT: D 702 ILE cc_start: 0.8458 (mp) cc_final: 0.8013 (tt) REVERT: D 731 PHE cc_start: 0.7511 (m-80) cc_final: 0.7011 (t80) REVERT: D 732 THR cc_start: 0.8661 (m) cc_final: 0.8427 (p) REVERT: D 801 MET cc_start: 0.8432 (ptt) cc_final: 0.8036 (ptp) REVERT: D 868 PHE cc_start: 0.8809 (m-10) cc_final: 0.7634 (t80) REVERT: D 1023 MET cc_start: 0.6960 (mmm) cc_final: 0.5867 (mtp) outliers start: 62 outliers final: 42 residues processed: 415 average time/residue: 0.4076 time to fit residues: 274.3051 Evaluate side-chains 414 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 364 time to evaluate : 3.673 ------------------------------------------------------------------------------- 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 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 1021 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 209 ILE 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 627 GLU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 797 LEU 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 209 ILE 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 797 LEU Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL 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 566 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 26 optimal weight: 7.9990 chunk 302 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 350 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.159079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106139 restraints weight = 49238.483| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.47 r_work: 0.3204 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 31192 Z= 0.198 Angle : 0.653 11.518 42260 Z= 0.333 Chirality : 0.042 0.181 4708 Planarity : 0.004 0.040 5280 Dihedral : 5.147 49.441 4024 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.98 % Allowed : 16.26 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3656 helix: 1.45 (0.10), residues: 2472 sheet: -1.23 (0.35), residues: 192 loop : -2.44 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 898 HIS 0.005 0.001 HIS C 765 PHE 0.035 0.002 PHE B1021 TYR 0.029 0.002 TYR C 191 ARG 0.008 0.000 ARG C1046 Details of bonding type rmsd hydrogen bonds : bond 0.04676 ( 1768) hydrogen bonds : angle 4.02475 ( 5244) SS BOND : bond 0.00733 ( 4) SS BOND : angle 2.92455 ( 8) covalent geometry : bond 0.00484 (31188) covalent geometry : angle 0.65193 (42252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24855.57 seconds wall clock time: 439 minutes 39.46 seconds (26379.46 seconds total)