Starting phenix.real_space_refine on Fri Mar 6 11:01:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrf_32725/03_2026/7wrf_32725.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrf_32725/03_2026/7wrf_32725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wrf_32725/03_2026/7wrf_32725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrf_32725/03_2026/7wrf_32725.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wrf_32725/03_2026/7wrf_32725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrf_32725/03_2026/7wrf_32725.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 S 140 5.16 5 Na 1 4.78 5 C 19820 2.51 5 N 5052 2.21 5 O 5452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30469 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "B" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "C" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "D" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' CA': 1, ' NA': 1, 'KX7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.52, per 1000 atoms: 0.21 Number of scatterers: 30469 At special positions: 0 Unit cell: (151.086, 151.086, 156.156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 140 16.00 Na 1 11.00 O 5452 8.00 N 5052 7.00 C 19820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.03 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.02 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.02 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.2 seconds 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7080 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 4 sheets defined 70.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 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: 5.42 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4884 1.31 - 1.44: 8856 1.44 - 1.57: 17236 1.57 - 1.70: 0 1.70 - 1.83: 212 Bond restraints: 31188 Sorted by residual: bond pdb=" N21 KX7 D1202 " pdb=" O23 KX7 D1202 " ideal model delta sigma weight residual 1.208 1.402 -0.194 2.00e-02 2.50e+03 9.36e+01 bond pdb=" N21 KX7 B1202 " pdb=" O23 KX7 B1202 " ideal model delta sigma weight residual 1.208 1.401 -0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" N21 KX7 A1203 " pdb=" O23 KX7 A1203 " ideal model delta sigma weight residual 1.208 1.401 -0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" N21 KX7 C1202 " pdb=" O23 KX7 C1202 " ideal model delta sigma weight residual 1.208 1.401 -0.193 2.00e-02 2.50e+03 9.28e+01 bond pdb=" C05 KX7 D1202 " pdb=" N07 KX7 D1202 " ideal model delta sigma weight residual 1.355 1.495 -0.140 2.00e-02 2.50e+03 4.89e+01 ... (remaining 31183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 39939 1.94 - 3.88: 1912 3.88 - 5.82: 297 5.82 - 7.76: 76 7.76 - 9.71: 28 Bond angle restraints: 42252 Sorted by residual: angle pdb=" N VAL B 791 " pdb=" CA VAL B 791 " pdb=" C VAL B 791 " ideal model delta sigma weight residual 112.96 108.21 4.75 1.00e+00 1.00e+00 2.26e+01 angle pdb=" N VAL A 791 " pdb=" CA VAL A 791 " pdb=" C VAL A 791 " ideal model delta sigma weight residual 112.96 108.25 4.71 1.00e+00 1.00e+00 2.22e+01 angle pdb=" N VAL C 791 " pdb=" CA VAL C 791 " pdb=" C VAL C 791 " ideal model delta sigma weight residual 112.96 108.26 4.70 1.00e+00 1.00e+00 2.21e+01 angle pdb=" N VAL D 791 " pdb=" CA VAL D 791 " pdb=" C VAL D 791 " ideal model delta sigma weight residual 112.96 108.28 4.68 1.00e+00 1.00e+00 2.19e+01 angle pdb=" C ILE A 701 " pdb=" N ILE A 702 " pdb=" CA ILE A 702 " ideal model delta sigma weight residual 120.33 123.78 -3.45 8.00e-01 1.56e+00 1.86e+01 ... (remaining 42247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.57: 17104 14.57 - 29.14: 884 29.14 - 43.71: 272 43.71 - 58.28: 16 58.28 - 72.85: 28 Dihedral angle restraints: 18304 sinusoidal: 7392 harmonic: 10912 Sorted by residual: dihedral pdb=" CA PRO B1012 " pdb=" C PRO B1012 " pdb=" N PHE B1013 " pdb=" CA PHE B1013 " ideal model delta harmonic sigma weight residual -180.00 -150.09 -29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA PRO D1012 " pdb=" C PRO D1012 " pdb=" N PHE D1013 " pdb=" CA PHE D1013 " ideal model delta harmonic sigma weight residual -180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA PRO A1012 " pdb=" C PRO A1012 " pdb=" N PHE A1013 " pdb=" CA PHE A1013 " ideal model delta harmonic sigma weight residual -180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2875 0.045 - 0.090: 1358 0.090 - 0.134: 352 0.134 - 0.179: 99 0.179 - 0.224: 24 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CG LEU A 521 " pdb=" CB LEU A 521 " pdb=" CD1 LEU A 521 " pdb=" CD2 LEU A 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU B 521 " pdb=" CB LEU B 521 " pdb=" CD1 LEU B 521 " pdb=" CD2 LEU B 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU D 521 " pdb=" CB LEU D 521 " pdb=" CD1 LEU D 521 " pdb=" CD2 LEU D 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 4705 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 141 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO D 142 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 142 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 142 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 141 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO A 142 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 141 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO B 142 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 142 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 142 " 0.034 5.00e-02 4.00e+02 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 8661 2.82 - 3.34: 28118 3.34 - 3.86: 48975 3.86 - 4.38: 56324 4.38 - 4.90: 96780 Nonbonded interactions: 238858 Sorted by model distance: nonbonded pdb=" O VAL A1065 " pdb=" OG1 THR A1069 " model vdw 2.294 3.040 nonbonded pdb=" O VAL C1065 " pdb=" OG1 THR C1069 " model vdw 2.295 3.040 nonbonded pdb=" O VAL B1065 " pdb=" OG1 THR B1069 " model vdw 2.295 3.040 nonbonded pdb=" O VAL D1065 " pdb=" OG1 THR D1069 " model vdw 2.295 3.040 nonbonded pdb=" O VAL D 728 " pdb=" OG1 THR D 732 " model vdw 2.324 3.040 ... (remaining 238853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 102 through 1201) selection = (chain 'B' and resid 102 through 1201) selection = (chain 'C' and resid 102 through 1201) selection = (chain 'D' and resid 102 through 1201) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 25.950 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.11), residues: 3656 helix: -2.03 (0.08), residues: 2412 sheet: -1.90 (0.32), residues: 208 loop : -3.28 (0.15), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1008 TYR 0.038 0.003 TYR A 772 PHE 0.031 0.003 PHE B 304 TRP 0.026 0.003 TRP B 377 HIS 0.007 0.002 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00808 (31188) covalent geometry : angle 0.98652 (42252) SS BOND : bond 0.00636 ( 4) SS BOND : angle 4.83437 ( 8) hydrogen bonds : bond 0.14823 ( 1768) hydrogen bonds : angle 6.41497 ( 5244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 827 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.8176 (ttt180) cc_final: 0.7920 (ttp-110) REVERT: A 280 GLN cc_start: 0.8309 (tt0) cc_final: 0.8104 (tm-30) REVERT: A 569 ILE cc_start: 0.9136 (tp) cc_final: 0.8904 (tp) REVERT: A 702 ILE cc_start: 0.8413 (mt) cc_final: 0.8152 (tt) REVERT: A 787 TYR cc_start: 0.7393 (t80) cc_final: 0.7114 (t80) REVERT: A 868 PHE cc_start: 0.8203 (m-10) cc_final: 0.7610 (t80) REVERT: A 1023 MET cc_start: 0.7034 (mmm) cc_final: 0.5993 (mtp) REVERT: B 162 ARG cc_start: 0.8118 (ttt180) cc_final: 0.7887 (ttp-110) REVERT: B 191 TYR cc_start: 0.7537 (t80) cc_final: 0.7231 (t80) REVERT: B 627 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7843 (mt-10) REVERT: B 691 LYS cc_start: 0.7529 (mtpt) cc_final: 0.7271 (mtpt) REVERT: B 702 ILE cc_start: 0.8410 (mt) cc_final: 0.8163 (tt) REVERT: B 787 TYR cc_start: 0.7387 (t80) cc_final: 0.7102 (t80) REVERT: B 868 PHE cc_start: 0.8192 (m-10) cc_final: 0.7601 (t80) REVERT: B 1023 MET cc_start: 0.6992 (mmm) cc_final: 0.5936 (mtp) REVERT: C 191 TYR cc_start: 0.7627 (t80) cc_final: 0.7354 (t80) REVERT: C 280 GLN cc_start: 0.8276 (tt0) cc_final: 0.8063 (tm-30) REVERT: C 569 ILE cc_start: 0.9143 (tp) cc_final: 0.8922 (tp) REVERT: C 627 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7856 (mt-10) REVERT: C 702 ILE cc_start: 0.8404 (mt) cc_final: 0.8160 (tt) REVERT: C 787 TYR cc_start: 0.7411 (t80) cc_final: 0.7151 (t80) REVERT: C 868 PHE cc_start: 0.8177 (m-10) cc_final: 0.7612 (t80) REVERT: C 1023 MET cc_start: 0.6850 (mmm) cc_final: 0.5837 (mtp) REVERT: C 1047 ASN cc_start: 0.7790 (m-40) cc_final: 0.7583 (m110) REVERT: D 191 TYR cc_start: 0.7609 (t80) cc_final: 0.7317 (t80) REVERT: D 280 GLN cc_start: 0.8337 (tt0) cc_final: 0.8136 (tm-30) REVERT: D 569 ILE cc_start: 0.9109 (tp) cc_final: 0.8899 (tp) REVERT: D 702 ILE cc_start: 0.8403 (mt) cc_final: 0.8141 (tt) REVERT: D 787 TYR cc_start: 0.7408 (t80) cc_final: 0.7139 (t80) REVERT: D 868 PHE cc_start: 0.8181 (m-10) cc_final: 0.7621 (t80) REVERT: D 1023 MET cc_start: 0.6889 (mmm) cc_final: 0.5893 (mtp) outliers start: 4 outliers final: 0 residues processed: 827 average time/residue: 0.2169 time to fit residues: 273.2944 Evaluate side-chains 427 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 257 HIS A 259 HIS A 438 GLN A 572 ASN A 675 GLN A 987 GLN B 136 HIS B 256 ASN B 257 HIS B 259 HIS B 438 GLN B 572 ASN B 675 GLN B 741 ASN C 136 HIS C 257 HIS C 259 HIS C 294 ASN C 438 GLN C 572 ASN C 675 GLN C 741 ASN D 136 HIS D 257 HIS D 259 HIS D 438 GLN D 572 ASN D 675 GLN D 987 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.159862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.107802 restraints weight = 48820.082| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.42 r_work: 0.3220 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 31192 Z= 0.234 Angle : 0.703 8.924 42260 Z= 0.369 Chirality : 0.044 0.147 4708 Planarity : 0.005 0.054 5280 Dihedral : 6.087 50.303 4024 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.16 % Allowed : 8.26 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.13), residues: 3656 helix: -0.19 (0.10), residues: 2440 sheet: -1.89 (0.32), residues: 192 loop : -3.26 (0.15), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 278 TYR 0.016 0.002 TYR B1005 PHE 0.032 0.002 PHE A 752 TRP 0.022 0.002 TRP A 898 HIS 0.005 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00560 (31188) covalent geometry : angle 0.70204 (42252) SS BOND : bond 0.00853 ( 4) SS BOND : angle 2.67642 ( 8) hydrogen bonds : bond 0.05750 ( 1768) hydrogen bonds : angle 4.58802 ( 5244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 458 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8109 (t80) cc_final: 0.7755 (t80) REVERT: A 280 GLN cc_start: 0.8533 (tt0) cc_final: 0.8220 (tp40) REVERT: A 491 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7923 (tp30) REVERT: A 702 ILE cc_start: 0.8508 (mt) cc_final: 0.8272 (tt) REVERT: A 787 TYR cc_start: 0.7927 (t80) cc_final: 0.7467 (t80) REVERT: A 800 VAL cc_start: 0.9312 (t) cc_final: 0.9100 (p) REVERT: A 868 PHE cc_start: 0.8863 (m-10) cc_final: 0.7693 (t80) REVERT: A 914 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8351 (mm-40) REVERT: A 1005 TYR cc_start: 0.6938 (m-10) cc_final: 0.5669 (m-80) REVERT: A 1021 PHE cc_start: 0.7528 (m-80) cc_final: 0.7286 (m-80) REVERT: A 1023 MET cc_start: 0.7040 (mmm) cc_final: 0.5978 (mtp) REVERT: B 491 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7859 (tp30) REVERT: B 569 ILE cc_start: 0.9172 (tp) cc_final: 0.8971 (tp) REVERT: B 702 ILE cc_start: 0.8512 (mt) cc_final: 0.8298 (tt) REVERT: B 787 TYR cc_start: 0.7907 (t80) cc_final: 0.7461 (t80) REVERT: B 801 MET cc_start: 0.8255 (ptm) cc_final: 0.8012 (ptt) REVERT: B 868 PHE cc_start: 0.8845 (m-10) cc_final: 0.7661 (t80) REVERT: B 1005 TYR cc_start: 0.6856 (m-10) cc_final: 0.5647 (m-80) REVERT: B 1021 PHE cc_start: 0.7556 (m-80) cc_final: 0.7312 (m-80) REVERT: B 1023 MET cc_start: 0.6981 (mmm) cc_final: 0.5904 (mtp) REVERT: C 191 TYR cc_start: 0.8126 (t80) cc_final: 0.7823 (t80) REVERT: C 280 GLN cc_start: 0.8520 (tt0) cc_final: 0.8204 (tp40) REVERT: C 353 MET cc_start: 0.6291 (mpp) cc_final: 0.5896 (ptp) REVERT: C 491 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7879 (tp30) REVERT: C 702 ILE cc_start: 0.8498 (mt) cc_final: 0.8297 (tt) REVERT: C 741 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8679 (m-40) REVERT: C 787 TYR cc_start: 0.7909 (t80) cc_final: 0.7460 (t80) REVERT: C 800 VAL cc_start: 0.9308 (t) cc_final: 0.9101 (p) REVERT: C 801 MET cc_start: 0.8419 (ptm) cc_final: 0.8187 (ptt) REVERT: C 864 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8658 (mp) REVERT: C 868 PHE cc_start: 0.8840 (m-10) cc_final: 0.7665 (t80) REVERT: C 1005 TYR cc_start: 0.6855 (m-10) cc_final: 0.5634 (m-80) REVERT: C 1021 PHE cc_start: 0.7564 (m-80) cc_final: 0.7320 (m-80) REVERT: C 1023 MET cc_start: 0.6948 (mmm) cc_final: 0.5876 (mtp) REVERT: D 280 GLN cc_start: 0.8559 (tt0) cc_final: 0.8252 (tp40) REVERT: D 353 MET cc_start: 0.6356 (mpp) cc_final: 0.5973 (ptp) REVERT: D 491 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7921 (tp30) REVERT: D 702 ILE cc_start: 0.8510 (mt) cc_final: 0.8275 (tt) REVERT: D 787 TYR cc_start: 0.7919 (t80) cc_final: 0.7463 (t80) REVERT: D 800 VAL cc_start: 0.9332 (t) cc_final: 0.9103 (p) REVERT: D 868 PHE cc_start: 0.8847 (m-10) cc_final: 0.7688 (t80) REVERT: D 1005 TYR cc_start: 0.6929 (m-10) cc_final: 0.5732 (m-80) REVERT: D 1023 MET cc_start: 0.7059 (mmm) cc_final: 0.5999 (mtp) REVERT: D 1066 LYS cc_start: 0.9007 (mtpp) cc_final: 0.8805 (mmtp) outliers start: 72 outliers final: 38 residues processed: 505 average time/residue: 0.2045 time to fit residues: 163.3679 Evaluate side-chains 434 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 394 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 741 ASN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 63 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 278 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 311 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 294 ASN ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN B 294 ASN ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 571 GLN D 741 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.161764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110453 restraints weight = 48565.966| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.37 r_work: 0.3256 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3079 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 : 0.595 7.588 42260 Z= 0.312 Chirality : 0.040 0.142 4708 Planarity : 0.004 0.049 5280 Dihedral : 5.724 50.480 4024 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.25 % Allowed : 10.25 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3656 helix: 0.62 (0.10), residues: 2472 sheet: -1.72 (0.34), residues: 192 loop : -2.95 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.013 0.002 TYR D 191 PHE 0.015 0.001 PHE B 779 TRP 0.019 0.002 TRP B 898 HIS 0.004 0.001 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00341 (31188) covalent geometry : angle 0.59353 (42252) SS BOND : bond 0.01244 ( 4) SS BOND : angle 3.25018 ( 8) hydrogen bonds : bond 0.04575 ( 1768) hydrogen bonds : angle 4.18926 ( 5244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 443 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8481 (tt0) cc_final: 0.8170 (tp40) REVERT: A 353 MET cc_start: 0.6497 (mpp) cc_final: 0.5958 (ptp) REVERT: A 396 MET cc_start: 0.7056 (mmp) cc_final: 0.6173 (mmp) REVERT: A 491 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7858 (tp30) REVERT: A 787 TYR cc_start: 0.7900 (t80) cc_final: 0.7445 (t80) REVERT: A 868 PHE cc_start: 0.8809 (m-10) cc_final: 0.7633 (t80) REVERT: A 1005 TYR cc_start: 0.6876 (m-10) cc_final: 0.5544 (m-80) REVERT: A 1023 MET cc_start: 0.6984 (mmm) cc_final: 0.5898 (mtp) REVERT: A 1068 ASN cc_start: 0.8438 (m-40) cc_final: 0.8220 (m-40) REVERT: B 191 TYR cc_start: 0.7938 (t80) cc_final: 0.7599 (t80) REVERT: B 353 MET cc_start: 0.6417 (mpp) cc_final: 0.5862 (ptp) REVERT: B 396 MET cc_start: 0.7057 (mmp) cc_final: 0.6185 (mmp) REVERT: B 491 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7852 (tp30) REVERT: B 787 TYR cc_start: 0.7936 (t80) cc_final: 0.7491 (t80) REVERT: B 868 PHE cc_start: 0.8772 (m-10) cc_final: 0.7603 (t80) REVERT: B 914 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8331 (mm-40) REVERT: B 1005 TYR cc_start: 0.6815 (m-10) cc_final: 0.5423 (m-80) REVERT: B 1023 MET cc_start: 0.6897 (mmm) cc_final: 0.5788 (mtp) REVERT: B 1066 LYS cc_start: 0.8903 (mmtp) cc_final: 0.8685 (mmmm) REVERT: B 1068 ASN cc_start: 0.8395 (m-40) cc_final: 0.8167 (m-40) REVERT: C 280 GLN cc_start: 0.8514 (tt0) cc_final: 0.8174 (tp40) REVERT: C 353 MET cc_start: 0.6417 (mpp) cc_final: 0.5904 (ptp) REVERT: C 396 MET cc_start: 0.6950 (mmp) cc_final: 0.6108 (mmp) REVERT: C 491 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7874 (tp30) REVERT: C 787 TYR cc_start: 0.7946 (t80) cc_final: 0.7502 (t80) REVERT: C 868 PHE cc_start: 0.8796 (m-10) cc_final: 0.7612 (t80) REVERT: C 1005 TYR cc_start: 0.6838 (m-10) cc_final: 0.5453 (m-80) REVERT: C 1023 MET cc_start: 0.6879 (mmm) cc_final: 0.5810 (mtp) REVERT: C 1068 ASN cc_start: 0.8355 (m-40) cc_final: 0.8120 (m-40) REVERT: D 280 GLN cc_start: 0.8495 (tt0) cc_final: 0.8181 (tp40) REVERT: D 353 MET cc_start: 0.6507 (mpp) cc_final: 0.6006 (ptp) REVERT: D 396 MET cc_start: 0.6985 (mmp) cc_final: 0.6274 (mmp) REVERT: D 689 ASP cc_start: 0.8348 (t0) cc_final: 0.8146 (t0) REVERT: D 787 TYR cc_start: 0.7907 (t80) cc_final: 0.7452 (t80) REVERT: D 868 PHE cc_start: 0.8800 (m-10) cc_final: 0.7623 (t80) REVERT: D 1005 TYR cc_start: 0.6897 (m-10) cc_final: 0.5544 (m-80) REVERT: D 1023 MET cc_start: 0.6956 (mmm) cc_final: 0.5864 (mtp) REVERT: D 1066 LYS cc_start: 0.8982 (mtpp) cc_final: 0.8769 (mmtp) REVERT: D 1068 ASN cc_start: 0.8378 (m-40) cc_final: 0.8157 (m-40) outliers start: 75 outliers final: 45 residues processed: 493 average time/residue: 0.1924 time to fit residues: 152.7650 Evaluate side-chains 429 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 384 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 40 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 333 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 297 optimal weight: 9.9990 chunk 223 optimal weight: 10.0000 chunk 311 optimal weight: 0.0270 chunk 284 optimal weight: 2.9990 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN B 571 GLN B 609 ASN B 990 ASN C 571 GLN C 609 ASN C 741 ASN C 990 ASN D 294 ASN ** D 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 609 ASN D 635 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 = 0.4070 r_free = 0.4070 target = 0.160803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109476 restraints weight = 48647.839| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.37 r_work: 0.3239 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31192 Z= 0.155 Angle : 0.581 6.495 42260 Z= 0.303 Chirality : 0.040 0.174 4708 Planarity : 0.004 0.044 5280 Dihedral : 5.383 50.227 4024 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.06 % Allowed : 11.54 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3656 helix: 1.00 (0.10), residues: 2480 sheet: -1.42 (0.35), residues: 192 loop : -2.73 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1079 TYR 0.025 0.002 TYR C 191 PHE 0.014 0.001 PHE C 752 TRP 0.018 0.001 TRP A 898 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00372 (31188) covalent geometry : angle 0.58011 (42252) SS BOND : bond 0.00795 ( 4) SS BOND : angle 2.44578 ( 8) hydrogen bonds : bond 0.04451 ( 1768) hydrogen bonds : angle 4.01827 ( 5244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 407 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8483 (tt0) cc_final: 0.8173 (tp40) REVERT: A 396 MET cc_start: 0.7171 (mmp) cc_final: 0.6427 (mmp) REVERT: A 488 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8004 (tt) REVERT: A 732 THR cc_start: 0.8774 (m) cc_final: 0.8505 (p) REVERT: A 788 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7802 (mmp) REVERT: A 868 PHE cc_start: 0.8811 (m-10) cc_final: 0.7635 (t80) REVERT: A 1023 MET cc_start: 0.6918 (mmm) cc_final: 0.5811 (mtp) REVERT: A 1068 ASN cc_start: 0.8385 (m-40) cc_final: 0.8129 (m-40) REVERT: B 396 MET cc_start: 0.7135 (mmp) cc_final: 0.6856 (mmp) REVERT: B 488 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7978 (tt) REVERT: B 491 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7848 (tp30) REVERT: B 605 LYS cc_start: 0.8365 (mmtp) cc_final: 0.8086 (mmtm) REVERT: B 702 ILE cc_start: 0.8475 (mp) cc_final: 0.8020 (tt) REVERT: B 732 THR cc_start: 0.8739 (m) cc_final: 0.8425 (p) REVERT: B 787 TYR cc_start: 0.7903 (t80) cc_final: 0.7447 (t80) REVERT: B 801 MET cc_start: 0.8296 (ptt) cc_final: 0.8051 (ptt) REVERT: B 868 PHE cc_start: 0.8796 (m-10) cc_final: 0.7608 (t80) REVERT: B 1023 MET cc_start: 0.6770 (mmm) cc_final: 0.5689 (mtp) REVERT: B 1068 ASN cc_start: 0.8356 (m-40) cc_final: 0.8092 (m-40) REVERT: C 280 GLN cc_start: 0.8527 (tt0) cc_final: 0.8231 (tp40) REVERT: C 395 LYS cc_start: 0.8523 (mmmm) cc_final: 0.8294 (mmmm) REVERT: C 396 MET cc_start: 0.6862 (mmp) cc_final: 0.6144 (mmp) REVERT: C 488 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7968 (tt) REVERT: C 491 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7875 (tp30) REVERT: C 732 THR cc_start: 0.8743 (m) cc_final: 0.8458 (p) REVERT: C 787 TYR cc_start: 0.7902 (t80) cc_final: 0.7453 (t80) REVERT: C 868 PHE cc_start: 0.8792 (m-10) cc_final: 0.7604 (t80) REVERT: C 1023 MET cc_start: 0.6744 (mmm) cc_final: 0.5653 (mtp) REVERT: C 1068 ASN cc_start: 0.8325 (m-40) cc_final: 0.8056 (m-40) REVERT: D 280 GLN cc_start: 0.8524 (tt0) cc_final: 0.8210 (tp40) REVERT: D 396 MET cc_start: 0.7001 (mmp) cc_final: 0.6507 (mmp) REVERT: D 488 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7949 (tt) REVERT: D 702 ILE cc_start: 0.8503 (mp) cc_final: 0.8014 (tt) REVERT: D 732 THR cc_start: 0.8797 (m) cc_final: 0.8472 (p) REVERT: D 788 MET cc_start: 0.8052 (ttm) cc_final: 0.7803 (mmp) REVERT: D 868 PHE cc_start: 0.8797 (m-10) cc_final: 0.7622 (t80) REVERT: D 1023 MET cc_start: 0.6871 (mmm) cc_final: 0.5828 (mtp) REVERT: D 1068 ASN cc_start: 0.8344 (m-40) cc_final: 0.8080 (m-40) outliers start: 102 outliers final: 52 residues processed: 481 average time/residue: 0.1970 time to fit residues: 152.4307 Evaluate side-chains 432 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 375 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1045 PHE 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 440 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 54 optimal weight: 3.9990 chunk 348 optimal weight: 0.7980 chunk 340 optimal weight: 6.9990 chunk 252 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 336 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 280 optimal weight: 7.9990 chunk 274 optimal weight: 9.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.158045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108052 restraints weight = 49590.500| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.61 r_work: 0.3166 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 31192 Z= 0.240 Angle : 0.650 7.245 42260 Z= 0.337 Chirality : 0.043 0.198 4708 Planarity : 0.004 0.045 5280 Dihedral : 5.549 54.833 4024 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.09 % Allowed : 13.46 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3656 helix: 1.05 (0.10), residues: 2464 sheet: -1.55 (0.34), residues: 192 loop : -2.76 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1046 TYR 0.028 0.002 TYR C 191 PHE 0.025 0.002 PHE A1021 TRP 0.021 0.002 TRP A 898 HIS 0.006 0.001 HIS D 765 Details of bonding type rmsd covalent geometry : bond 0.00582 (31188) covalent geometry : angle 0.64831 (42252) SS BOND : bond 0.01070 ( 4) SS BOND : angle 3.91017 ( 8) hydrogen bonds : bond 0.05157 ( 1768) hydrogen bonds : angle 4.15929 ( 5244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 392 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8588 (tt0) cc_final: 0.8297 (tp40) REVERT: A 304 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: A 488 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7898 (tt) REVERT: A 689 ASP cc_start: 0.8425 (t0) cc_final: 0.8056 (m-30) REVERT: A 702 ILE cc_start: 0.8491 (mp) cc_final: 0.8009 (tt) REVERT: A 732 THR cc_start: 0.8880 (m) cc_final: 0.8602 (p) REVERT: A 868 PHE cc_start: 0.8879 (m-10) cc_final: 0.7685 (t80) REVERT: A 1023 MET cc_start: 0.6914 (mmm) cc_final: 0.5872 (mtp) REVERT: A 1068 ASN cc_start: 0.8408 (m-40) cc_final: 0.8123 (m-40) REVERT: B 488 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7911 (tt) REVERT: B 491 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7928 (tp30) REVERT: B 605 LYS cc_start: 0.8253 (mmtp) cc_final: 0.7979 (mmtm) REVERT: B 689 ASP cc_start: 0.8412 (t0) cc_final: 0.8102 (m-30) REVERT: B 702 ILE cc_start: 0.8455 (mp) cc_final: 0.8013 (tt) REVERT: B 732 THR cc_start: 0.8839 (m) cc_final: 0.8599 (p) REVERT: B 788 MET cc_start: 0.8161 (ttm) cc_final: 0.7711 (mmp) REVERT: B 868 PHE cc_start: 0.8868 (m-10) cc_final: 0.7692 (t80) REVERT: B 1023 MET cc_start: 0.6844 (mmm) cc_final: 0.5762 (mtp) REVERT: B 1068 ASN cc_start: 0.8416 (m-40) cc_final: 0.8137 (m-40) REVERT: C 280 GLN cc_start: 0.8579 (tt0) cc_final: 0.8251 (tp40) REVERT: C 304 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.6680 (m-80) REVERT: C 395 LYS cc_start: 0.8479 (mmmm) cc_final: 0.8200 (mmmm) REVERT: C 396 MET cc_start: 0.7252 (mmp) cc_final: 0.6758 (mmp) REVERT: C 488 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7967 (tt) REVERT: C 491 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7958 (tp30) REVERT: C 689 ASP cc_start: 0.8308 (t0) cc_final: 0.7971 (m-30) REVERT: C 732 THR cc_start: 0.8834 (m) cc_final: 0.8603 (p) REVERT: C 788 MET cc_start: 0.8180 (ttm) cc_final: 0.7739 (mmp) REVERT: C 801 MET cc_start: 0.8447 (ptt) cc_final: 0.8156 (ptt) REVERT: C 868 PHE cc_start: 0.8866 (m-10) cc_final: 0.7706 (t80) REVERT: C 1023 MET cc_start: 0.6850 (mmm) cc_final: 0.5769 (mtp) REVERT: C 1046 ARG cc_start: 0.7517 (ttm170) cc_final: 0.7234 (ttm110) REVERT: C 1068 ASN cc_start: 0.8401 (m-40) cc_final: 0.8117 (m-40) REVERT: D 280 GLN cc_start: 0.8598 (tt0) cc_final: 0.8270 (tp40) REVERT: D 294 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7597 (p0) REVERT: D 396 MET cc_start: 0.7353 (mmp) cc_final: 0.6860 (mmp) REVERT: D 488 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8020 (tt) REVERT: D 646 TYR cc_start: 0.6144 (t80) cc_final: 0.5868 (t80) REVERT: D 689 ASP cc_start: 0.8312 (t0) cc_final: 0.7990 (m-30) REVERT: D 702 ILE cc_start: 0.8490 (mp) cc_final: 0.8019 (tt) REVERT: D 732 THR cc_start: 0.8883 (m) cc_final: 0.8622 (p) REVERT: D 788 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7929 (mmp) REVERT: D 868 PHE cc_start: 0.8882 (m-10) cc_final: 0.7744 (t80) REVERT: D 1021 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.6611 (t80) REVERT: D 1023 MET cc_start: 0.6873 (mmm) cc_final: 0.5814 (mtp) REVERT: D 1068 ASN cc_start: 0.8452 (m-40) cc_final: 0.8193 (m-40) outliers start: 103 outliers final: 55 residues processed: 464 average time/residue: 0.1914 time to fit residues: 143.2364 Evaluate side-chains 426 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 362 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU 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 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 797 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain B residue 1078 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain C residue 1078 MET Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1045 PHE Chi-restraints excluded: chain D residue 1078 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 117 optimal weight: 20.0000 chunk 303 optimal weight: 6.9990 chunk 360 optimal weight: 0.7980 chunk 187 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 270 optimal weight: 0.0070 chunk 223 optimal weight: 9.9990 chunk 337 optimal weight: 0.9990 overall best weight: 2.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 571 GLN D 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.158503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107343 restraints weight = 48596.417| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.40 r_work: 0.3216 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31192 Z= 0.174 Angle : 0.603 7.340 42260 Z= 0.312 Chirality : 0.041 0.190 4708 Planarity : 0.004 0.044 5280 Dihedral : 5.392 49.835 4024 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.79 % Allowed : 14.51 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3656 helix: 1.27 (0.11), residues: 2460 sheet: -1.59 (0.34), residues: 192 loop : -2.66 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1046 TYR 0.030 0.002 TYR C 191 PHE 0.013 0.001 PHE A1013 TRP 0.020 0.002 TRP A 898 HIS 0.004 0.001 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00422 (31188) covalent geometry : angle 0.60142 (42252) SS BOND : bond 0.00793 ( 4) SS BOND : angle 3.15349 ( 8) hydrogen bonds : bond 0.04569 ( 1768) hydrogen bonds : angle 4.02600 ( 5244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 371 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8560 (tt0) cc_final: 0.8246 (tp40) REVERT: A 304 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.6689 (m-80) REVERT: A 353 MET cc_start: 0.6754 (mpp) cc_final: 0.6085 (pmm) REVERT: A 396 MET cc_start: 0.7424 (mmp) cc_final: 0.6848 (mmp) REVERT: A 488 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7877 (tt) REVERT: A 689 ASP cc_start: 0.8332 (t0) cc_final: 0.8102 (m-30) REVERT: A 702 ILE cc_start: 0.8432 (mp) cc_final: 0.7976 (tt) REVERT: A 732 THR cc_start: 0.8914 (m) cc_final: 0.8649 (p) REVERT: A 868 PHE cc_start: 0.8802 (m-10) cc_final: 0.7638 (t80) REVERT: A 1023 MET cc_start: 0.6924 (mmm) cc_final: 0.5872 (mtp) REVERT: A 1068 ASN cc_start: 0.8366 (m-40) cc_final: 0.8086 (m-40) REVERT: B 304 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.7259 (m-80) REVERT: B 353 MET cc_start: 0.6698 (mpp) cc_final: 0.6238 (pmm) REVERT: B 396 MET cc_start: 0.7466 (mmp) cc_final: 0.6918 (mmp) REVERT: B 488 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7804 (tt) REVERT: B 627 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8516 (mp0) REVERT: B 689 ASP cc_start: 0.8331 (t0) cc_final: 0.7991 (m-30) REVERT: B 702 ILE cc_start: 0.8425 (mp) cc_final: 0.8007 (tt) REVERT: B 732 THR cc_start: 0.8850 (m) cc_final: 0.8619 (p) REVERT: B 788 MET cc_start: 0.8131 (ttm) cc_final: 0.7729 (mmp) REVERT: B 801 MET cc_start: 0.8455 (ptt) cc_final: 0.8154 (ptt) REVERT: B 868 PHE cc_start: 0.8810 (m-10) cc_final: 0.7625 (t80) REVERT: B 1023 MET cc_start: 0.6896 (mmm) cc_final: 0.5843 (mtp) REVERT: B 1068 ASN cc_start: 0.8326 (m-40) cc_final: 0.8037 (m-40) REVERT: C 141 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7962 (p) REVERT: C 280 GLN cc_start: 0.8520 (tt0) cc_final: 0.8226 (tp40) REVERT: C 304 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: C 353 MET cc_start: 0.6711 (mpp) cc_final: 0.6094 (pmm) REVERT: C 396 MET cc_start: 0.7378 (mmp) cc_final: 0.6909 (mmp) REVERT: C 488 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7816 (tt) REVERT: C 491 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7862 (tp30) REVERT: C 627 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8498 (mp0) REVERT: C 689 ASP cc_start: 0.8301 (t0) cc_final: 0.7969 (m-30) REVERT: C 732 THR cc_start: 0.8854 (m) cc_final: 0.8635 (p) REVERT: C 788 MET cc_start: 0.8113 (ttm) cc_final: 0.7774 (mmp) REVERT: C 801 MET cc_start: 0.8274 (ptt) cc_final: 0.8038 (ptt) REVERT: C 868 PHE cc_start: 0.8795 (m-10) cc_final: 0.7610 (t80) REVERT: C 989 ASN cc_start: 0.7458 (t0) cc_final: 0.7168 (t0) REVERT: C 1023 MET cc_start: 0.6886 (mmm) cc_final: 0.5826 (mtp) REVERT: C 1046 ARG cc_start: 0.7675 (ttm170) cc_final: 0.7417 (ttm110) REVERT: C 1068 ASN cc_start: 0.8324 (m-40) cc_final: 0.8035 (m-40) REVERT: D 280 GLN cc_start: 0.8595 (tt0) cc_final: 0.8271 (tp40) REVERT: D 294 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7548 (p0) REVERT: D 353 MET cc_start: 0.6758 (mpp) cc_final: 0.6140 (pmm) REVERT: D 396 MET cc_start: 0.7305 (mmp) cc_final: 0.6888 (mmp) REVERT: D 488 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7937 (tt) REVERT: D 689 ASP cc_start: 0.8341 (t0) cc_final: 0.8038 (m-30) REVERT: D 702 ILE cc_start: 0.8468 (mp) cc_final: 0.8024 (tt) REVERT: D 732 THR cc_start: 0.8891 (m) cc_final: 0.8644 (p) REVERT: D 868 PHE cc_start: 0.8809 (m-10) cc_final: 0.7636 (t80) REVERT: D 1021 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6673 (t80) REVERT: D 1023 MET cc_start: 0.6794 (mmm) cc_final: 0.5730 (mtp) REVERT: D 1049 ASP cc_start: 0.7265 (m-30) cc_final: 0.6723 (m-30) REVERT: D 1059 MET cc_start: 0.7577 (mpp) cc_final: 0.7234 (mmm) REVERT: D 1068 ASN cc_start: 0.8372 (m-40) cc_final: 0.8116 (m-40) outliers start: 93 outliers final: 51 residues processed: 442 average time/residue: 0.1903 time to fit residues: 136.1405 Evaluate side-chains 419 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 358 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 302 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain 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 209 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain B residue 1078 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain C residue 1078 MET Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1045 PHE Chi-restraints excluded: chain D residue 1078 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 246 optimal weight: 4.9990 chunk 341 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 242 optimal weight: 5.9990 chunk 295 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.158830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106355 restraints weight = 49755.402| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.51 r_work: 0.3208 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31192 Z= 0.177 Angle : 0.608 8.072 42260 Z= 0.314 Chirality : 0.041 0.183 4708 Planarity : 0.004 0.045 5280 Dihedral : 5.323 48.933 4024 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.67 % Allowed : 14.72 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3656 helix: 1.31 (0.11), residues: 2472 sheet: -1.57 (0.34), residues: 192 loop : -2.67 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1046 TYR 0.030 0.002 TYR D 191 PHE 0.035 0.001 PHE C1021 TRP 0.020 0.002 TRP A 898 HIS 0.004 0.001 HIS C 765 Details of bonding type rmsd covalent geometry : bond 0.00430 (31188) covalent geometry : angle 0.60669 (42252) SS BOND : bond 0.00722 ( 4) SS BOND : angle 2.76718 ( 8) hydrogen bonds : bond 0.04597 ( 1768) hydrogen bonds : angle 4.00225 ( 5244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 367 time to evaluate : 1.148 Fit side-chains REVERT: A 280 GLN cc_start: 0.8587 (tt0) cc_final: 0.8265 (tp40) REVERT: A 304 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.6710 (m-80) REVERT: A 353 MET cc_start: 0.6734 (mpp) cc_final: 0.6088 (pmm) REVERT: A 488 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7852 (tt) REVERT: A 627 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8558 (mp0) REVERT: A 689 ASP cc_start: 0.8365 (t0) cc_final: 0.8076 (m-30) REVERT: A 702 ILE cc_start: 0.8444 (mp) cc_final: 0.7993 (tt) REVERT: A 732 THR cc_start: 0.8897 (m) cc_final: 0.8636 (p) REVERT: A 868 PHE cc_start: 0.8812 (m-10) cc_final: 0.7641 (t80) REVERT: A 1023 MET cc_start: 0.6929 (mmm) cc_final: 0.5854 (mtp) REVERT: B 353 MET cc_start: 0.6646 (mpp) cc_final: 0.6178 (pmm) REVERT: B 396 MET cc_start: 0.7369 (mmp) cc_final: 0.6864 (mmp) REVERT: B 689 ASP cc_start: 0.8374 (t0) cc_final: 0.8032 (m-30) REVERT: B 702 ILE cc_start: 0.8433 (mp) cc_final: 0.8025 (tt) REVERT: B 732 THR cc_start: 0.8879 (m) cc_final: 0.8632 (p) REVERT: B 788 MET cc_start: 0.8089 (ttm) cc_final: 0.7729 (mmp) REVERT: B 801 MET cc_start: 0.8487 (ptt) cc_final: 0.8202 (ptt) REVERT: B 868 PHE cc_start: 0.8819 (m-10) cc_final: 0.7636 (t80) REVERT: B 1023 MET cc_start: 0.6883 (mmm) cc_final: 0.5804 (mtp) REVERT: B 1059 MET cc_start: 0.7485 (mpp) cc_final: 0.7089 (mmm) REVERT: C 141 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7928 (p) REVERT: C 280 GLN cc_start: 0.8555 (tt0) cc_final: 0.8266 (tp40) REVERT: C 304 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.6724 (m-80) REVERT: C 353 MET cc_start: 0.6675 (mpp) cc_final: 0.6048 (pmm) REVERT: C 396 MET cc_start: 0.7409 (mmp) cc_final: 0.6998 (mmp) REVERT: C 488 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7838 (tt) REVERT: C 491 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7837 (tp30) REVERT: C 689 ASP cc_start: 0.8350 (t0) cc_final: 0.8016 (m-30) REVERT: C 732 THR cc_start: 0.8883 (m) cc_final: 0.8651 (p) REVERT: C 788 MET cc_start: 0.8055 (ttm) cc_final: 0.7719 (mmp) REVERT: C 801 MET cc_start: 0.8384 (ptt) cc_final: 0.8149 (ptt) REVERT: C 868 PHE cc_start: 0.8799 (m-10) cc_final: 0.7618 (t80) REVERT: C 989 ASN cc_start: 0.7448 (t0) cc_final: 0.7149 (t0) REVERT: C 1023 MET cc_start: 0.6939 (mmm) cc_final: 0.5841 (mtp) REVERT: C 1046 ARG cc_start: 0.7671 (ttm170) cc_final: 0.7406 (ttm110) REVERT: C 1059 MET cc_start: 0.7413 (mpp) cc_final: 0.7018 (mmm) REVERT: C 1068 ASN cc_start: 0.8265 (m-40) cc_final: 0.7972 (m-40) REVERT: D 141 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7950 (p) REVERT: D 280 GLN cc_start: 0.8585 (tt0) cc_final: 0.8263 (tp40) REVERT: D 353 MET cc_start: 0.6731 (mpp) cc_final: 0.6131 (pmm) REVERT: D 396 MET cc_start: 0.7328 (mmp) cc_final: 0.6973 (mmp) REVERT: D 488 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7986 (tt) REVERT: D 627 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8534 (mp0) REVERT: D 689 ASP cc_start: 0.8352 (t0) cc_final: 0.8020 (m-30) REVERT: D 702 ILE cc_start: 0.8470 (mp) cc_final: 0.8039 (tt) REVERT: D 732 THR cc_start: 0.8880 (m) cc_final: 0.8630 (p) REVERT: D 868 PHE cc_start: 0.8813 (m-10) cc_final: 0.7641 (t80) REVERT: D 1021 PHE cc_start: 0.7252 (OUTLIER) cc_final: 0.6670 (t80) REVERT: D 1023 MET cc_start: 0.6931 (mmm) cc_final: 0.5830 (mtp) REVERT: D 1059 MET cc_start: 0.7629 (mpp) cc_final: 0.7339 (mmm) REVERT: D 1068 ASN cc_start: 0.8297 (m-40) cc_final: 0.8039 (m-40) outliers start: 89 outliers final: 56 residues processed: 431 average time/residue: 0.1883 time to fit residues: 131.4644 Evaluate side-chains 424 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 360 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 209 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain 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 209 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 358 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain C residue 1078 MET Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 209 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 584 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1045 PHE Chi-restraints excluded: chain D residue 1078 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 78 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 265 optimal weight: 0.9990 chunk 255 optimal weight: 0.9980 chunk 295 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 14 optimal weight: 0.0370 chunk 135 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 366 optimal weight: 10.0000 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 HIS D 306 GLN D 500 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.161741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111277 restraints weight = 48780.611| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.38 r_work: 0.3272 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4080 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= 0.116 Angle : 0.567 8.050 42260 Z= 0.292 Chirality : 0.039 0.165 4708 Planarity : 0.004 0.045 5280 Dihedral : 5.080 44.780 4024 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.77 % Allowed : 16.23 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3656 helix: 1.52 (0.11), residues: 2484 sheet: -1.14 (0.36), residues: 184 loop : -2.50 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1046 TYR 0.030 0.001 TYR D 191 PHE 0.021 0.001 PHE A 776 TRP 0.019 0.001 TRP B 898 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00261 (31188) covalent geometry : angle 0.56653 (42252) SS BOND : bond 0.00583 ( 4) SS BOND : angle 1.97168 ( 8) hydrogen bonds : bond 0.03765 ( 1768) hydrogen bonds : angle 3.83469 ( 5244) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 392 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8536 (tt0) cc_final: 0.8210 (tp40) REVERT: A 304 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.6675 (m-80) REVERT: A 353 MET cc_start: 0.6774 (mpp) cc_final: 0.6343 (pmm) REVERT: A 396 MET cc_start: 0.6985 (mmp) cc_final: 0.5883 (mmp) REVERT: A 488 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7811 (tt) REVERT: A 566 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8709 (mp) REVERT: A 689 ASP cc_start: 0.8313 (t0) cc_final: 0.8057 (m-30) REVERT: A 731 PHE cc_start: 0.7419 (m-80) cc_final: 0.7042 (t80) REVERT: A 732 THR cc_start: 0.8663 (m) cc_final: 0.8441 (p) REVERT: A 868 PHE cc_start: 0.8744 (m-10) cc_final: 0.7550 (t80) REVERT: A 1023 MET cc_start: 0.6882 (mmm) cc_final: 0.5835 (mtp) REVERT: A 1059 MET cc_start: 0.7623 (mpp) cc_final: 0.7333 (mmm) REVERT: B 353 MET cc_start: 0.6619 (mpp) cc_final: 0.6207 (pmm) REVERT: B 566 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8853 (mp) REVERT: B 646 TYR cc_start: 0.6068 (t80) cc_final: 0.5746 (t80) REVERT: B 689 ASP cc_start: 0.8361 (t0) cc_final: 0.8138 (m-30) REVERT: B 731 PHE cc_start: 0.7496 (m-80) cc_final: 0.7060 (t80) REVERT: B 732 THR cc_start: 0.8600 (m) cc_final: 0.8394 (p) REVERT: B 788 MET cc_start: 0.8095 (ttm) cc_final: 0.7682 (mmt) REVERT: B 801 MET cc_start: 0.8392 (ptt) cc_final: 0.8107 (ptt) REVERT: B 868 PHE cc_start: 0.8751 (m-10) cc_final: 0.7565 (t80) REVERT: B 1023 MET cc_start: 0.6868 (mmm) cc_final: 0.5788 (mtp) REVERT: B 1059 MET cc_start: 0.7684 (mpp) cc_final: 0.7365 (mmm) REVERT: C 141 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7817 (p) REVERT: C 280 GLN cc_start: 0.8537 (tt0) cc_final: 0.8221 (tp40) REVERT: C 353 MET cc_start: 0.6641 (mpp) cc_final: 0.6235 (pmm) REVERT: C 396 MET cc_start: 0.7300 (mmp) cc_final: 0.6896 (mmp) REVERT: C 488 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7842 (tt) REVERT: C 689 ASP cc_start: 0.8292 (t0) cc_final: 0.7986 (m-30) REVERT: C 731 PHE cc_start: 0.7484 (m-80) cc_final: 0.7041 (t80) REVERT: C 788 MET cc_start: 0.8088 (ttm) cc_final: 0.7692 (mmt) REVERT: C 801 MET cc_start: 0.8304 (ptt) cc_final: 0.8076 (ptt) REVERT: C 868 PHE cc_start: 0.8742 (m-10) cc_final: 0.7541 (t80) REVERT: C 1023 MET cc_start: 0.6864 (mmm) cc_final: 0.5787 (mtp) REVERT: C 1046 ARG cc_start: 0.7524 (ttm170) cc_final: 0.7262 (ttm110) REVERT: C 1059 MET cc_start: 0.7560 (mpp) cc_final: 0.7256 (mmm) REVERT: D 280 GLN cc_start: 0.8529 (tt0) cc_final: 0.8214 (tp40) REVERT: D 353 MET cc_start: 0.6703 (mpp) cc_final: 0.6311 (pmm) REVERT: D 396 MET cc_start: 0.7422 (mmp) cc_final: 0.7020 (mmp) REVERT: D 689 ASP cc_start: 0.8315 (t0) cc_final: 0.7989 (m-30) REVERT: D 702 ILE cc_start: 0.8488 (mp) cc_final: 0.8094 (tt) REVERT: D 731 PHE cc_start: 0.7504 (m-80) cc_final: 0.7023 (t80) REVERT: D 732 THR cc_start: 0.8799 (m) cc_final: 0.8589 (p) REVERT: D 868 PHE cc_start: 0.8779 (m-10) cc_final: 0.7561 (t80) REVERT: D 989 ASN cc_start: 0.7228 (t0) cc_final: 0.6978 (t0) REVERT: D 1021 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6748 (t80) REVERT: D 1023 MET cc_start: 0.6896 (mmm) cc_final: 0.5763 (mtp) REVERT: D 1059 MET cc_start: 0.7695 (mpp) cc_final: 0.7462 (mmm) outliers start: 59 outliers final: 23 residues processed: 435 average time/residue: 0.1822 time to fit residues: 128.4938 Evaluate side-chains 393 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 363 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 488 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain 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 676 ASN Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 1021 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 227 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 79 optimal weight: 0.3980 chunk 159 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 267 optimal weight: 0.5980 chunk 229 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 366 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 500 HIS C 635 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.161701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111011 restraints weight = 48578.493| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.39 r_work: 0.3267 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31192 Z= 0.120 Angle : 0.581 10.178 42260 Z= 0.296 Chirality : 0.039 0.180 4708 Planarity : 0.004 0.042 5280 Dihedral : 4.914 49.527 4024 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.56 % Allowed : 16.80 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.14), residues: 3656 helix: 1.60 (0.11), residues: 2488 sheet: -1.01 (0.36), residues: 184 loop : -2.44 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1046 TYR 0.030 0.001 TYR D 191 PHE 0.028 0.001 PHE B1021 TRP 0.019 0.001 TRP C 453 HIS 0.003 0.001 HIS D 500 Details of bonding type rmsd covalent geometry : bond 0.00277 (31188) covalent geometry : angle 0.58017 (42252) SS BOND : bond 0.00586 ( 4) SS BOND : angle 2.02172 ( 8) hydrogen bonds : bond 0.03779 ( 1768) hydrogen bonds : angle 3.81266 ( 5244) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 365 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8521 (tt0) cc_final: 0.8199 (tp40) REVERT: A 304 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.6675 (m-80) REVERT: A 353 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.6276 (pmm) REVERT: A 396 MET cc_start: 0.7020 (mmp) cc_final: 0.5910 (mmp) REVERT: A 488 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7848 (tt) REVERT: A 566 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 605 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7962 (mmtm) REVERT: A 616 GLU cc_start: 0.7876 (mp0) cc_final: 0.7617 (mp0) REVERT: A 689 ASP cc_start: 0.8374 (t0) cc_final: 0.8095 (m-30) REVERT: A 731 PHE cc_start: 0.7385 (m-80) cc_final: 0.7030 (t80) REVERT: A 732 THR cc_start: 0.8658 (m) cc_final: 0.8422 (p) REVERT: A 868 PHE cc_start: 0.8722 (m-10) cc_final: 0.7517 (t80) REVERT: A 1023 MET cc_start: 0.6884 (mmm) cc_final: 0.5816 (mtp) REVERT: A 1059 MET cc_start: 0.7682 (mpp) cc_final: 0.7396 (mmm) REVERT: B 353 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6273 (pmm) REVERT: B 396 MET cc_start: 0.6992 (mmp) cc_final: 0.5824 (mmp) REVERT: B 566 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8825 (mp) REVERT: B 605 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7953 (mmtm) REVERT: B 646 TYR cc_start: 0.6156 (t80) cc_final: 0.5877 (t80) REVERT: B 689 ASP cc_start: 0.8428 (t0) cc_final: 0.8154 (m-30) REVERT: B 702 ILE cc_start: 0.8469 (mp) cc_final: 0.8053 (tt) REVERT: B 731 PHE cc_start: 0.7540 (m-80) cc_final: 0.7078 (t80) REVERT: B 732 THR cc_start: 0.8556 (m) cc_final: 0.8337 (p) REVERT: B 788 MET cc_start: 0.8041 (ttm) cc_final: 0.7632 (mmt) REVERT: B 801 MET cc_start: 0.8357 (ptt) cc_final: 0.8060 (ptt) REVERT: B 868 PHE cc_start: 0.8744 (m-10) cc_final: 0.7527 (t80) REVERT: B 1023 MET cc_start: 0.6849 (mmm) cc_final: 0.5748 (mtp) REVERT: B 1059 MET cc_start: 0.7718 (mpp) cc_final: 0.7395 (mmm) REVERT: C 141 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7940 (p) REVERT: C 280 GLN cc_start: 0.8530 (tt0) cc_final: 0.8220 (tp40) REVERT: C 353 MET cc_start: 0.6606 (mpp) cc_final: 0.6224 (pmm) REVERT: C 396 MET cc_start: 0.7363 (mmp) cc_final: 0.6991 (mmp) REVERT: C 488 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7782 (tt) REVERT: C 605 LYS cc_start: 0.8204 (mmtp) cc_final: 0.7922 (mmtm) REVERT: C 616 GLU cc_start: 0.7953 (mp0) cc_final: 0.7688 (mp0) REVERT: C 627 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8429 (mp0) REVERT: C 689 ASP cc_start: 0.8425 (t0) cc_final: 0.8154 (m-30) REVERT: C 731 PHE cc_start: 0.7585 (m-80) cc_final: 0.7025 (t80) REVERT: C 788 MET cc_start: 0.7997 (ttm) cc_final: 0.7675 (mmp) REVERT: C 801 MET cc_start: 0.8229 (ptt) cc_final: 0.8000 (ptt) REVERT: C 868 PHE cc_start: 0.8727 (m-10) cc_final: 0.7532 (t80) REVERT: C 1023 MET cc_start: 0.6846 (mmm) cc_final: 0.5745 (mtp) REVERT: C 1046 ARG cc_start: 0.7490 (ttm170) cc_final: 0.7214 (ttm110) REVERT: C 1059 MET cc_start: 0.7631 (mpp) cc_final: 0.7313 (mmm) REVERT: D 280 GLN cc_start: 0.8524 (tt0) cc_final: 0.8181 (tp40) REVERT: D 353 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6300 (pmm) REVERT: D 616 GLU cc_start: 0.7922 (mp0) cc_final: 0.7667 (mp0) REVERT: D 627 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8435 (mp0) REVERT: D 689 ASP cc_start: 0.8375 (t0) cc_final: 0.8030 (m-30) REVERT: D 731 PHE cc_start: 0.7466 (m-80) cc_final: 0.7007 (t80) REVERT: D 732 THR cc_start: 0.8623 (m) cc_final: 0.8396 (p) REVERT: D 868 PHE cc_start: 0.8741 (m-10) cc_final: 0.7537 (t80) REVERT: D 1021 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6742 (t80) REVERT: D 1023 MET cc_start: 0.6995 (mmm) cc_final: 0.5847 (mtp) REVERT: D 1059 MET cc_start: 0.7765 (mpp) cc_final: 0.7539 (mmm) outliers start: 52 outliers final: 26 residues processed: 404 average time/residue: 0.1987 time to fit residues: 131.7620 Evaluate side-chains 392 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 355 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 353 MET Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 1078 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 1021 PHE 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 1 optimal weight: 8.9990 chunk 176 optimal weight: 0.9980 chunk 338 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 265 optimal weight: 0.5980 chunk 312 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 635 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.159688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108558 restraints weight = 48510.726| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.39 r_work: 0.3231 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31192 Z= 0.165 Angle : 0.620 11.435 42260 Z= 0.316 Chirality : 0.041 0.179 4708 Planarity : 0.004 0.043 5280 Dihedral : 4.994 47.121 4024 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.35 % Allowed : 16.95 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.14), residues: 3656 helix: 1.58 (0.11), residues: 2476 sheet: -0.99 (0.36), residues: 184 loop : -2.45 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1046 TYR 0.028 0.002 TYR D 191 PHE 0.022 0.001 PHE A 776 TRP 0.021 0.001 TRP A 453 HIS 0.003 0.001 HIS C 765 Details of bonding type rmsd covalent geometry : bond 0.00399 (31188) covalent geometry : angle 0.61808 (42252) SS BOND : bond 0.00775 ( 4) SS BOND : angle 3.63328 ( 8) hydrogen bonds : bond 0.04312 ( 1768) hydrogen bonds : angle 3.90482 ( 5244) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 358 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8542 (tt0) cc_final: 0.8217 (tp40) REVERT: A 304 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.6732 (m-80) REVERT: A 353 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6334 (pmm) REVERT: A 396 MET cc_start: 0.6898 (mmp) cc_final: 0.6210 (mmp) REVERT: A 445 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8271 (mm-30) REVERT: A 488 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7909 (tt) REVERT: A 566 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8715 (mp) REVERT: A 616 GLU cc_start: 0.7987 (mp0) cc_final: 0.7697 (mp0) REVERT: A 627 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8475 (mp0) REVERT: A 689 ASP cc_start: 0.8386 (t0) cc_final: 0.8073 (m-30) REVERT: A 731 PHE cc_start: 0.7381 (m-80) cc_final: 0.7005 (t80) REVERT: A 732 THR cc_start: 0.8698 (m) cc_final: 0.8470 (p) REVERT: A 868 PHE cc_start: 0.8773 (m-10) cc_final: 0.7625 (t80) REVERT: A 1023 MET cc_start: 0.6922 (mmm) cc_final: 0.5812 (mtp) REVERT: A 1059 MET cc_start: 0.7728 (mpp) cc_final: 0.7444 (mmm) REVERT: B 198 ASP cc_start: 0.8075 (m-30) cc_final: 0.7867 (m-30) REVERT: B 353 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.6259 (pmm) REVERT: B 396 MET cc_start: 0.6978 (mmp) cc_final: 0.5821 (mmp) REVERT: B 566 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8775 (mp) REVERT: B 605 LYS cc_start: 0.8237 (mmtp) cc_final: 0.7981 (mmtm) REVERT: B 627 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8487 (mp0) REVERT: B 646 TYR cc_start: 0.6222 (t80) cc_final: 0.5940 (t80) REVERT: B 689 ASP cc_start: 0.8415 (t0) cc_final: 0.8100 (m-30) REVERT: B 702 ILE cc_start: 0.8480 (mp) cc_final: 0.8065 (tt) REVERT: B 731 PHE cc_start: 0.7546 (m-80) cc_final: 0.7073 (t80) REVERT: B 732 THR cc_start: 0.8613 (m) cc_final: 0.8393 (p) REVERT: B 788 MET cc_start: 0.8107 (ttm) cc_final: 0.7703 (mmt) REVERT: B 801 MET cc_start: 0.8396 (ptt) cc_final: 0.8114 (ptt) REVERT: B 868 PHE cc_start: 0.8789 (m-10) cc_final: 0.7618 (t80) REVERT: B 1023 MET cc_start: 0.6907 (mmm) cc_final: 0.5787 (mtp) REVERT: B 1059 MET cc_start: 0.7532 (mpp) cc_final: 0.7178 (mmm) REVERT: C 141 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7994 (p) REVERT: C 280 GLN cc_start: 0.8560 (tt0) cc_final: 0.8254 (tp40) REVERT: C 353 MET cc_start: 0.6578 (mpp) cc_final: 0.6176 (pmm) REVERT: C 396 MET cc_start: 0.7336 (mmp) cc_final: 0.6962 (mmp) REVERT: C 488 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7882 (tt) REVERT: C 605 LYS cc_start: 0.8218 (mmtp) cc_final: 0.7953 (mmtm) REVERT: C 616 GLU cc_start: 0.8062 (mp0) cc_final: 0.7758 (mp0) REVERT: C 627 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8511 (mp0) REVERT: C 689 ASP cc_start: 0.8403 (t0) cc_final: 0.8026 (m-30) REVERT: C 731 PHE cc_start: 0.7570 (m-80) cc_final: 0.7009 (t80) REVERT: C 788 MET cc_start: 0.8057 (ttm) cc_final: 0.7684 (mmt) REVERT: C 801 MET cc_start: 0.8296 (ptt) cc_final: 0.8057 (ptt) REVERT: C 868 PHE cc_start: 0.8796 (m-10) cc_final: 0.7600 (t80) REVERT: C 1023 MET cc_start: 0.6906 (mmm) cc_final: 0.5790 (mtp) REVERT: C 1046 ARG cc_start: 0.7446 (ttm170) cc_final: 0.7152 (ttm110) REVERT: C 1059 MET cc_start: 0.7559 (mpp) cc_final: 0.7241 (mmm) REVERT: D 280 GLN cc_start: 0.8556 (tt0) cc_final: 0.8244 (tp40) REVERT: D 353 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.6259 (pmm) REVERT: D 616 GLU cc_start: 0.7989 (mp0) cc_final: 0.7693 (mp0) REVERT: D 627 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8531 (mp0) REVERT: D 689 ASP cc_start: 0.8400 (t0) cc_final: 0.8036 (m-30) REVERT: D 702 ILE cc_start: 0.8501 (mp) cc_final: 0.8062 (tt) REVERT: D 731 PHE cc_start: 0.7502 (m-80) cc_final: 0.7039 (t80) REVERT: D 732 THR cc_start: 0.8698 (m) cc_final: 0.8471 (p) REVERT: D 868 PHE cc_start: 0.8804 (m-10) cc_final: 0.7632 (t80) REVERT: D 1021 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6741 (t80) REVERT: D 1023 MET cc_start: 0.6987 (mmm) cc_final: 0.5811 (mtp) REVERT: D 1059 MET cc_start: 0.7733 (mpp) cc_final: 0.7501 (mmm) outliers start: 45 outliers final: 29 residues processed: 389 average time/residue: 0.2015 time to fit residues: 127.2166 Evaluate side-chains 397 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 358 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 353 MET Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 1078 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 141 THR 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 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 1078 MET Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 1021 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 364 optimal weight: 0.9990 chunk 174 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 286 optimal weight: 0.3980 chunk 213 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 chunk 271 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 990 ASN C 990 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.162270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111849 restraints weight = 48579.476| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.39 r_work: 0.3281 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31192 Z= 0.113 Angle : 0.582 10.950 42260 Z= 0.294 Chirality : 0.039 0.169 4708 Planarity : 0.003 0.040 5280 Dihedral : 4.908 45.830 4024 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.35 % Allowed : 17.10 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.14), residues: 3656 helix: 1.66 (0.11), residues: 2496 sheet: -0.85 (0.36), residues: 184 loop : -2.51 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 203 TYR 0.025 0.001 TYR B 191 PHE 0.034 0.001 PHE B1021 TRP 0.018 0.001 TRP B 898 HIS 0.003 0.001 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00256 (31188) covalent geometry : angle 0.58032 (42252) SS BOND : bond 0.00694 ( 4) SS BOND : angle 2.82314 ( 8) hydrogen bonds : bond 0.03645 ( 1768) hydrogen bonds : angle 3.77388 ( 5244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11549.53 seconds wall clock time: 197 minutes 6.30 seconds (11826.30 seconds total)