Starting phenix.real_space_refine on Sun Jul 5 21:12:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wrf_32725/07_2026/7wrf_32725.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrf_32725/07_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_32725/07_2026/7wrf_32725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrf_32725/07_2026/7wrf_32725.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wrf_32725/07_2026/7wrf_32725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrf_32725/07_2026/7wrf_32725.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wrf_32725/07_2026/7wrf_32725.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wrf_32725/07_2026/7wrf_32725.cif" } 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-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30469 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "B" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "C" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "D" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' CA': 1, ' NA': 1, 'KX7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.66, per 1000 atoms: 0.19 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: 2.38 Conformation dependent library (CDL) restraints added in 1.3 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: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 125 through 136 removed outlier: 3.860A pdb=" N LEU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 204 removed outlier: 3.735A pdb=" N TYR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.695A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.830A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 removed outlier: 3.576A pdb=" N LEU A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 385 removed outlier: 4.102A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.787A pdb=" N TYR A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.728A pdb=" N ALA A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 502 through 516 removed outlier: 3.680A pdb=" N TYR A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 532 Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.586A pdb=" N ALA A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 582 removed outlier: 3.718A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 602 Processing helix chain 'A' and resid 607 through 636 removed outlier: 3.773A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 636 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.766A pdb=" N ILE A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 removed outlier: 3.635A pdb=" N GLY A 684 " --> pdb=" O LYS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.692A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.603A pdb=" N VAL A 705 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 702 through 706' Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 759 removed outlier: 3.540A pdb=" N ASP A 759 " --> pdb=" O VAL A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 790 Processing helix chain 'A' and resid 791 through 795 Processing helix chain 'A' and resid 796 through 817 removed outlier: 3.523A pdb=" N VAL A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 847 removed outlier: 4.187A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 853 through 860 Processing helix chain 'A' and resid 863 through 890 Processing helix chain 'A' and resid 895 through 901 Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 925 through 929 removed outlier: 3.955A pdb=" N HIS A 928 " --> pdb=" O ASP A 925 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS A 929 " --> pdb=" O PHE A 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 925 through 929' Processing helix chain 'A' and resid 952 through 969 Proline residue: A 958 - end of helix Processing helix chain 'A' and resid 969 through 1006 removed outlier: 3.620A pdb=" N LEU A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1014 No H-bonds generated for 'chain 'A' and resid 1012 through 1014' Processing helix chain 'A' and resid 1015 through 1030 removed outlier: 3.631A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1071 removed outlier: 3.859A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A1071 " --> pdb=" O ILE A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1104 removed outlier: 3.635A pdb=" N MET A1078 " --> pdb=" O ASN A1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 136 removed outlier: 3.860A pdb=" N LEU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 204 removed outlier: 3.734A pdb=" N TYR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.695A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.829A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 removed outlier: 3.576A pdb=" N LEU B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 370 through 385 removed outlier: 4.102A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.786A pdb=" N TYR B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.728A pdb=" N ALA B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 468 Processing helix chain 'B' and resid 470 through 481 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 502 through 516 removed outlier: 3.680A pdb=" N TYR B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 532 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.585A pdb=" N ALA B 563 " --> pdb=" O HIS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 582 removed outlier: 3.719A pdb=" N VAL B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 607 through 636 removed outlier: 3.774A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 636 " --> pdb=" O CYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.766A pdb=" N ILE B 669 " --> pdb=" O ASP B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 removed outlier: 3.635A pdb=" N GLY B 684 " --> pdb=" O LYS B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.693A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.603A pdb=" N VAL B 705 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 706 " --> pdb=" O PRO B 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 702 through 706' Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 759 removed outlier: 3.541A pdb=" N ASP B 759 " --> pdb=" O VAL B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 790 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 796 through 817 removed outlier: 3.523A pdb=" N VAL B 800 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 847 removed outlier: 4.186A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 853 through 860 Processing helix chain 'B' and resid 863 through 890 Processing helix chain 'B' and resid 895 through 901 Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 925 through 929 removed outlier: 3.955A pdb=" N HIS B 928 " --> pdb=" O ASP B 925 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS B 929 " --> pdb=" O PHE B 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 925 through 929' Processing helix chain 'B' and resid 952 through 969 Proline residue: B 958 - end of helix Processing helix chain 'B' and resid 969 through 1006 removed outlier: 3.620A pdb=" N LEU B 975 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1014 No H-bonds generated for 'chain 'B' and resid 1012 through 1014' Processing helix chain 'B' and resid 1015 through 1030 removed outlier: 3.631A pdb=" N ALA B1019 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1071 removed outlier: 3.859A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET B1059 " --> pdb=" O TRP B1055 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA B1071 " --> pdb=" O ILE B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1104 removed outlier: 3.635A pdb=" N MET B1078 " --> pdb=" O ASN B1074 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 136 removed outlier: 3.860A pdb=" N LEU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 204 removed outlier: 3.736A pdb=" N TYR C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.695A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 341 removed outlier: 3.829A pdb=" N VAL C 338 " --> pdb=" O GLN C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 removed outlier: 3.575A pdb=" N LEU C 362 " --> pdb=" O LEU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 370 through 385 removed outlier: 4.103A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 402 through 418 removed outlier: 3.786A pdb=" N TYR C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.728A pdb=" N ALA C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 468 Processing helix chain 'C' and resid 470 through 481 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 502 through 516 removed outlier: 3.681A pdb=" N TYR C 506 " --> pdb=" O SER C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 532 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.585A pdb=" N ALA C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 582 removed outlier: 3.718A pdb=" N VAL C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 602 Processing helix chain 'C' and resid 607 through 636 removed outlier: 3.774A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 636 " --> pdb=" O CYS C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 644 Processing helix chain 'C' and resid 655 through 663 Processing helix chain 'C' and resid 665 through 670 removed outlier: 3.766A pdb=" N ILE C 669 " --> pdb=" O ASP C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 684 removed outlier: 3.635A pdb=" N GLY C 684 " --> pdb=" O LYS C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 701 removed outlier: 3.694A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 706 removed outlier: 3.604A pdb=" N VAL C 705 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY C 706 " --> pdb=" O PRO C 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 702 through 706' Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 759 removed outlier: 3.540A pdb=" N ASP C 759 " --> pdb=" O VAL C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 765 through 790 Processing helix chain 'C' and resid 791 through 795 Processing helix chain 'C' and resid 796 through 817 removed outlier: 3.523A pdb=" N VAL C 800 " --> pdb=" O ASP C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 847 removed outlier: 4.186A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 850 No H-bonds generated for 'chain 'C' and resid 848 through 850' Processing helix chain 'C' and resid 853 through 860 Processing helix chain 'C' and resid 863 through 890 Processing helix chain 'C' and resid 895 through 901 Processing helix chain 'C' and resid 904 through 910 Processing helix chain 'C' and resid 925 through 929 removed outlier: 3.955A pdb=" N HIS C 928 " --> pdb=" O ASP C 925 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS C 929 " --> pdb=" O PHE C 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 925 through 929' Processing helix chain 'C' and resid 952 through 969 Proline residue: C 958 - end of helix Processing helix chain 'C' and resid 969 through 1006 removed outlier: 3.620A pdb=" N LEU C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1014 No H-bonds generated for 'chain 'C' and resid 1012 through 1014' Processing helix chain 'C' and resid 1015 through 1030 removed outlier: 3.631A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1071 removed outlier: 3.859A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET C1059 " --> pdb=" O TRP C1055 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C1071 " --> pdb=" O ILE C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1104 removed outlier: 3.634A pdb=" N MET C1078 " --> pdb=" O ASN C1074 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 136 removed outlier: 3.860A pdb=" N LEU D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 204 removed outlier: 3.736A pdb=" N TYR D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 309 through 322 removed outlier: 3.695A pdb=" N LEU D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 341 removed outlier: 3.829A pdb=" N VAL D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 removed outlier: 3.575A pdb=" N LEU D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 369 Processing helix chain 'D' and resid 370 through 385 removed outlier: 4.102A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 402 through 418 removed outlier: 3.786A pdb=" N TYR D 410 " --> pdb=" O ASN D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.728A pdb=" N ALA D 442 " --> pdb=" O GLN D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 468 Processing helix chain 'D' and resid 470 through 481 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'D' and resid 502 through 516 removed outlier: 3.680A pdb=" N TYR D 506 " --> pdb=" O SER D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 532 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.585A pdb=" N ALA D 563 " --> pdb=" O HIS D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 582 removed outlier: 3.718A pdb=" N VAL D 579 " --> pdb=" O GLU D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 602 Processing helix chain 'D' and resid 607 through 636 removed outlier: 3.774A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP D 636 " --> pdb=" O CYS D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 644 Processing helix chain 'D' and resid 655 through 663 Processing helix chain 'D' and resid 665 through 670 removed outlier: 3.765A pdb=" N ILE D 669 " --> pdb=" O ASP D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 684 removed outlier: 3.635A pdb=" N GLY D 684 " --> pdb=" O LYS D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 701 removed outlier: 3.694A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 706 removed outlier: 3.603A pdb=" N VAL D 705 " --> pdb=" O ILE D 702 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY D 706 " --> pdb=" O PRO D 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 702 through 706' Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'D' and resid 733 through 759 removed outlier: 3.540A pdb=" N ASP D 759 " --> pdb=" O VAL D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 790 Processing helix chain 'D' and resid 791 through 795 Processing helix chain 'D' and resid 796 through 817 removed outlier: 3.522A pdb=" N VAL D 800 " --> pdb=" O ASP D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 847 removed outlier: 4.186A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 850 No H-bonds generated for 'chain 'D' and resid 848 through 850' Processing helix chain 'D' and resid 853 through 860 Processing helix chain 'D' and resid 863 through 890 Processing helix chain 'D' and resid 895 through 901 Processing helix chain 'D' and resid 904 through 910 Processing helix chain 'D' and resid 925 through 929 removed outlier: 3.955A pdb=" N HIS D 928 " --> pdb=" O ASP D 925 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS D 929 " --> pdb=" O PHE D 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 925 through 929' Processing helix chain 'D' and resid 952 through 969 Proline residue: D 958 - end of helix Processing helix chain 'D' and resid 969 through 1006 removed outlier: 3.620A pdb=" N LEU D 975 " --> pdb=" O LEU D 971 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1014 No H-bonds generated for 'chain 'D' and resid 1012 through 1014' Processing helix chain 'D' and resid 1015 through 1030 removed outlier: 3.631A pdb=" N ALA D1019 " --> pdb=" O PHE D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1046 through 1071 removed outlier: 3.859A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET D1059 " --> pdb=" O TRP D1055 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA D1071 " --> pdb=" O ILE D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1074 through 1104 removed outlier: 3.636A pdb=" N MET D1078 " --> pdb=" O ASN D1074 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121 removed outlier: 6.922A pdb=" N LEU A 120 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 179 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE A 214 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR A 181 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL A 328 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS A 303 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 119 through 121 removed outlier: 6.923A pdb=" N LEU B 120 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE B 179 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE B 214 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR B 181 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL B 328 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS B 303 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 119 through 121 removed outlier: 6.922A pdb=" N LEU C 120 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE C 179 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE C 214 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR C 181 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL C 328 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS C 303 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 119 through 121 removed outlier: 6.921A pdb=" N LEU D 120 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE D 179 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE D 214 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR D 181 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL D 328 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS D 303 " --> pdb=" O VAL D 328 " (cutoff:3.500A) 1768 hydrogen bonds defined for protein. 5244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.11 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4884 1.31 - 1.44: 8856 1.44 - 1.57: 17236 1.57 - 1.70: 0 1.70 - 1.83: 212 Bond restraints: 31188 Sorted by residual: bond pdb=" N21 KX7 D1202 " pdb=" O23 KX7 D1202 " ideal model delta sigma weight residual 1.208 1.402 -0.194 2.00e-02 2.50e+03 9.36e+01 bond pdb=" N21 KX7 B1202 " pdb=" O23 KX7 B1202 " ideal model delta sigma weight residual 1.208 1.401 -0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" N21 KX7 A1203 " pdb=" O23 KX7 A1203 " ideal model delta sigma weight residual 1.208 1.401 -0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" N21 KX7 C1202 " pdb=" O23 KX7 C1202 " ideal model delta sigma weight residual 1.208 1.401 -0.193 2.00e-02 2.50e+03 9.28e+01 bond pdb=" C05 KX7 D1202 " pdb=" N07 KX7 D1202 " ideal model delta sigma weight residual 1.355 1.495 -0.140 2.00e-02 2.50e+03 4.89e+01 ... (remaining 31183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 39939 1.94 - 3.88: 1912 3.88 - 5.82: 297 5.82 - 7.76: 76 7.76 - 9.71: 28 Bond angle restraints: 42252 Sorted by residual: angle pdb=" N VAL B 791 " pdb=" CA VAL B 791 " pdb=" C VAL B 791 " ideal model delta sigma weight residual 112.96 108.21 4.75 1.00e+00 1.00e+00 2.26e+01 angle pdb=" N VAL A 791 " pdb=" CA VAL A 791 " pdb=" C VAL A 791 " ideal model delta sigma weight residual 112.96 108.25 4.71 1.00e+00 1.00e+00 2.22e+01 angle pdb=" N VAL C 791 " pdb=" CA VAL C 791 " pdb=" C VAL C 791 " ideal model delta sigma weight residual 112.96 108.26 4.70 1.00e+00 1.00e+00 2.21e+01 angle pdb=" N VAL D 791 " pdb=" CA VAL D 791 " pdb=" C VAL D 791 " ideal model delta sigma weight residual 112.96 108.28 4.68 1.00e+00 1.00e+00 2.19e+01 angle pdb=" C ILE A 701 " pdb=" N ILE A 702 " pdb=" CA ILE A 702 " ideal model delta sigma weight residual 120.33 123.78 -3.45 8.00e-01 1.56e+00 1.86e+01 ... (remaining 42247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.57: 17104 14.57 - 29.14: 884 29.14 - 43.71: 272 43.71 - 58.28: 16 58.28 - 72.85: 28 Dihedral angle restraints: 18304 sinusoidal: 7392 harmonic: 10912 Sorted by residual: dihedral pdb=" CA PRO B1012 " pdb=" C PRO B1012 " pdb=" N PHE B1013 " pdb=" CA PHE B1013 " ideal model delta harmonic sigma weight residual -180.00 -150.09 -29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA PRO D1012 " pdb=" C PRO D1012 " pdb=" N PHE D1013 " pdb=" CA PHE D1013 " ideal model delta harmonic sigma weight residual -180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA PRO A1012 " pdb=" C PRO A1012 " pdb=" N PHE A1013 " pdb=" CA PHE A1013 " ideal model delta harmonic sigma weight residual -180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2875 0.045 - 0.090: 1358 0.090 - 0.134: 352 0.134 - 0.179: 99 0.179 - 0.224: 24 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CG LEU A 521 " pdb=" CB LEU A 521 " pdb=" CD1 LEU A 521 " pdb=" CD2 LEU A 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU B 521 " pdb=" CB LEU B 521 " pdb=" CD1 LEU B 521 " pdb=" CD2 LEU B 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU D 521 " pdb=" CB LEU D 521 " pdb=" CD1 LEU D 521 " pdb=" CD2 LEU D 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 4705 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 141 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO D 142 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 142 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 142 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 141 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO A 142 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 141 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO B 142 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 142 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 142 " 0.034 5.00e-02 4.00e+02 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 8661 2.82 - 3.34: 28118 3.34 - 3.86: 48975 3.86 - 4.38: 56324 4.38 - 4.90: 96780 Nonbonded interactions: 238858 Sorted by model distance: nonbonded pdb=" O VAL A1065 " pdb=" OG1 THR A1069 " model vdw 2.294 3.040 nonbonded pdb=" O VAL C1065 " pdb=" OG1 THR C1069 " model vdw 2.295 3.040 nonbonded pdb=" O VAL B1065 " pdb=" OG1 THR B1069 " model vdw 2.295 3.040 nonbonded pdb=" O VAL D1065 " pdb=" OG1 THR D1069 " model vdw 2.295 3.040 nonbonded pdb=" O VAL D 728 " pdb=" OG1 THR D 732 " model vdw 2.324 3.040 ... (remaining 238853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 102 through 1201) selection = (chain 'B' and resid 102 through 1201) selection = (chain 'C' and resid 102 through 1201) selection = (chain 'D' and resid 102 through 1201) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.600 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.194 31192 Z= 0.352 Angle : 0.989 9.705 42260 Z= 0.544 Chirality : 0.056 0.224 4708 Planarity : 0.007 0.062 5280 Dihedral : 10.460 72.845 11212 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.12 % Allowed : 1.80 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.11), residues: 3656 helix: -2.03 (0.08), residues: 2412 sheet: -1.90 (0.32), residues: 208 loop : -3.28 (0.15), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1008 TYR 0.038 0.003 TYR A 772 PHE 0.031 0.003 PHE B 304 TRP 0.026 0.003 TRP B 377 HIS 0.007 0.002 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00808 / 0.35 (31188) covalent geometry : angle 0.98652 / 0.54 (42252) SS BOND : bond 0.00636 / 0.29 ( 4) SS BOND : angle 4.83437 / 2.79 ( 8) hydrogen bonds : bond 0.14823 / 9.91 ( 1768) hydrogen bonds : angle 6.41497 / 4.41 ( 5244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 827 time to evaluate : 1.068 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: 0.1986 time to fit residues: 251.3810 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 : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 HIS A 257 HIS A 259 HIS A 438 GLN A 572 ASN A 675 GLN A 987 GLN B 136 HIS B 256 ASN B 257 HIS B 259 HIS B 438 GLN B 572 ASN B 675 GLN B 741 ASN C 136 HIS C 257 HIS C 259 HIS C 294 ASN C 438 GLN C 572 ASN C 675 GLN C 741 ASN D 136 HIS D 257 HIS D 259 HIS D 438 GLN D 572 ASN D 675 GLN D 987 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.159862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.107802 restraints weight = 48820.082| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.42 r_work: 0.3220 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 31192 Z= 0.234 Angle : 0.703 8.924 42260 Z= 0.369 Chirality : 0.044 0.147 4708 Planarity : 0.005 0.054 5280 Dihedral : 6.087 50.303 4024 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.16 % Allowed : 8.26 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.13), residues: 3656 helix: -0.19 (0.10), residues: 2440 sheet: -1.89 (0.32), residues: 192 loop : -3.26 (0.15), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 278 TYR 0.016 0.002 TYR B1005 PHE 0.032 0.002 PHE A 752 TRP 0.022 0.002 TRP A 898 HIS 0.005 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.23 (31188) covalent geometry : angle 0.70204 / 0.37 (42252) SS BOND : bond 0.00853 / 0.39 ( 4) SS BOND : angle 2.67642 / 1.55 ( 8) hydrogen bonds : bond 0.05750 / 3.92 ( 1768) hydrogen bonds : angle 4.58802 / 3.16 ( 5244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 458 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8109 (t80) cc_final: 0.7755 (t80) REVERT: A 280 GLN cc_start: 0.8533 (tt0) cc_final: 0.8220 (tp40) REVERT: A 491 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7923 (tp30) REVERT: A 702 ILE cc_start: 0.8508 (mt) cc_final: 0.8272 (tt) REVERT: A 787 TYR cc_start: 0.7927 (t80) cc_final: 0.7467 (t80) REVERT: A 800 VAL cc_start: 0.9312 (t) cc_final: 0.9100 (p) REVERT: A 868 PHE cc_start: 0.8863 (m-10) cc_final: 0.7693 (t80) REVERT: A 914 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8351 (mm-40) REVERT: A 1005 TYR cc_start: 0.6938 (m-10) cc_final: 0.5669 (m-80) REVERT: A 1021 PHE cc_start: 0.7528 (m-80) cc_final: 0.7286 (m-80) REVERT: A 1023 MET cc_start: 0.7040 (mmm) cc_final: 0.5978 (mtp) REVERT: B 491 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7859 (tp30) REVERT: B 569 ILE cc_start: 0.9172 (tp) cc_final: 0.8971 (tp) REVERT: B 702 ILE cc_start: 0.8512 (mt) cc_final: 0.8298 (tt) REVERT: B 787 TYR cc_start: 0.7907 (t80) cc_final: 0.7461 (t80) REVERT: B 801 MET cc_start: 0.8255 (ptm) cc_final: 0.8012 (ptt) REVERT: B 868 PHE cc_start: 0.8845 (m-10) cc_final: 0.7661 (t80) REVERT: B 1005 TYR cc_start: 0.6856 (m-10) cc_final: 0.5647 (m-80) REVERT: B 1021 PHE cc_start: 0.7556 (m-80) cc_final: 0.7312 (m-80) REVERT: B 1023 MET cc_start: 0.6981 (mmm) cc_final: 0.5904 (mtp) REVERT: C 191 TYR cc_start: 0.8126 (t80) cc_final: 0.7823 (t80) REVERT: C 280 GLN cc_start: 0.8520 (tt0) cc_final: 0.8209 (tp40) REVERT: C 353 MET cc_start: 0.6291 (mpp) cc_final: 0.5897 (ptp) REVERT: C 491 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7879 (tp30) REVERT: C 702 ILE cc_start: 0.8498 (mt) cc_final: 0.8297 (tt) REVERT: C 741 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8679 (m-40) REVERT: C 787 TYR cc_start: 0.7909 (t80) cc_final: 0.7460 (t80) REVERT: C 800 VAL cc_start: 0.9308 (t) cc_final: 0.9101 (p) REVERT: C 801 MET cc_start: 0.8419 (ptm) cc_final: 0.8187 (ptt) REVERT: C 864 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8658 (mp) REVERT: C 868 PHE cc_start: 0.8840 (m-10) cc_final: 0.7665 (t80) REVERT: C 1005 TYR cc_start: 0.6855 (m-10) cc_final: 0.5634 (m-80) REVERT: C 1021 PHE cc_start: 0.7564 (m-80) cc_final: 0.7320 (m-80) REVERT: C 1023 MET cc_start: 0.6948 (mmm) cc_final: 0.5876 (mtp) REVERT: D 280 GLN cc_start: 0.8559 (tt0) cc_final: 0.8252 (tp40) REVERT: D 353 MET cc_start: 0.6356 (mpp) cc_final: 0.5974 (ptp) REVERT: D 491 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7921 (tp30) REVERT: D 702 ILE cc_start: 0.8510 (mt) cc_final: 0.8275 (tt) REVERT: D 787 TYR cc_start: 0.7919 (t80) cc_final: 0.7463 (t80) REVERT: D 800 VAL cc_start: 0.9332 (t) cc_final: 0.9103 (p) REVERT: D 868 PHE cc_start: 0.8847 (m-10) cc_final: 0.7688 (t80) REVERT: D 1005 TYR cc_start: 0.6929 (m-10) cc_final: 0.5732 (m-80) REVERT: D 1023 MET cc_start: 0.7059 (mmm) cc_final: 0.5999 (mtp) REVERT: D 1066 LYS cc_start: 0.9007 (mtpp) cc_final: 0.8805 (mmtp) outliers start: 72 outliers final: 38 residues processed: 505 average time/residue: 0.1762 time to fit residues: 141.2380 Evaluate side-chains 435 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 395 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 741 ASN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 63 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 278 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 311 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 294 ASN ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN B 294 ASN ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 571 GLN D 741 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.161761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110448 restraints weight = 48555.480| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.37 r_work: 0.3256 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31192 Z= 0.146 Angle : 0.595 7.856 42260 Z= 0.311 Chirality : 0.040 0.145 4708 Planarity : 0.004 0.048 5280 Dihedral : 5.713 50.284 4024 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.19 % Allowed : 10.28 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.14), residues: 3656 helix: 0.63 (0.10), residues: 2472 sheet: -1.70 (0.34), residues: 192 loop : -2.94 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 160 TYR 0.014 0.002 TYR C1005 PHE 0.015 0.001 PHE B 779 TRP 0.019 0.002 TRP B 898 HIS 0.004 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (31188) covalent geometry : angle 0.59316 / 0.31 (42252) SS BOND : bond 0.01137 / 0.52 ( 4) SS BOND : angle 3.30435 / 1.91 ( 8) hydrogen bonds : bond 0.04546 / 3.08 ( 1768) hydrogen bonds : angle 4.17729 / 2.87 ( 5244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 443 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8479 (tt0) cc_final: 0.8166 (tp40) REVERT: A 353 MET cc_start: 0.6478 (mpp) cc_final: 0.5943 (ptp) REVERT: A 396 MET cc_start: 0.7034 (mmp) cc_final: 0.6168 (mmp) REVERT: A 491 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7847 (tp30) REVERT: A 787 TYR cc_start: 0.7891 (t80) cc_final: 0.7433 (t80) REVERT: A 868 PHE cc_start: 0.8797 (m-10) cc_final: 0.7588 (t80) REVERT: A 1005 TYR cc_start: 0.6884 (m-10) cc_final: 0.5538 (m-80) REVERT: A 1023 MET cc_start: 0.6952 (mmm) cc_final: 0.5867 (mtp) REVERT: A 1068 ASN cc_start: 0.8428 (m-40) cc_final: 0.8206 (m-40) REVERT: B 191 TYR cc_start: 0.7869 (t80) cc_final: 0.7524 (t80) REVERT: B 353 MET cc_start: 0.6412 (mpp) cc_final: 0.5862 (ptp) REVERT: B 396 MET cc_start: 0.7039 (mmp) cc_final: 0.6180 (mmp) REVERT: B 491 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7860 (tp30) REVERT: B 689 ASP cc_start: 0.8366 (t0) cc_final: 0.8122 (t0) REVERT: B 787 TYR cc_start: 0.7927 (t80) cc_final: 0.7479 (t80) REVERT: B 868 PHE cc_start: 0.8764 (m-10) cc_final: 0.7560 (t80) REVERT: B 1005 TYR cc_start: 0.6834 (m-10) cc_final: 0.5413 (m-80) REVERT: B 1023 MET cc_start: 0.6870 (mmm) cc_final: 0.5760 (mtp) REVERT: B 1068 ASN cc_start: 0.8386 (m-40) cc_final: 0.8155 (m-40) REVERT: C 280 GLN cc_start: 0.8502 (tt0) cc_final: 0.8163 (tp40) REVERT: C 353 MET cc_start: 0.6414 (mpp) cc_final: 0.5905 (ptp) REVERT: C 396 MET cc_start: 0.6976 (mmp) cc_final: 0.6136 (mmp) REVERT: C 491 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7882 (tp30) REVERT: C 787 TYR cc_start: 0.7921 (t80) cc_final: 0.7463 (t80) REVERT: C 868 PHE cc_start: 0.8787 (m-10) cc_final: 0.7568 (t80) REVERT: C 1005 TYR cc_start: 0.6880 (m-10) cc_final: 0.5461 (m-80) REVERT: C 1023 MET cc_start: 0.6861 (mmm) cc_final: 0.5755 (mtp) REVERT: C 1068 ASN cc_start: 0.8345 (m-40) cc_final: 0.8106 (m-40) REVERT: D 280 GLN cc_start: 0.8492 (tt0) cc_final: 0.8177 (tp40) REVERT: D 353 MET cc_start: 0.6568 (mpp) cc_final: 0.5992 (ptp) REVERT: D 396 MET cc_start: 0.6968 (mmp) cc_final: 0.6274 (mmp) REVERT: D 689 ASP cc_start: 0.8361 (t0) cc_final: 0.8157 (t0) REVERT: D 787 TYR cc_start: 0.7896 (t80) cc_final: 0.7437 (t80) REVERT: D 868 PHE cc_start: 0.8792 (m-10) cc_final: 0.7581 (t80) REVERT: D 1005 TYR cc_start: 0.6905 (m-10) cc_final: 0.5536 (m-80) REVERT: D 1023 MET cc_start: 0.6951 (mmm) cc_final: 0.5874 (mtp) REVERT: D 1066 LYS cc_start: 0.9005 (mtpp) cc_final: 0.8792 (mmtp) REVERT: D 1068 ASN cc_start: 0.8367 (m-40) cc_final: 0.8141 (m-40) outliers start: 73 outliers final: 43 residues processed: 492 average time/residue: 0.1976 time to fit residues: 156.5648 Evaluate side-chains 424 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 381 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 40 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 51 optimal weight: 0.5980 chunk 134 optimal weight: 8.9990 chunk 333 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 311 optimal weight: 0.0980 chunk 284 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 571 GLN B 990 ASN C 571 GLN C 609 ASN C 990 ASN D 294 ASN D 609 ASN D 635 ASN D 990 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.159154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107481 restraints weight = 48649.259| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.38 r_work: 0.3211 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31192 Z= 0.195 Angle : 0.620 6.398 42260 Z= 0.322 Chirality : 0.042 0.184 4708 Planarity : 0.004 0.045 5280 Dihedral : 5.485 48.488 4024 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.31 % Allowed : 11.93 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3656 helix: 0.91 (0.10), residues: 2476 sheet: -1.47 (0.35), residues: 192 loop : -2.80 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 278 TYR 0.027 0.002 TYR C 191 PHE 0.018 0.002 PHE C 752 TRP 0.020 0.002 TRP A 898 HIS 0.005 0.001 HIS C 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 (31188) covalent geometry : angle 0.61835 / 0.32 (42252) SS BOND : bond 0.00842 / 0.38 ( 4) SS BOND : angle 2.88576 / 1.67 ( 8) hydrogen bonds : bond 0.04907 / 3.33 ( 1768) hydrogen bonds : angle 4.11731 / 2.83 ( 5244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 406 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8536 (tt0) cc_final: 0.8233 (tp40) REVERT: A 304 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.6739 (m-80) REVERT: A 396 MET cc_start: 0.7444 (mmp) cc_final: 0.6750 (mmp) REVERT: A 488 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8055 (tt) REVERT: A 732 THR cc_start: 0.8796 (m) cc_final: 0.8519 (p) REVERT: A 788 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7837 (mmp) REVERT: A 868 PHE cc_start: 0.8833 (m-10) cc_final: 0.7656 (t80) REVERT: A 914 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8288 (mm-40) REVERT: A 1023 MET cc_start: 0.6851 (mmm) cc_final: 0.5792 (mtp) REVERT: A 1068 ASN cc_start: 0.8439 (m-40) cc_final: 0.8180 (m-40) REVERT: B 304 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.6656 (m-80) REVERT: B 396 MET cc_start: 0.7421 (mmp) cc_final: 0.7207 (mmp) REVERT: B 488 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7992 (tt) REVERT: B 491 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7869 (tp30) REVERT: B 702 ILE cc_start: 0.8487 (mp) cc_final: 0.8027 (tt) REVERT: B 732 THR cc_start: 0.8763 (m) cc_final: 0.8443 (p) REVERT: B 788 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7829 (mmp) REVERT: B 801 MET cc_start: 0.8323 (ptt) cc_final: 0.8084 (ptt) REVERT: B 868 PHE cc_start: 0.8811 (m-10) cc_final: 0.7636 (t80) REVERT: B 1023 MET cc_start: 0.6780 (mmm) cc_final: 0.5722 (mtp) REVERT: B 1068 ASN cc_start: 0.8411 (m-40) cc_final: 0.8149 (m-40) REVERT: C 280 GLN cc_start: 0.8539 (tt0) cc_final: 0.8229 (tp40) REVERT: C 396 MET cc_start: 0.7058 (mmp) cc_final: 0.6393 (mmp) REVERT: C 488 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7990 (tt) REVERT: C 491 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7898 (tp30) REVERT: C 732 THR cc_start: 0.8738 (m) cc_final: 0.8446 (p) REVERT: C 788 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7863 (mmp) REVERT: C 868 PHE cc_start: 0.8799 (m-10) cc_final: 0.7625 (t80) REVERT: C 1023 MET cc_start: 0.6760 (mmm) cc_final: 0.5691 (mtp) REVERT: C 1068 ASN cc_start: 0.8408 (m-40) cc_final: 0.8137 (m-40) REVERT: D 280 GLN cc_start: 0.8538 (tt0) cc_final: 0.8241 (tp40) REVERT: D 304 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: D 395 LYS cc_start: 0.8608 (mmmm) cc_final: 0.8364 (mmmm) REVERT: D 396 MET cc_start: 0.7305 (mmp) cc_final: 0.6776 (mmp) REVERT: D 488 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7981 (tt) REVERT: D 702 ILE cc_start: 0.8507 (mp) cc_final: 0.8022 (tt) REVERT: D 732 THR cc_start: 0.8817 (m) cc_final: 0.8487 (p) REVERT: D 788 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7857 (mmp) REVERT: D 868 PHE cc_start: 0.8841 (m-10) cc_final: 0.7658 (t80) REVERT: D 914 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8212 (mm-40) REVERT: D 1023 MET cc_start: 0.6950 (mmm) cc_final: 0.5865 (mtp) REVERT: D 1066 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8819 (mmtp) REVERT: D 1068 ASN cc_start: 0.8430 (m-40) cc_final: 0.8167 (m-40) outliers start: 110 outliers final: 58 residues processed: 483 average time/residue: 0.1878 time to fit residues: 146.5214 Evaluate side-chains 452 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 383 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 788 MET Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 54 optimal weight: 6.9990 chunk 348 optimal weight: 1.9990 chunk 340 optimal weight: 4.9990 chunk 252 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 336 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 280 optimal weight: 2.9990 chunk 274 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN D 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.160424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107621 restraints weight = 49412.757| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.47 r_work: 0.3222 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31192 Z= 0.157 Angle : 0.585 6.614 42260 Z= 0.303 Chirality : 0.040 0.185 4708 Planarity : 0.004 0.044 5280 Dihedral : 5.414 51.678 4024 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.85 % Allowed : 13.67 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3656 helix: 1.15 (0.11), residues: 2476 sheet: -1.45 (0.35), residues: 192 loop : -2.73 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1046 TYR 0.030 0.002 TYR C 191 PHE 0.025 0.001 PHE B1021 TRP 0.020 0.001 TRP A 898 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (31188) covalent geometry : angle 0.58249 / 0.30 (42252) SS BOND : bond 0.00992 / 0.45 ( 4) SS BOND : angle 3.69354 / 2.12 ( 8) hydrogen bonds : bond 0.04426 / 3.01 ( 1768) hydrogen bonds : angle 3.99231 / 2.75 ( 5244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 390 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8521 (tt0) cc_final: 0.8197 (tp40) REVERT: A 304 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.6822 (m-80) REVERT: A 488 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7898 (tt) REVERT: A 689 ASP cc_start: 0.8331 (t0) cc_final: 0.8022 (m-30) REVERT: A 732 THR cc_start: 0.8852 (m) cc_final: 0.8598 (p) REVERT: A 868 PHE cc_start: 0.8823 (m-10) cc_final: 0.7660 (t80) REVERT: A 1021 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7299 (t80) REVERT: A 1023 MET cc_start: 0.6760 (mmm) cc_final: 0.5742 (mtp) REVERT: A 1068 ASN cc_start: 0.8343 (m-40) cc_final: 0.8067 (m-40) REVERT: B 304 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.6719 (m-80) REVERT: B 488 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7875 (tt) REVERT: B 491 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7837 (tp30) REVERT: B 689 ASP cc_start: 0.8375 (t0) cc_final: 0.8055 (m-30) REVERT: B 702 ILE cc_start: 0.8485 (mp) cc_final: 0.8043 (tt) REVERT: B 732 THR cc_start: 0.8803 (m) cc_final: 0.8578 (p) REVERT: B 788 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7834 (mmp) REVERT: B 801 MET cc_start: 0.8400 (ptt) cc_final: 0.8187 (ptt) REVERT: B 868 PHE cc_start: 0.8814 (m-10) cc_final: 0.7631 (t80) REVERT: B 1023 MET cc_start: 0.6755 (mmm) cc_final: 0.5731 (mtp) REVERT: B 1068 ASN cc_start: 0.8261 (m-40) cc_final: 0.7970 (m-40) REVERT: C 280 GLN cc_start: 0.8532 (tt0) cc_final: 0.8219 (tp40) REVERT: C 396 MET cc_start: 0.7306 (mmp) cc_final: 0.6813 (mmp) REVERT: C 488 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7948 (tt) REVERT: C 491 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7858 (tp30) REVERT: C 689 ASP cc_start: 0.8317 (t0) cc_final: 0.7994 (m-30) REVERT: C 732 THR cc_start: 0.8792 (m) cc_final: 0.8578 (p) REVERT: C 788 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7834 (mmp) REVERT: C 801 MET cc_start: 0.8359 (ptt) cc_final: 0.8040 (ptt) REVERT: C 868 PHE cc_start: 0.8803 (m-10) cc_final: 0.7627 (t80) REVERT: C 1023 MET cc_start: 0.6760 (mmm) cc_final: 0.5738 (mtp) REVERT: C 1068 ASN cc_start: 0.8288 (m-40) cc_final: 0.8006 (m-40) REVERT: D 280 GLN cc_start: 0.8532 (tt0) cc_final: 0.8201 (tp40) REVERT: D 294 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7517 (p0) REVERT: D 304 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.6800 (m-80) REVERT: D 396 MET cc_start: 0.7252 (mmp) cc_final: 0.6941 (mmp) REVERT: D 488 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8016 (tt) REVERT: D 689 ASP cc_start: 0.8331 (t0) cc_final: 0.7997 (m-30) REVERT: D 702 ILE cc_start: 0.8441 (mp) cc_final: 0.7966 (tt) REVERT: D 732 THR cc_start: 0.8853 (m) cc_final: 0.8609 (p) REVERT: D 868 PHE cc_start: 0.8843 (m-10) cc_final: 0.7661 (t80) REVERT: D 1021 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.6627 (t80) REVERT: D 1023 MET cc_start: 0.6825 (mmm) cc_final: 0.5794 (mtp) REVERT: D 1049 ASP cc_start: 0.7280 (m-30) cc_final: 0.6925 (m-30) REVERT: D 1068 ASN cc_start: 0.8304 (m-40) cc_final: 0.8028 (m-40) outliers start: 95 outliers final: 47 residues processed: 450 average time/residue: 0.1786 time to fit residues: 130.6783 Evaluate side-chains 429 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 370 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain B residue 1078 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 788 MET Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1045 PHE Chi-restraints excluded: chain D residue 1078 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 117 optimal weight: 20.0000 chunk 303 optimal weight: 20.0000 chunk 360 optimal weight: 0.7980 chunk 187 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 337 optimal weight: 5.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 ASN B 635 ASN C 635 ASN C 990 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.155680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102434 restraints weight = 49502.611| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.52 r_work: 0.3148 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 31192 Z= 0.324 Angle : 0.717 7.336 42260 Z= 0.371 Chirality : 0.046 0.205 4708 Planarity : 0.005 0.046 5280 Dihedral : 5.705 56.785 4024 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.49 % Allowed : 13.58 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3656 helix: 0.91 (0.10), residues: 2468 sheet: -1.81 (0.33), residues: 192 loop : -2.79 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 901 TYR 0.027 0.002 TYR C 191 PHE 0.022 0.002 PHE D1013 TRP 0.024 0.002 TRP A 898 HIS 0.008 0.001 HIS B 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00785 / 0.32 (31188) covalent geometry : angle 0.71518 / 0.37 (42252) SS BOND : bond 0.00940 / 0.43 ( 4) SS BOND : angle 4.14767 / 2.39 ( 8) hydrogen bonds : bond 0.05810 / 3.95 ( 1768) hydrogen bonds : angle 4.32757 / 2.99 ( 5244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 379 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8628 (tt0) cc_final: 0.8307 (tp40) REVERT: A 304 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.6717 (m-80) REVERT: A 353 MET cc_start: 0.6768 (mpp) cc_final: 0.6092 (pmm) REVERT: A 395 LYS cc_start: 0.8623 (mmmm) cc_final: 0.8294 (mmmm) REVERT: A 488 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7939 (tt) REVERT: A 613 GLU cc_start: 0.8590 (mp0) cc_final: 0.8224 (mp0) REVERT: A 689 ASP cc_start: 0.8451 (t0) cc_final: 0.8147 (m-30) REVERT: A 732 THR cc_start: 0.8912 (m) cc_final: 0.8619 (p) REVERT: A 868 PHE cc_start: 0.8875 (m-10) cc_final: 0.7725 (t80) REVERT: A 1021 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7419 (t80) REVERT: A 1023 MET cc_start: 0.7061 (mmm) cc_final: 0.5941 (mtp) REVERT: A 1059 MET cc_start: 0.7522 (mpp) cc_final: 0.7147 (mmm) REVERT: B 141 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7885 (p) REVERT: B 304 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: B 353 MET cc_start: 0.6704 (mpp) cc_final: 0.6223 (pmm) REVERT: B 401 ASP cc_start: 0.8329 (t70) cc_final: 0.8012 (m-30) REVERT: B 402 GLU cc_start: 0.7957 (tt0) cc_final: 0.7690 (tt0) REVERT: B 488 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7851 (tt) REVERT: B 689 ASP cc_start: 0.8430 (t0) cc_final: 0.8080 (m-30) REVERT: B 702 ILE cc_start: 0.8468 (mp) cc_final: 0.8051 (tt) REVERT: B 732 THR cc_start: 0.8868 (m) cc_final: 0.8623 (p) REVERT: B 1023 MET cc_start: 0.6995 (mmm) cc_final: 0.5892 (mtp) REVERT: B 1046 ARG cc_start: 0.7309 (ttm170) cc_final: 0.7019 (ttm110) REVERT: B 1059 MET cc_start: 0.7471 (mpp) cc_final: 0.7103 (mmm) REVERT: C 280 GLN cc_start: 0.8612 (tt0) cc_final: 0.8288 (tp40) REVERT: C 353 MET cc_start: 0.6738 (mpp) cc_final: 0.6090 (pmm) REVERT: C 395 LYS cc_start: 0.8460 (mmmm) cc_final: 0.8234 (mmmm) REVERT: C 401 ASP cc_start: 0.8278 (t70) cc_final: 0.7947 (m-30) REVERT: C 402 GLU cc_start: 0.7989 (tt0) cc_final: 0.7721 (tt0) REVERT: C 488 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7866 (tt) REVERT: C 491 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7947 (tp30) REVERT: C 627 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8603 (mp0) REVERT: C 646 TYR cc_start: 0.6096 (t80) cc_final: 0.5754 (t80) REVERT: C 689 ASP cc_start: 0.8406 (t0) cc_final: 0.8065 (m-30) REVERT: C 732 THR cc_start: 0.8817 (m) cc_final: 0.8572 (p) REVERT: C 801 MET cc_start: 0.8445 (ptt) cc_final: 0.8178 (ptt) REVERT: C 868 PHE cc_start: 0.8882 (m-10) cc_final: 0.7738 (t80) REVERT: C 1023 MET cc_start: 0.6969 (mmm) cc_final: 0.5829 (mtp) REVERT: C 1059 MET cc_start: 0.7501 (mpp) cc_final: 0.7151 (mmm) REVERT: D 280 GLN cc_start: 0.8612 (tt0) cc_final: 0.8305 (tp40) REVERT: D 304 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.6703 (m-80) REVERT: D 353 MET cc_start: 0.6731 (mpp) cc_final: 0.6096 (pmm) REVERT: D 395 LYS cc_start: 0.8521 (mmmm) cc_final: 0.8268 (mmmm) REVERT: D 488 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7992 (tt) REVERT: D 689 ASP cc_start: 0.8382 (t0) cc_final: 0.8074 (m-30) REVERT: D 702 ILE cc_start: 0.8497 (mp) cc_final: 0.8057 (tt) REVERT: D 732 THR cc_start: 0.8886 (m) cc_final: 0.8604 (p) REVERT: D 868 PHE cc_start: 0.8884 (m-10) cc_final: 0.7731 (t80) REVERT: D 1021 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6670 (t80) REVERT: D 1023 MET cc_start: 0.7059 (mmm) cc_final: 0.5920 (mtp) REVERT: D 1049 ASP cc_start: 0.7232 (m-30) cc_final: 0.6865 (m-30) REVERT: D 1059 MET cc_start: 0.7564 (mpp) cc_final: 0.7161 (mmm) outliers start: 116 outliers final: 64 residues processed: 468 average time/residue: 0.1816 time to fit residues: 137.8762 Evaluate side-chains 430 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 356 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain B residue 1078 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain C residue 1078 MET Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1045 PHE Chi-restraints excluded: chain D residue 1078 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.6881 > 50: distance: 11 - 20: 3.031 distance: 37 - 55: 6.729 distance: 51 - 55: 9.134 distance: 55 - 56: 18.224 distance: 56 - 57: 10.026 distance: 56 - 59: 8.310 distance: 57 - 58: 17.906 distance: 57 - 60: 30.183 distance: 60 - 61: 25.339 distance: 61 - 62: 18.963 distance: 61 - 64: 21.618 distance: 62 - 63: 11.865 distance: 62 - 67: 3.951 distance: 64 - 65: 23.025 distance: 64 - 66: 12.549 distance: 67 - 68: 9.905 distance: 68 - 69: 11.898 distance: 68 - 71: 14.216 distance: 69 - 70: 12.044 distance: 69 - 75: 3.192 distance: 71 - 72: 6.165 distance: 72 - 73: 4.643 distance: 72 - 74: 6.449 distance: 76 - 77: 20.305 distance: 76 - 79: 14.367 distance: 77 - 78: 18.488 distance: 77 - 84: 25.127 distance: 78 - 113: 16.912 distance: 79 - 80: 11.047 distance: 80 - 81: 3.853 distance: 81 - 82: 8.304 distance: 81 - 83: 5.610 distance: 84 - 85: 9.582 distance: 85 - 86: 7.986 distance: 85 - 88: 12.829 distance: 86 - 87: 24.411 distance: 86 - 94: 24.022 distance: 88 - 89: 8.323 distance: 89 - 90: 7.050 distance: 90 - 92: 4.304 distance: 91 - 93: 4.895 distance: 92 - 93: 5.299 distance: 94 - 95: 14.436 distance: 95 - 96: 18.201 distance: 95 - 98: 15.292 distance: 96 - 97: 19.138 distance: 96 - 105: 25.088 distance: 98 - 99: 10.474 distance: 99 - 100: 10.803 distance: 99 - 101: 12.290 distance: 100 - 102: 7.453 distance: 102 - 104: 3.094 distance: 103 - 104: 3.749 distance: 105 - 106: 8.955 distance: 106 - 107: 31.510 distance: 106 - 109: 8.684 distance: 107 - 108: 27.617 distance: 107 - 113: 17.077 distance: 109 - 110: 9.214 distance: 109 - 111: 9.517 distance: 110 - 112: 6.174 distance: 113 - 114: 36.075 distance: 114 - 115: 28.653 distance: 114 - 117: 25.139 distance: 115 - 116: 24.664 distance: 115 - 118: 8.177 distance: 118 - 119: 5.931 distance: 119 - 120: 17.912 distance: 119 - 122: 16.295 distance: 120 - 121: 22.066 distance: 120 - 127: 13.936 distance: 121 - 145: 24.206 distance: 122 - 123: 8.469 distance: 123 - 124: 16.740 distance: 124 - 125: 6.101 distance: 124 - 126: 4.667 distance: 127 - 128: 3.175 distance: 127 - 133: 4.547 distance: 128 - 129: 9.656 distance: 128 - 131: 6.551 distance: 129 - 130: 13.676 distance: 129 - 134: 10.477 distance: 130 - 154: 14.007 distance: 131 - 132: 4.734 distance: 132 - 133: 11.500