Starting phenix.real_space_refine on Sun Jul 5 21:06:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wre_32724/07_2026/7wre_32724.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wre_32724/07_2026/7wre_32724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wre_32724/07_2026/7wre_32724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wre_32724/07_2026/7wre_32724.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wre_32724/07_2026/7wre_32724.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wre_32724/07_2026/7wre_32724.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wre_32724/07_2026/7wre_32724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wre_32724/07_2026/7wre_32724.map" } resolution = 2.52 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 140 5.16 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 44 residue(s): 0.04s 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: 30468 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: 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: "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: 5.70, per 1000 atoms: 0.19 Number of scatterers: 30468 At special positions: 0 Unit cell: (153.114, 153.114, 156.156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 140 16.00 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=2.38 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.38 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.38 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.38 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7080 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 4 sheets defined 70.1% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 125 through 136 removed outlier: 3.787A 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: 3.677A pdb=" N TYR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.926A 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: 3.654A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.631A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.827A pdb=" N ARG A 368 " --> pdb=" O THR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 385 removed outlier: 3.914A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.564A pdb=" N THR A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.654A pdb=" N ALA A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 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 Processing helix chain 'A' and resid 518 through 532 Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.639A pdb=" N ALA A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 582 removed outlier: 3.677A 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: 3.522A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (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: 3.597A pdb=" N ILE A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.795A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 4.051A pdb=" N GLY A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 788 removed outlier: 3.520A pdb=" N LEU A 769 " --> pdb=" O HIS A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 795 Processing helix chain 'A' and resid 796 through 817 Processing helix chain 'A' and resid 821 through 847 removed outlier: 4.298A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.300A 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 852 through 860 removed outlier: 4.559A pdb=" N LYS A 856 " --> pdb=" O ASN A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 890 Processing helix chain 'A' and resid 895 through 904 removed outlier: 3.654A pdb=" N SER A 902 " --> pdb=" O TRP A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 911 through 913 No H-bonds generated for 'chain 'A' and resid 911 through 913' Processing helix chain 'A' and resid 925 through 929 removed outlier: 3.856A pdb=" N HIS A 928 " --> pdb=" O ASP A 925 " (cutoff:3.500A) removed outlier: 3.794A 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 removed outlier: 3.573A pdb=" N ILE A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1006 removed outlier: 3.667A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1027 removed outlier: 3.513A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1070 removed outlier: 3.977A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1104 removed outlier: 3.792A pdb=" N MET A1078 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A1104 " --> pdb=" O ALA A1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 136 removed outlier: 3.787A 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: 3.677A pdb=" N TYR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.926A 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: 3.654A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.631A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.827A pdb=" N ARG B 368 " --> pdb=" O THR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 385 removed outlier: 3.914A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.563A pdb=" N THR B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.655A pdb=" N ALA B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 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 Processing helix chain 'B' and resid 518 through 532 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.639A pdb=" N ALA B 563 " --> pdb=" O HIS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 582 removed outlier: 3.677A 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: 3.521A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (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: 3.597A pdb=" N ILE B 669 " --> pdb=" O ASP B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.795A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 4.052A pdb=" N GLY B 706 " --> pdb=" O PRO B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 759 Processing helix chain 'B' and resid 765 through 788 removed outlier: 3.520A pdb=" N LEU B 769 " --> pdb=" O HIS B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 796 through 817 Processing helix chain 'B' and resid 821 through 847 removed outlier: 4.297A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.300A 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 852 through 860 removed outlier: 4.559A pdb=" N LYS B 856 " --> pdb=" O ASN B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 890 Processing helix chain 'B' and resid 895 through 904 removed outlier: 3.654A pdb=" N SER B 902 " --> pdb=" O TRP B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 911 through 913 No H-bonds generated for 'chain 'B' and resid 911 through 913' Processing helix chain 'B' and resid 925 through 929 removed outlier: 3.856A pdb=" N HIS B 928 " --> pdb=" O ASP B 925 " (cutoff:3.500A) removed outlier: 3.795A 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 removed outlier: 3.572A pdb=" N ILE B 969 " --> pdb=" O LEU B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 1006 removed outlier: 3.667A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1027 removed outlier: 3.513A pdb=" N ALA B1019 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1070 removed outlier: 3.977A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET B1059 " --> pdb=" O TRP B1055 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1104 removed outlier: 3.792A pdb=" N MET B1078 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B1104 " --> pdb=" O ALA B1100 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 136 removed outlier: 3.787A 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: 3.677A pdb=" N TYR C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 3.927A 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: 3.653A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 341 removed outlier: 3.631A pdb=" N VAL C 338 " --> pdb=" O GLN C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 365 through 369 removed outlier: 3.827A pdb=" N ARG C 368 " --> pdb=" O THR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 385 removed outlier: 3.914A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 418 removed outlier: 3.563A pdb=" N THR C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.654A pdb=" N ALA C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 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 Processing helix chain 'C' and resid 518 through 532 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.639A pdb=" N ALA C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 582 removed outlier: 3.676A 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: 3.522A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (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: 3.597A pdb=" N ILE C 669 " --> pdb=" O ASP C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 removed outlier: 3.795A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 706 removed outlier: 4.051A pdb=" N GLY C 706 " --> pdb=" O PRO C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 759 Processing helix chain 'C' and resid 765 through 788 removed outlier: 3.521A pdb=" N LEU C 769 " --> pdb=" O HIS C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 795 Processing helix chain 'C' and resid 796 through 817 Processing helix chain 'C' and resid 821 through 847 removed outlier: 4.297A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.299A 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 852 through 860 removed outlier: 4.560A pdb=" N LYS C 856 " --> pdb=" O ASN C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 890 Processing helix chain 'C' and resid 895 through 904 removed outlier: 3.655A pdb=" N SER C 902 " --> pdb=" O TRP C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 910 Processing helix chain 'C' and resid 911 through 913 No H-bonds generated for 'chain 'C' and resid 911 through 913' Processing helix chain 'C' and resid 925 through 929 removed outlier: 3.856A pdb=" N HIS C 928 " --> pdb=" O ASP C 925 " (cutoff:3.500A) removed outlier: 3.794A 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 removed outlier: 3.572A pdb=" N ILE C 969 " --> pdb=" O LEU C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1006 removed outlier: 3.668A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1027 removed outlier: 3.513A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1070 removed outlier: 3.978A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET C1059 " --> pdb=" O TRP C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1104 removed outlier: 3.791A pdb=" N MET C1078 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C1104 " --> pdb=" O ALA C1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 136 removed outlier: 3.787A 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: 3.677A pdb=" N TYR D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 3.926A 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: 3.653A pdb=" N LEU D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 341 removed outlier: 3.631A pdb=" N VAL D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 365 through 369 removed outlier: 3.827A pdb=" N ARG D 368 " --> pdb=" O THR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 385 removed outlier: 3.914A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 418 removed outlier: 3.564A pdb=" N THR D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.654A pdb=" N ALA D 442 " --> pdb=" O GLN D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 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 Processing helix chain 'D' and resid 518 through 532 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.639A pdb=" N ALA D 563 " --> pdb=" O HIS D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 582 removed outlier: 3.677A 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: 3.522A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (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: 3.598A pdb=" N ILE D 669 " --> pdb=" O ASP D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 removed outlier: 3.795A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 706 removed outlier: 4.052A pdb=" N GLY D 706 " --> pdb=" O PRO D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'D' and resid 733 through 759 Processing helix chain 'D' and resid 765 through 788 removed outlier: 3.520A pdb=" N LEU D 769 " --> pdb=" O HIS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 795 Processing helix chain 'D' and resid 796 through 817 Processing helix chain 'D' and resid 821 through 847 removed outlier: 4.298A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.300A 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 852 through 860 removed outlier: 4.560A pdb=" N LYS D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 890 Processing helix chain 'D' and resid 895 through 904 removed outlier: 3.654A pdb=" N SER D 902 " --> pdb=" O TRP D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 910 Processing helix chain 'D' and resid 911 through 913 No H-bonds generated for 'chain 'D' and resid 911 through 913' Processing helix chain 'D' and resid 925 through 929 removed outlier: 3.856A pdb=" N HIS D 928 " --> pdb=" O ASP D 925 " (cutoff:3.500A) removed outlier: 3.794A 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 removed outlier: 3.573A pdb=" N ILE D 969 " --> pdb=" O LEU D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 1006 removed outlier: 3.667A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1015 through 1027 removed outlier: 3.513A pdb=" N ALA D1019 " --> pdb=" O PHE D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1046 through 1070 removed outlier: 3.977A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET D1059 " --> pdb=" O TRP D1055 " (cutoff:3.500A) Processing helix chain 'D' and resid 1074 through 1104 removed outlier: 3.792A pdb=" N MET D1078 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS D1104 " --> pdb=" O ALA D1100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 121 removed outlier: 6.171A pdb=" N ALA A 211 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU A 261 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY A 213 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL A 263 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA A 215 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA A 177 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE A 212 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE A 179 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE A 214 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR A 181 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL A 328 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N CYS A 303 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 327 " --> pdb=" O THR A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 121 removed outlier: 6.171A pdb=" N ALA B 211 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU B 261 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY B 213 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL B 263 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALA B 215 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA B 177 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE B 212 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE B 179 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE B 214 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR B 181 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL B 328 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS B 303 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 327 " --> pdb=" O THR B 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 121 removed outlier: 6.171A pdb=" N ALA C 211 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU C 261 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY C 213 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL C 263 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALA C 215 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA C 177 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE C 212 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 6.260A 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: 6.688A pdb=" N THR C 181 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL C 328 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS C 303 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL C 327 " --> pdb=" O THR C 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 118 through 121 removed outlier: 6.170A pdb=" N ALA D 211 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU D 261 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY D 213 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL D 263 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA D 215 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA D 177 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE D 212 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE D 179 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE D 214 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR D 181 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL D 328 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS D 303 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL D 327 " --> pdb=" O THR D 392 " (cutoff:3.500A) 1784 hydrogen bonds defined for protein. 5292 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: 4.70 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4892 1.31 - 1.44: 8876 1.44 - 1.57: 17208 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 1.399 -0.191 2.00e-02 2.50e+03 9.17e+01 bond pdb=" N21 KX7 C1202 " pdb=" O23 KX7 C1202 " ideal model delta sigma weight residual 1.208 1.399 -0.191 2.00e-02 2.50e+03 9.09e+01 bond pdb=" N21 KX7 A1202 " pdb=" O23 KX7 A1202 " ideal model delta sigma weight residual 1.208 1.398 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" N21 KX7 B1202 " pdb=" O23 KX7 B1202 " ideal model delta sigma weight residual 1.208 1.398 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C05 KX7 D1202 " pdb=" N07 KX7 D1202 " ideal model delta sigma weight residual 1.355 1.486 -0.131 2.00e-02 2.50e+03 4.29e+01 ... (remaining 31183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 39533 2.16 - 4.33: 2281 4.33 - 6.49: 298 6.49 - 8.66: 100 8.66 - 10.82: 40 Bond angle restraints: 42252 Sorted by residual: angle pdb=" N SER C 917 " pdb=" CA SER C 917 " pdb=" C SER C 917 " ideal model delta sigma weight residual 111.36 121.66 -10.30 1.09e+00 8.42e-01 8.93e+01 angle pdb=" N SER A 917 " pdb=" CA SER A 917 " pdb=" C SER A 917 " ideal model delta sigma weight residual 111.36 121.63 -10.27 1.09e+00 8.42e-01 8.88e+01 angle pdb=" N SER D 917 " pdb=" CA SER D 917 " pdb=" C SER D 917 " ideal model delta sigma weight residual 111.36 121.50 -10.14 1.09e+00 8.42e-01 8.65e+01 angle pdb=" N SER B 917 " pdb=" CA SER B 917 " pdb=" C SER B 917 " ideal model delta sigma weight residual 111.36 121.35 -9.99 1.09e+00 8.42e-01 8.41e+01 angle pdb=" N ASP A 920 " pdb=" CA ASP A 920 " pdb=" C ASP A 920 " ideal model delta sigma weight residual 111.36 120.96 -9.60 1.09e+00 8.42e-01 7.76e+01 ... (remaining 42247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.80: 16879 14.80 - 29.60: 1111 29.60 - 44.40: 262 44.40 - 59.20: 20 59.20 - 74.01: 32 Dihedral angle restraints: 18304 sinusoidal: 7392 harmonic: 10912 Sorted by residual: dihedral pdb=" CA LYS D 573 " pdb=" C LYS D 573 " pdb=" N LYS D 574 " pdb=" CA LYS D 574 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LYS A 573 " pdb=" C LYS A 573 " pdb=" N LYS A 574 " pdb=" CA LYS A 574 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LYS C 573 " pdb=" C LYS C 573 " pdb=" N LYS C 574 " pdb=" CA LYS C 574 " ideal model delta harmonic sigma weight residual 180.00 156.13 23.87 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3237 0.065 - 0.130: 1186 0.130 - 0.195: 237 0.195 - 0.260: 31 0.260 - 0.325: 17 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CA SER A 917 " pdb=" N SER A 917 " pdb=" C SER A 917 " pdb=" CB SER A 917 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA SER C 917 " pdb=" N SER C 917 " pdb=" C SER C 917 " pdb=" CB SER C 917 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA SER D 917 " pdb=" N SER D 917 " pdb=" C SER D 917 " pdb=" CB SER D 917 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 4705 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 752 " 0.002 2.00e-02 2.50e+03 2.36e-02 9.75e+00 pdb=" CG PHE B 752 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 752 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 752 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE B 752 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 752 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE B 752 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 752 " -0.002 2.00e-02 2.50e+03 2.34e-02 9.56e+00 pdb=" CG PHE A 752 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 752 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 752 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE A 752 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 752 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 752 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 752 " 0.002 2.00e-02 2.50e+03 2.33e-02 9.52e+00 pdb=" CG PHE C 752 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE C 752 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE C 752 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE C 752 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 752 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE C 752 " -0.006 2.00e-02 2.50e+03 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4616 2.75 - 3.29: 29038 3.29 - 3.82: 49502 3.82 - 4.36: 58912 4.36 - 4.90: 99149 Nonbonded interactions: 241217 Sorted by model distance: nonbonded pdb=" OD1 ASP A 920 " pdb=" NH2 ARG B 901 " model vdw 2.212 3.120 nonbonded pdb=" OD1 ASP C 920 " pdb=" NH2 ARG D 901 " model vdw 2.213 3.120 nonbonded pdb=" NH2 ARG A 901 " pdb=" OD1 ASP D 920 " model vdw 2.224 3.120 nonbonded pdb=" OD1 ASP B 920 " pdb=" NH2 ARG C 901 " model vdw 2.251 3.120 nonbonded pdb=" OG SER D 205 " pdb=" OE1 GLU D 206 " model vdw 2.259 3.040 ... (remaining 241212 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.880 Find NCS groups from input model: 0.290 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:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 : 0.013 0.354 31192 Z= 0.567 Angle : 1.210 25.269 42260 Z= 0.670 Chirality : 0.068 0.325 4708 Planarity : 0.007 0.066 5280 Dihedral : 10.862 74.005 11212 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.15 % Favored : 93.52 % Rotamer: Outliers : 0.24 % Allowed : 3.25 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.69 (0.11), residues: 3656 helix: -1.98 (0.08), residues: 2400 sheet: -2.21 (0.32), residues: 192 loop : -3.18 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 829 TYR 0.051 0.004 TYR A 772 PHE 0.043 0.004 PHE C 832 TRP 0.031 0.004 TRP A 651 HIS 0.016 0.004 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.01264 / 0.53 (31188) covalent geometry : angle 1.17886 / 0.66 (42252) SS BOND : bond 0.35249 / 16.19 ( 4) SS BOND : angle 19.71736 / 11.17 ( 8) hydrogen bonds : bond 0.17052 / 10.99 ( 1784) hydrogen bonds : angle 6.96062 / 4.94 ( 5292) *********************** 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 667 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 659 time to evaluate : 0.913 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: 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 189 MET cc_start: 0.8251 (mpp) cc_final: 0.7924 (mtt) REVERT: A 198 ASP cc_start: 0.8432 (m-30) cc_final: 0.7986 (m-30) REVERT: B 189 MET cc_start: 0.8248 (mpp) cc_final: 0.7927 (mtt) REVERT: C 189 MET cc_start: 0.8259 (mpp) cc_final: 0.7931 (mtt) REVERT: D 189 MET cc_start: 0.8253 (mpp) cc_final: 0.7920 (mtt) REVERT: D 198 ASP cc_start: 0.8428 (m-30) cc_final: 0.7979 (m-30) outliers start: 8 outliers final: 4 residues processed: 667 average time/residue: 0.6777 time to fit residues: 522.2681 Evaluate side-chains 388 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 384 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 144 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 HIS A 257 HIS A 259 HIS A 270 HIS A 294 ASN A 438 GLN A 667 HIS A 671 GLN A 675 GLN B 136 HIS B 257 HIS B 259 HIS B 270 HIS B 294 ASN B 438 GLN B 667 HIS B 671 GLN B 675 GLN C 136 HIS C 257 HIS C 259 HIS C 270 HIS C 294 ASN C 438 GLN C 667 HIS C 671 GLN C 675 GLN D 136 HIS D 257 HIS D 259 HIS D 270 HIS D 294 ASN D 438 GLN D 667 HIS D 671 GLN D 675 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.123572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.085813 restraints weight = 69665.172| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.80 r_work: 0.3186 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 31192 Z= 0.196 Angle : 0.713 8.095 42260 Z= 0.379 Chirality : 0.043 0.150 4708 Planarity : 0.006 0.083 5280 Dihedral : 6.225 55.721 4032 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.70 % Allowed : 11.42 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.13), residues: 3656 helix: -0.11 (0.10), residues: 2436 sheet: -2.18 (0.33), residues: 204 loop : -2.79 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1079 TYR 0.017 0.002 TYR B 787 PHE 0.019 0.002 PHE C 779 TRP 0.028 0.002 TRP A 453 HIS 0.006 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (31188) covalent geometry : angle 0.71237 / 0.38 (42252) SS BOND : bond 0.00606 / 0.28 ( 4) SS BOND : angle 2.91965 / 1.66 ( 8) hydrogen bonds : bond 0.05845 / 3.92 ( 1784) hydrogen bonds : angle 4.72306 / 3.33 ( 5292) *********************** 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 521 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 431 time to evaluate : 1.139 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: 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 189 MET cc_start: 0.7856 (mpp) cc_final: 0.7526 (mtm) REVERT: A 282 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.8002 (pp20) REVERT: A 353 MET cc_start: 0.7777 (mpp) cc_final: 0.7502 (pmm) REVERT: A 401 ASP cc_start: 0.9078 (t0) cc_final: 0.8853 (t0) REVERT: A 462 MET cc_start: 0.8902 (tmm) cc_final: 0.8662 (tmm) REVERT: A 518 ASP cc_start: 0.8471 (t0) cc_final: 0.8074 (t0) REVERT: A 800 VAL cc_start: 0.9396 (t) cc_final: 0.9073 (m) REVERT: A 942 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8649 (pt0) REVERT: A 1018 PHE cc_start: 0.8000 (m-10) cc_final: 0.7684 (m-10) REVERT: B 189 MET cc_start: 0.7876 (mpp) cc_final: 0.7563 (mtm) REVERT: B 353 MET cc_start: 0.7761 (mpp) cc_final: 0.7526 (pmm) REVERT: B 401 ASP cc_start: 0.9079 (t0) cc_final: 0.8856 (t0) REVERT: B 457 ASP cc_start: 0.7795 (t0) cc_final: 0.7541 (t0) REVERT: B 462 MET cc_start: 0.8899 (tmm) cc_final: 0.8694 (tmm) REVERT: B 518 ASP cc_start: 0.8455 (t0) cc_final: 0.8050 (t0) REVERT: B 689 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8224 (p0) REVERT: B 800 VAL cc_start: 0.9393 (t) cc_final: 0.9067 (m) REVERT: B 942 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8691 (pt0) REVERT: B 1078 MET cc_start: 0.7139 (mmt) cc_final: 0.6933 (mmt) REVERT: C 189 MET cc_start: 0.7853 (mpp) cc_final: 0.7535 (mtm) REVERT: C 282 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: C 353 MET cc_start: 0.7760 (mpp) cc_final: 0.7497 (pmm) REVERT: C 360 ARG cc_start: 0.8616 (ptm160) cc_final: 0.8373 (ptm160) REVERT: C 401 ASP cc_start: 0.9091 (t0) cc_final: 0.8860 (t0) REVERT: C 462 MET cc_start: 0.8899 (tmm) cc_final: 0.8658 (tmm) REVERT: C 518 ASP cc_start: 0.8435 (t0) cc_final: 0.8025 (t0) REVERT: C 689 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8200 (p0) REVERT: C 800 VAL cc_start: 0.9399 (t) cc_final: 0.9076 (m) REVERT: C 942 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8725 (pt0) REVERT: D 189 MET cc_start: 0.7859 (mpp) cc_final: 0.7535 (mtm) REVERT: D 282 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7992 (pp20) REVERT: D 353 MET cc_start: 0.7783 (mpp) cc_final: 0.7502 (pmm) REVERT: D 368 ARG cc_start: 0.7868 (tpt90) cc_final: 0.7633 (pmm-80) REVERT: D 401 ASP cc_start: 0.9079 (t0) cc_final: 0.8858 (t0) REVERT: D 457 ASP cc_start: 0.7781 (t0) cc_final: 0.7405 (t0) REVERT: D 462 MET cc_start: 0.8900 (tmm) cc_final: 0.8659 (tmm) REVERT: D 518 ASP cc_start: 0.8461 (t0) cc_final: 0.8084 (t0) REVERT: D 689 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8157 (p0) REVERT: D 800 VAL cc_start: 0.9401 (t) cc_final: 0.9082 (m) REVERT: D 942 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8697 (pt0) REVERT: D 1078 MET cc_start: 0.7060 (mmt) cc_final: 0.6856 (mmt) outliers start: 90 outliers final: 25 residues processed: 494 average time/residue: 0.6094 time to fit residues: 352.7744 Evaluate side-chains 376 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 341 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 64 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 278 optimal weight: 30.0000 chunk 223 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 609 ASN A 741 ASN A 761 HIS A 997 GLN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN B 609 ASN B 761 HIS ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN C 609 ASN C 761 HIS D 572 ASN D 609 ASN D 761 HIS D 997 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.121136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.082717 restraints weight = 69698.770| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.85 r_work: 0.3127 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 31192 Z= 0.304 Angle : 0.745 9.020 42260 Z= 0.392 Chirality : 0.046 0.148 4708 Planarity : 0.005 0.057 5280 Dihedral : 5.998 51.913 4024 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.16 % Allowed : 13.79 % Favored : 83.05 % 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: -0.80 (0.13), residues: 3656 helix: 0.46 (0.10), residues: 2460 sheet: -1.99 (0.36), residues: 188 loop : -2.64 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1083 TYR 0.017 0.002 TYR A 772 PHE 0.024 0.002 PHE D1021 TRP 0.026 0.002 TRP D 453 HIS 0.008 0.002 HIS D 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.30 (31188) covalent geometry : angle 0.74238 / 0.39 (42252) SS BOND : bond 0.01124 / 0.52 ( 4) SS BOND : angle 4.73396 / 2.69 ( 8) hydrogen bonds : bond 0.06133 / 4.09 ( 1784) hydrogen bonds : angle 4.69568 / 3.31 ( 5292) *********************** 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 463 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 358 time to evaluate : 1.201 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: symmetry clash revert: symmetry clash REVERT: A 141 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8561 (p) REVERT: A 189 MET cc_start: 0.7823 (mpp) cc_final: 0.7479 (mtm) REVERT: A 462 MET cc_start: 0.8924 (tmm) cc_final: 0.8723 (tmm) REVERT: A 518 ASP cc_start: 0.8484 (t0) cc_final: 0.8207 (t0) REVERT: A 942 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8783 (pt0) REVERT: A 985 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8475 (mp) REVERT: A 1023 MET cc_start: 0.7589 (mmp) cc_final: 0.6407 (ttm) REVERT: A 1059 MET cc_start: 0.7969 (mpp) cc_final: 0.7292 (pmm) REVERT: B 141 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8549 (p) REVERT: B 189 MET cc_start: 0.7814 (mpp) cc_final: 0.7504 (mtm) REVERT: B 462 MET cc_start: 0.8882 (tmm) cc_final: 0.8646 (tmm) REVERT: B 518 ASP cc_start: 0.8468 (t0) cc_final: 0.8206 (t0) REVERT: B 689 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8235 (p0) REVERT: B 942 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8774 (pt0) REVERT: B 985 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8479 (mp) REVERT: B 1023 MET cc_start: 0.7574 (mmp) cc_final: 0.6385 (ttm) REVERT: B 1059 MET cc_start: 0.7966 (mpp) cc_final: 0.7280 (pmm) REVERT: C 141 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8570 (p) REVERT: C 189 MET cc_start: 0.7834 (mpp) cc_final: 0.7535 (mtm) REVERT: C 282 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7974 (pp20) REVERT: C 462 MET cc_start: 0.8918 (tmm) cc_final: 0.8717 (tmm) REVERT: C 518 ASP cc_start: 0.8470 (t0) cc_final: 0.8206 (t0) REVERT: C 689 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8232 (p0) REVERT: C 942 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8784 (pt0) REVERT: C 985 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8507 (mp) REVERT: C 1023 MET cc_start: 0.7572 (mmp) cc_final: 0.6400 (ttm) REVERT: C 1059 MET cc_start: 0.7980 (mpp) cc_final: 0.7284 (pmm) REVERT: C 1066 LYS cc_start: 0.9295 (mtpp) cc_final: 0.9042 (mtmm) REVERT: D 141 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8568 (p) REVERT: D 189 MET cc_start: 0.7882 (mpp) cc_final: 0.7530 (mtm) REVERT: D 282 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7985 (pp20) REVERT: D 360 ARG cc_start: 0.8425 (ppp-140) cc_final: 0.8199 (ppp80) REVERT: D 368 ARG cc_start: 0.7909 (tpt90) cc_final: 0.7685 (pmm-80) REVERT: D 457 ASP cc_start: 0.7993 (t0) cc_final: 0.7640 (t0) REVERT: D 495 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8766 (tm-30) REVERT: D 518 ASP cc_start: 0.8460 (t0) cc_final: 0.8178 (t0) REVERT: D 637 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7788 (mp0) REVERT: D 689 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8226 (p0) REVERT: D 942 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8801 (pt0) REVERT: D 985 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8487 (mp) REVERT: D 1023 MET cc_start: 0.7588 (mmp) cc_final: 0.6403 (ttm) REVERT: D 1059 MET cc_start: 0.7978 (mpp) cc_final: 0.7275 (pmm) outliers start: 105 outliers final: 43 residues processed: 440 average time/residue: 0.5851 time to fit residues: 307.8070 Evaluate side-chains 385 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 325 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1095 LEU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 864 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 989 ASN Chi-restraints excluded: chain D residue 1095 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 13 optimal weight: 20.0000 chunk 371 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 333 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 297 optimal weight: 20.0000 chunk 223 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 ASN B 449 ASN C 449 ASN D 449 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.122436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.084345 restraints weight = 68699.645| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.81 r_work: 0.3161 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31192 Z= 0.194 Angle : 0.658 8.693 42260 Z= 0.343 Chirality : 0.043 0.137 4708 Planarity : 0.004 0.036 5280 Dihedral : 5.769 53.774 4024 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.16 % Allowed : 14.90 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3656 helix: 0.91 (0.10), residues: 2448 sheet: -2.02 (0.38), residues: 176 loop : -2.41 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1083 TYR 0.015 0.002 TYR A 727 PHE 0.024 0.002 PHE A 779 TRP 0.024 0.002 TRP D 898 HIS 0.005 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (31188) covalent geometry : angle 0.65474 / 0.34 (42252) SS BOND : bond 0.00572 / 0.26 ( 4) SS BOND : angle 4.80048 / 2.73 ( 8) hydrogen bonds : bond 0.05185 / 3.47 ( 1784) hydrogen bonds : angle 4.42193 / 3.11 ( 5292) *********************** 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 472 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 367 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8494 (p) REVERT: A 189 MET cc_start: 0.7756 (mpp) cc_final: 0.7473 (mtm) REVERT: A 353 MET cc_start: 0.7747 (mpp) cc_final: 0.7383 (pmm) REVERT: A 360 ARG cc_start: 0.8744 (ptm160) cc_final: 0.8443 (ppp80) REVERT: A 457 ASP cc_start: 0.7917 (t0) cc_final: 0.7625 (t0) REVERT: A 462 MET cc_start: 0.8944 (tmm) cc_final: 0.8705 (tmm) REVERT: A 518 ASP cc_start: 0.8430 (t0) cc_final: 0.8208 (t70) REVERT: A 942 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8744 (pt0) REVERT: A 985 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8531 (mp) REVERT: A 1023 MET cc_start: 0.7553 (mmp) cc_final: 0.6406 (ttm) REVERT: B 141 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8478 (p) REVERT: B 189 MET cc_start: 0.7746 (mpp) cc_final: 0.7431 (mtm) REVERT: B 191 TYR cc_start: 0.8267 (t80) cc_final: 0.7969 (t80) REVERT: B 194 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8800 (mt-10) REVERT: B 353 MET cc_start: 0.7759 (mpp) cc_final: 0.7415 (pmm) REVERT: B 360 ARG cc_start: 0.8744 (ptm160) cc_final: 0.8450 (ppp80) REVERT: B 457 ASP cc_start: 0.7931 (t0) cc_final: 0.7645 (t0) REVERT: B 462 MET cc_start: 0.8924 (tmm) cc_final: 0.8655 (tmm) REVERT: B 518 ASP cc_start: 0.8413 (t0) cc_final: 0.8207 (t70) REVERT: B 689 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8163 (p0) REVERT: B 942 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8734 (pt0) REVERT: B 985 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8527 (mp) REVERT: C 141 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8512 (p) REVERT: C 189 MET cc_start: 0.7773 (mpp) cc_final: 0.7476 (mtm) REVERT: C 191 TYR cc_start: 0.8240 (t80) cc_final: 0.7969 (t80) REVERT: C 194 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8799 (mt-10) REVERT: C 353 MET cc_start: 0.7823 (mpp) cc_final: 0.7451 (pmm) REVERT: C 457 ASP cc_start: 0.7941 (t0) cc_final: 0.7648 (t0) REVERT: C 462 MET cc_start: 0.8928 (tmm) cc_final: 0.8688 (tmm) REVERT: C 518 ASP cc_start: 0.8407 (t0) cc_final: 0.8198 (t70) REVERT: C 689 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8151 (p0) REVERT: C 942 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8734 (pt0) REVERT: C 985 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8504 (mp) REVERT: C 1023 MET cc_start: 0.7451 (mmp) cc_final: 0.6276 (ttm) REVERT: D 141 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8528 (p) REVERT: D 189 MET cc_start: 0.7832 (mpp) cc_final: 0.7546 (mtm) REVERT: D 191 TYR cc_start: 0.8264 (t80) cc_final: 0.7987 (t80) REVERT: D 194 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8795 (mt-10) REVERT: D 353 MET cc_start: 0.7642 (mpp) cc_final: 0.7295 (pmm) REVERT: D 360 ARG cc_start: 0.8651 (ppp-140) cc_final: 0.8445 (ppp80) REVERT: D 457 ASP cc_start: 0.7901 (t0) cc_final: 0.7610 (t0) REVERT: D 462 MET cc_start: 0.8965 (tmm) cc_final: 0.8746 (tmm) REVERT: D 495 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8766 (mm-30) REVERT: D 518 ASP cc_start: 0.8435 (t0) cc_final: 0.8226 (t70) REVERT: D 689 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8159 (p0) REVERT: D 942 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8738 (pt0) REVERT: D 985 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8527 (mp) REVERT: D 1023 MET cc_start: 0.7491 (mmp) cc_final: 0.6315 (ttm) outliers start: 105 outliers final: 43 residues processed: 444 average time/residue: 0.5464 time to fit residues: 290.1588 Evaluate side-chains 368 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 310 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1015 PHE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 262 LEU 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 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 262 LEU 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 516 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 134 optimal weight: 3.9990 chunk 349 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 348 optimal weight: 4.9990 chunk 340 optimal weight: 1.9990 chunk 252 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 336 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 973 ASN B 973 ASN C 973 ASN D 973 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.123701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.085791 restraints weight = 68506.157| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.80 r_work: 0.3186 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31192 Z= 0.148 Angle : 0.620 10.954 42260 Z= 0.322 Chirality : 0.041 0.161 4708 Planarity : 0.004 0.043 5280 Dihedral : 5.585 50.059 4024 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.70 % Allowed : 16.14 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3656 helix: 1.19 (0.10), residues: 2456 sheet: -1.93 (0.36), residues: 188 loop : -2.18 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 197 TYR 0.019 0.002 TYR A 191 PHE 0.031 0.001 PHE A1021 TRP 0.024 0.002 TRP D 453 HIS 0.005 0.001 HIS D 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (31188) covalent geometry : angle 0.61817 / 0.32 (42252) SS BOND : bond 0.00664 / 0.31 ( 4) SS BOND : angle 3.11115 / 1.77 ( 8) hydrogen bonds : bond 0.04591 / 3.08 ( 1784) hydrogen bonds : angle 4.24112 / 2.98 ( 5292) *********************** 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 468 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 378 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8539 (p) REVERT: A 189 MET cc_start: 0.7712 (mpp) cc_final: 0.7463 (mtm) REVERT: A 191 TYR cc_start: 0.8282 (t80) cc_final: 0.8021 (t80) REVERT: A 194 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8864 (mt-10) REVERT: A 353 MET cc_start: 0.7671 (mpp) cc_final: 0.7342 (pmm) REVERT: A 360 ARG cc_start: 0.8868 (ptm160) cc_final: 0.8648 (ppp80) REVERT: A 462 MET cc_start: 0.8935 (tmm) cc_final: 0.8705 (tmm) REVERT: A 731 PHE cc_start: 0.8130 (m-10) cc_final: 0.7542 (t80) REVERT: A 942 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8707 (pt0) REVERT: A 1023 MET cc_start: 0.7474 (mmp) cc_final: 0.6380 (ttp) REVERT: A 1059 MET cc_start: 0.7977 (mpp) cc_final: 0.7204 (pmm) REVERT: A 1066 LYS cc_start: 0.9197 (mtpp) cc_final: 0.8979 (mtmm) REVERT: B 141 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8529 (p) REVERT: B 189 MET cc_start: 0.7724 (mpp) cc_final: 0.7446 (mtm) REVERT: B 353 MET cc_start: 0.7665 (mpp) cc_final: 0.7338 (pmm) REVERT: B 360 ARG cc_start: 0.8861 (ptm160) cc_final: 0.8644 (ppp80) REVERT: B 462 MET cc_start: 0.8938 (tmm) cc_final: 0.8646 (tmm) REVERT: B 689 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8126 (p0) REVERT: B 731 PHE cc_start: 0.8108 (m-10) cc_final: 0.7540 (t80) REVERT: B 942 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8704 (pt0) REVERT: B 1023 MET cc_start: 0.7384 (mmp) cc_final: 0.6253 (ttm) REVERT: B 1059 MET cc_start: 0.7985 (mpp) cc_final: 0.7203 (pmm) REVERT: B 1066 LYS cc_start: 0.9193 (mtpp) cc_final: 0.8972 (mtmm) REVERT: C 141 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8543 (p) REVERT: C 179 ILE cc_start: 0.8717 (pt) cc_final: 0.8440 (pp) REVERT: C 189 MET cc_start: 0.7753 (mpp) cc_final: 0.7482 (mtm) REVERT: C 191 TYR cc_start: 0.8187 (t80) cc_final: 0.7934 (t80) REVERT: C 194 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8798 (mt-10) REVERT: C 353 MET cc_start: 0.7800 (mpp) cc_final: 0.7481 (pmm) REVERT: C 462 MET cc_start: 0.8944 (tmm) cc_final: 0.8714 (tmm) REVERT: C 689 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8126 (p0) REVERT: C 731 PHE cc_start: 0.8098 (m-10) cc_final: 0.7509 (t80) REVERT: C 942 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8721 (pt0) REVERT: C 985 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8521 (mp) REVERT: C 1023 MET cc_start: 0.7505 (mmp) cc_final: 0.6412 (ttp) REVERT: C 1059 MET cc_start: 0.7979 (mpp) cc_final: 0.7183 (pmm) REVERT: D 141 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8538 (p) REVERT: D 179 ILE cc_start: 0.8710 (pt) cc_final: 0.8432 (pp) REVERT: D 189 MET cc_start: 0.7766 (mpp) cc_final: 0.7500 (mtm) REVERT: D 191 TYR cc_start: 0.8225 (t80) cc_final: 0.8000 (t80) REVERT: D 194 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8829 (mt-10) REVERT: D 353 MET cc_start: 0.7679 (mpp) cc_final: 0.7395 (pmm) REVERT: D 360 ARG cc_start: 0.8665 (ppp-140) cc_final: 0.8448 (ppp80) REVERT: D 457 ASP cc_start: 0.7884 (t0) cc_final: 0.7592 (t0) REVERT: D 495 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8782 (mm-30) REVERT: D 689 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8128 (p0) REVERT: D 731 PHE cc_start: 0.8211 (m-10) cc_final: 0.7572 (t80) REVERT: D 788 MET cc_start: 0.8174 (tmm) cc_final: 0.7860 (tmm) REVERT: D 942 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8721 (pt0) REVERT: D 1023 MET cc_start: 0.7496 (mmp) cc_final: 0.6403 (ttp) REVERT: D 1059 MET cc_start: 0.7977 (mpp) cc_final: 0.7138 (pmm) outliers start: 90 outliers final: 36 residues processed: 449 average time/residue: 0.5177 time to fit residues: 281.2465 Evaluate side-chains 377 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 329 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1015 PHE Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 1015 PHE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1015 PHE Chi-restraints excluded: chain D residue 141 THR 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 505 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 942 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 323 optimal weight: 1.9990 chunk 344 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 303 optimal weight: 9.9990 chunk 360 optimal weight: 0.9980 chunk 187 optimal weight: 20.0000 chunk 214 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 973 ASN D 973 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.121829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.083807 restraints weight = 68810.146| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.79 r_work: 0.3149 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31192 Z= 0.223 Angle : 0.666 9.684 42260 Z= 0.350 Chirality : 0.044 0.160 4708 Planarity : 0.004 0.034 5280 Dihedral : 5.521 47.770 4024 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.46 % Allowed : 16.53 % Favored : 80.02 % 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: 0.21 (0.14), residues: 3656 helix: 1.22 (0.10), residues: 2456 sheet: -1.90 (0.36), residues: 188 loop : -2.16 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 452 TYR 0.016 0.002 TYR B 191 PHE 0.031 0.002 PHE B1021 TRP 0.021 0.002 TRP B 786 HIS 0.005 0.001 HIS D 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 (31188) covalent geometry : angle 0.66420 / 0.35 (42252) SS BOND : bond 0.00721 / 0.33 ( 4) SS BOND : angle 3.24799 / 1.85 ( 8) hydrogen bonds : bond 0.05126 / 3.44 ( 1784) hydrogen bonds : angle 4.32931 / 3.05 ( 5292) *********************** 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 448 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 333 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8591 (p) REVERT: A 162 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.8243 (mtm-85) REVERT: A 189 MET cc_start: 0.7820 (mpp) cc_final: 0.7528 (mtm) REVERT: A 194 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8784 (mt-10) REVERT: A 353 MET cc_start: 0.7711 (mpp) cc_final: 0.7405 (pmm) REVERT: A 462 MET cc_start: 0.8917 (tmm) cc_final: 0.8624 (tmm) REVERT: A 731 PHE cc_start: 0.8089 (m-10) cc_final: 0.7520 (t80) REVERT: A 942 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8728 (pt0) REVERT: A 985 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8488 (mp) REVERT: A 1023 MET cc_start: 0.7426 (mmp) cc_final: 0.6362 (ttp) REVERT: A 1059 MET cc_start: 0.7786 (mpp) cc_final: 0.7054 (pmm) REVERT: A 1066 LYS cc_start: 0.9217 (mtpp) cc_final: 0.8999 (mtmm) REVERT: B 141 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8600 (p) REVERT: B 162 ARG cc_start: 0.8436 (ttp-110) cc_final: 0.8233 (mtm-85) REVERT: B 189 MET cc_start: 0.7809 (mpp) cc_final: 0.7508 (mtm) REVERT: B 191 TYR cc_start: 0.8350 (t80) cc_final: 0.8138 (t80) REVERT: B 194 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8711 (mt-10) REVERT: B 353 MET cc_start: 0.7693 (mpp) cc_final: 0.7393 (pmm) REVERT: B 462 MET cc_start: 0.8893 (tmm) cc_final: 0.8525 (tmm) REVERT: B 689 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8115 (p0) REVERT: B 731 PHE cc_start: 0.7992 (m-10) cc_final: 0.7549 (t80) REVERT: B 942 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8738 (pt0) REVERT: B 985 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8487 (mp) REVERT: B 1023 MET cc_start: 0.7425 (mmp) cc_final: 0.6336 (ttp) REVERT: B 1059 MET cc_start: 0.7777 (mpp) cc_final: 0.7096 (pmm) REVERT: B 1066 LYS cc_start: 0.9214 (mtpp) cc_final: 0.8997 (mtmm) REVERT: C 141 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8596 (p) REVERT: C 189 MET cc_start: 0.7827 (mpp) cc_final: 0.7502 (mtm) REVERT: C 191 TYR cc_start: 0.8324 (t80) cc_final: 0.8120 (t80) REVERT: C 194 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8730 (mt-10) REVERT: C 353 MET cc_start: 0.7818 (mpp) cc_final: 0.7500 (pmm) REVERT: C 462 MET cc_start: 0.8930 (tmm) cc_final: 0.8641 (tmm) REVERT: C 689 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8120 (p0) REVERT: C 731 PHE cc_start: 0.8159 (m-10) cc_final: 0.7560 (t80) REVERT: C 942 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8760 (pt0) REVERT: C 985 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8475 (mp) REVERT: C 1023 MET cc_start: 0.7422 (mmp) cc_final: 0.6348 (ttp) REVERT: C 1059 MET cc_start: 0.7771 (mpp) cc_final: 0.7091 (pmm) REVERT: D 141 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8578 (p) REVERT: D 189 MET cc_start: 0.7804 (mpp) cc_final: 0.7524 (mtm) REVERT: D 191 TYR cc_start: 0.8322 (t80) cc_final: 0.8108 (t80) REVERT: D 194 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8736 (mt-10) REVERT: D 353 MET cc_start: 0.7707 (mpp) cc_final: 0.7384 (pmm) REVERT: D 360 ARG cc_start: 0.8662 (ppp-140) cc_final: 0.8452 (ppp80) REVERT: D 457 ASP cc_start: 0.7949 (t0) cc_final: 0.7625 (t0) REVERT: D 495 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8748 (mm-30) REVERT: D 689 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8140 (p0) REVERT: D 731 PHE cc_start: 0.8174 (m-10) cc_final: 0.7563 (t80) REVERT: D 788 MET cc_start: 0.8222 (tmm) cc_final: 0.7847 (tmm) REVERT: D 942 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8753 (pt0) REVERT: D 985 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8494 (mp) REVERT: D 1023 MET cc_start: 0.7419 (mmp) cc_final: 0.6339 (ttp) REVERT: D 1059 MET cc_start: 0.7775 (mpp) cc_final: 0.7032 (pmm) outliers start: 115 outliers final: 57 residues processed: 424 average time/residue: 0.5218 time to fit residues: 266.9411 Evaluate side-chains 392 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 320 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1015 PHE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 157 LEU 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 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1015 PHE Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1015 PHE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 ILE 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 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 929 CYS 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 1095 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 98 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 116 optimal weight: 30.0000 chunk 351 optimal weight: 0.8980 chunk 246 optimal weight: 0.9980 chunk 341 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 242 optimal weight: 5.9990 chunk 295 optimal weight: 7.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 973 ASN D 973 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.123655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.085820 restraints weight = 68335.232| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.82 r_work: 0.3189 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31192 Z= 0.143 Angle : 0.619 10.907 42260 Z= 0.326 Chirality : 0.042 0.150 4708 Planarity : 0.004 0.032 5280 Dihedral : 5.413 48.766 4024 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.28 % Allowed : 18.03 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3656 helix: 1.48 (0.10), residues: 2460 sheet: -1.84 (0.36), residues: 188 loop : -1.97 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 368 TYR 0.015 0.002 TYR B 191 PHE 0.036 0.001 PHE D1021 TRP 0.024 0.002 TRP A 453 HIS 0.004 0.001 HIS D 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (31188) covalent geometry : angle 0.61809 / 0.33 (42252) SS BOND : bond 0.00558 / 0.26 ( 4) SS BOND : angle 2.39935 / 1.36 ( 8) hydrogen bonds : bond 0.04433 / 2.99 ( 1784) hydrogen bonds : angle 4.13759 / 2.91 ( 5292) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 344 time to evaluate : 0.979 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 141 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8503 (p) REVERT: A 162 ARG cc_start: 0.8469 (ttp-110) cc_final: 0.8214 (mtm-85) REVERT: A 179 ILE cc_start: 0.8703 (pt) cc_final: 0.8456 (pp) REVERT: A 189 MET cc_start: 0.7713 (mpp) cc_final: 0.7392 (mtm) REVERT: A 194 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8807 (mt-10) REVERT: A 353 MET cc_start: 0.7715 (mpp) cc_final: 0.7444 (pmm) REVERT: A 731 PHE cc_start: 0.8118 (m-10) cc_final: 0.7552 (t80) REVERT: A 942 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8676 (pt0) REVERT: A 985 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8490 (mp) REVERT: A 1023 MET cc_start: 0.7553 (mmp) cc_final: 0.6481 (ttp) REVERT: A 1066 LYS cc_start: 0.9196 (mtpp) cc_final: 0.8974 (mtmm) REVERT: B 141 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8519 (p) REVERT: B 162 ARG cc_start: 0.8425 (ttp-110) cc_final: 0.8184 (mtm-85) REVERT: B 179 ILE cc_start: 0.8699 (pt) cc_final: 0.8449 (pp) REVERT: B 189 MET cc_start: 0.7697 (mpp) cc_final: 0.7369 (mtm) REVERT: B 194 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8839 (mt-10) REVERT: B 353 MET cc_start: 0.7700 (mpp) cc_final: 0.7439 (pmm) REVERT: B 462 MET cc_start: 0.8878 (tmm) cc_final: 0.8530 (tmm) REVERT: B 689 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8061 (p0) REVERT: B 731 PHE cc_start: 0.8113 (m-10) cc_final: 0.7540 (t80) REVERT: B 942 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8714 (pt0) REVERT: B 985 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8488 (mp) REVERT: B 1023 MET cc_start: 0.7390 (mmp) cc_final: 0.6341 (ttp) REVERT: B 1066 LYS cc_start: 0.9189 (mtpp) cc_final: 0.8967 (mtmm) REVERT: C 141 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8503 (p) REVERT: C 179 ILE cc_start: 0.8708 (pt) cc_final: 0.8373 (pp) REVERT: C 189 MET cc_start: 0.7725 (mpp) cc_final: 0.7405 (mtm) REVERT: C 194 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8733 (mt-10) REVERT: C 255 ASN cc_start: 0.8771 (m110) cc_final: 0.8560 (p0) REVERT: C 353 MET cc_start: 0.7804 (mpp) cc_final: 0.7486 (pmm) REVERT: C 462 MET cc_start: 0.8924 (tmm) cc_final: 0.8721 (tmm) REVERT: C 689 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8052 (p0) REVERT: C 731 PHE cc_start: 0.8113 (m-10) cc_final: 0.7534 (t80) REVERT: C 942 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8716 (pt0) REVERT: C 985 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8503 (mp) REVERT: C 1023 MET cc_start: 0.7545 (mmp) cc_final: 0.6464 (ttp) REVERT: D 141 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8523 (p) REVERT: D 179 ILE cc_start: 0.8709 (pt) cc_final: 0.8443 (pp) REVERT: D 189 MET cc_start: 0.7732 (mpp) cc_final: 0.7526 (mtm) REVERT: D 194 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8751 (mt-10) REVERT: D 353 MET cc_start: 0.7684 (mpp) cc_final: 0.7331 (pmm) REVERT: D 457 ASP cc_start: 0.7840 (t0) cc_final: 0.7529 (t0) REVERT: D 495 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8758 (tm-30) REVERT: D 689 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8098 (p0) REVERT: D 731 PHE cc_start: 0.8104 (m-10) cc_final: 0.7531 (t80) REVERT: D 788 MET cc_start: 0.8241 (tmm) cc_final: 0.7822 (tmm) REVERT: D 942 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8703 (pt0) REVERT: D 985 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8494 (mp) REVERT: D 1023 MET cc_start: 0.7570 (mmp) cc_final: 0.6496 (ttp) outliers start: 76 outliers final: 36 residues processed: 403 average time/residue: 0.5497 time to fit residues: 264.8358 Evaluate side-chains 374 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 323 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1015 PHE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 ILE 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 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 339 optimal weight: 8.9990 chunk 241 optimal weight: 0.0980 chunk 197 optimal weight: 6.9990 chunk 326 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 78 optimal weight: 0.0980 chunk 28 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 295 optimal weight: 9.9990 chunk 201 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.124770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.087169 restraints weight = 68011.853| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.80 r_work: 0.3215 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31192 Z= 0.127 Angle : 0.625 12.184 42260 Z= 0.327 Chirality : 0.041 0.174 4708 Planarity : 0.004 0.070 5280 Dihedral : 5.265 46.233 4024 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.07 % Allowed : 18.24 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.14), residues: 3656 helix: 1.65 (0.10), residues: 2456 sheet: -1.68 (0.36), residues: 188 loop : -1.91 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 162 TYR 0.022 0.002 TYR C 191 PHE 0.039 0.001 PHE B1021 TRP 0.017 0.001 TRP B 898 HIS 0.004 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (31188) covalent geometry : angle 0.62334 / 0.33 (42252) SS BOND : bond 0.00548 / 0.25 ( 4) SS BOND : angle 3.81717 / 2.16 ( 8) hydrogen bonds : bond 0.04098 / 2.77 ( 1784) hydrogen bonds : angle 4.04193 / 2.85 ( 5292) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 359 time to evaluate : 1.104 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: A 162 ARG cc_start: 0.8517 (ttp-110) cc_final: 0.8306 (mtm-85) REVERT: A 179 ILE cc_start: 0.8714 (pt) cc_final: 0.8363 (pp) REVERT: A 189 MET cc_start: 0.7667 (mpp) cc_final: 0.7369 (mtm) REVERT: A 194 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8861 (mt-10) REVERT: A 353 MET cc_start: 0.7679 (mpp) cc_final: 0.7370 (pmm) REVERT: A 731 PHE cc_start: 0.8071 (m-10) cc_final: 0.7527 (t80) REVERT: A 942 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8634 (pt0) REVERT: A 985 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8492 (mp) REVERT: A 1023 MET cc_start: 0.7557 (mmp) cc_final: 0.6488 (ttp) REVERT: A 1059 MET cc_start: 0.7903 (mpp) cc_final: 0.7349 (pmm) REVERT: B 162 ARG cc_start: 0.8532 (ttp-110) cc_final: 0.8311 (mtm-85) REVERT: B 179 ILE cc_start: 0.8717 (pt) cc_final: 0.8364 (pp) REVERT: B 189 MET cc_start: 0.7648 (mpp) cc_final: 0.7322 (mtm) REVERT: B 194 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8830 (mt-10) REVERT: B 353 MET cc_start: 0.7670 (mpp) cc_final: 0.7362 (pmm) REVERT: B 457 ASP cc_start: 0.7856 (t0) cc_final: 0.7635 (t0) REVERT: B 462 MET cc_start: 0.8927 (tmm) cc_final: 0.8608 (tmm) REVERT: B 689 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8062 (p0) REVERT: B 731 PHE cc_start: 0.8090 (m-10) cc_final: 0.7536 (t80) REVERT: B 942 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8667 (pt0) REVERT: B 985 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8487 (mp) REVERT: B 992 GLN cc_start: 0.9055 (mt0) cc_final: 0.8824 (tt0) REVERT: B 1023 MET cc_start: 0.7412 (mmp) cc_final: 0.6391 (ttp) REVERT: B 1059 MET cc_start: 0.7911 (mpp) cc_final: 0.7346 (pmm) REVERT: C 141 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8559 (p) REVERT: C 179 ILE cc_start: 0.8712 (pt) cc_final: 0.8380 (pp) REVERT: C 189 MET cc_start: 0.7680 (mpp) cc_final: 0.7394 (mtm) REVERT: C 194 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8842 (mt-10) REVERT: C 353 MET cc_start: 0.7761 (mpp) cc_final: 0.7445 (pmm) REVERT: C 689 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8048 (p0) REVERT: C 731 PHE cc_start: 0.8089 (m-10) cc_final: 0.7507 (t80) REVERT: C 942 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8658 (pt0) REVERT: C 992 GLN cc_start: 0.9053 (mt0) cc_final: 0.8825 (tt0) REVERT: C 1023 MET cc_start: 0.7592 (mmp) cc_final: 0.6550 (ttp) REVERT: C 1059 MET cc_start: 0.7912 (mpp) cc_final: 0.7345 (pmm) REVERT: D 141 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8534 (p) REVERT: D 162 ARG cc_start: 0.8372 (ttm110) cc_final: 0.8172 (mtm-85) REVERT: D 179 ILE cc_start: 0.8707 (pt) cc_final: 0.8377 (pp) REVERT: D 194 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8819 (mt-10) REVERT: D 353 MET cc_start: 0.7672 (mpp) cc_final: 0.7318 (pmm) REVERT: D 457 ASP cc_start: 0.7759 (t0) cc_final: 0.7452 (t0) REVERT: D 495 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8711 (tm-30) REVERT: D 689 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8079 (p0) REVERT: D 731 PHE cc_start: 0.8096 (m-10) cc_final: 0.7544 (t80) REVERT: D 788 MET cc_start: 0.8209 (tmm) cc_final: 0.7988 (tmm) REVERT: D 863 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8505 (mmt) REVERT: D 942 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8659 (pt0) REVERT: D 985 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8501 (mp) REVERT: D 1023 MET cc_start: 0.7577 (mmp) cc_final: 0.6525 (ttp) REVERT: D 1059 MET cc_start: 0.7908 (mpp) cc_final: 0.7345 (pmm) outliers start: 69 outliers final: 40 residues processed: 416 average time/residue: 0.5471 time to fit residues: 272.7185 Evaluate side-chains 376 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 323 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1015 PHE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 255 ASN Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 310 ARG Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 24 optimal weight: 9.9990 chunk 174 optimal weight: 0.8980 chunk 279 optimal weight: 20.0000 chunk 356 optimal weight: 3.9990 chunk 216 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 256 ASN D 741 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.126249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.088764 restraints weight = 68217.250| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.77 r_work: 0.3244 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31192 Z= 0.120 Angle : 0.623 13.216 42260 Z= 0.323 Chirality : 0.041 0.180 4708 Planarity : 0.004 0.069 5280 Dihedral : 5.103 44.019 4024 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.01 % Allowed : 19.20 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.14), residues: 3656 helix: 1.69 (0.10), residues: 2472 sheet: -1.63 (0.36), residues: 188 loop : -2.13 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 197 TYR 0.019 0.001 TYR B 191 PHE 0.040 0.001 PHE A1021 TRP 0.032 0.001 TRP D 786 HIS 0.006 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (31188) covalent geometry : angle 0.62051 / 0.32 (42252) SS BOND : bond 0.00461 / 0.21 ( 4) SS BOND : angle 3.69011 / 2.09 ( 8) hydrogen bonds : bond 0.03703 / 2.50 ( 1784) hydrogen bonds : angle 3.94771 / 2.78 ( 5292) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 365 time to evaluate : 0.974 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 162 ARG cc_start: 0.8563 (ttp-110) cc_final: 0.8339 (mtm-85) REVERT: A 179 ILE cc_start: 0.8748 (pt) cc_final: 0.8540 (pp) REVERT: A 189 MET cc_start: 0.7640 (mpp) cc_final: 0.7327 (mtm) REVERT: A 194 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8891 (mt-10) REVERT: A 353 MET cc_start: 0.7640 (mpp) cc_final: 0.7309 (pmm) REVERT: A 731 PHE cc_start: 0.8062 (m-10) cc_final: 0.7531 (t80) REVERT: A 1023 MET cc_start: 0.7617 (mmp) cc_final: 0.6615 (ttp) REVERT: A 1059 MET cc_start: 0.7872 (mpp) cc_final: 0.7274 (pmm) REVERT: B 179 ILE cc_start: 0.8752 (pt) cc_final: 0.8520 (pp) REVERT: B 189 MET cc_start: 0.7632 (mpp) cc_final: 0.7303 (mtm) REVERT: B 194 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8868 (mt-10) REVERT: B 353 MET cc_start: 0.7633 (mpp) cc_final: 0.7315 (pmm) REVERT: B 462 MET cc_start: 0.8909 (tmm) cc_final: 0.8594 (tmm) REVERT: B 689 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8004 (p0) REVERT: B 731 PHE cc_start: 0.8075 (m-10) cc_final: 0.7543 (t80) REVERT: B 992 GLN cc_start: 0.9097 (mt0) cc_final: 0.8852 (tt0) REVERT: B 1023 MET cc_start: 0.7411 (mmp) cc_final: 0.6355 (ttp) REVERT: B 1059 MET cc_start: 0.7873 (mpp) cc_final: 0.7277 (pmm) REVERT: C 162 ARG cc_start: 0.8505 (mtm-85) cc_final: 0.8303 (mtm-85) REVERT: C 179 ILE cc_start: 0.8747 (pt) cc_final: 0.8491 (pp) REVERT: C 189 MET cc_start: 0.7658 (mpp) cc_final: 0.7344 (mtm) REVERT: C 191 TYR cc_start: 0.8410 (t80) cc_final: 0.8205 (t80) REVERT: C 194 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8863 (mt-10) REVERT: C 353 MET cc_start: 0.7790 (mpp) cc_final: 0.7463 (pmm) REVERT: C 462 MET cc_start: 0.8862 (tmm) cc_final: 0.8624 (tmm) REVERT: C 689 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8049 (p0) REVERT: C 731 PHE cc_start: 0.8123 (m-10) cc_final: 0.7567 (t80) REVERT: C 985 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8433 (mp) REVERT: C 992 GLN cc_start: 0.9092 (mt0) cc_final: 0.8849 (tt0) REVERT: C 1023 MET cc_start: 0.7614 (mmp) cc_final: 0.6569 (ttp) REVERT: C 1059 MET cc_start: 0.7865 (mpp) cc_final: 0.7289 (pmm) REVERT: C 1076 GLU cc_start: 0.9010 (pp20) cc_final: 0.8740 (pm20) REVERT: D 179 ILE cc_start: 0.8746 (pt) cc_final: 0.8544 (pp) REVERT: D 189 MET cc_start: 0.7375 (mtm) cc_final: 0.7064 (mtt) REVERT: D 194 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8871 (mt-10) REVERT: D 353 MET cc_start: 0.7776 (mpp) cc_final: 0.7400 (pmm) REVERT: D 457 ASP cc_start: 0.7876 (t0) cc_final: 0.7490 (t0) REVERT: D 495 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8694 (tm-30) REVERT: D 689 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8022 (p0) REVERT: D 731 PHE cc_start: 0.8099 (m-10) cc_final: 0.7552 (t80) REVERT: D 788 MET cc_start: 0.8145 (tmm) cc_final: 0.7688 (tmm) REVERT: D 863 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8485 (mmt) REVERT: D 992 GLN cc_start: 0.9103 (mt0) cc_final: 0.8886 (tt0) REVERT: D 1023 MET cc_start: 0.7610 (mmp) cc_final: 0.6594 (ttp) REVERT: D 1059 MET cc_start: 0.7868 (mpp) cc_final: 0.7259 (pmm) outliers start: 67 outliers final: 35 residues processed: 421 average time/residue: 0.5521 time to fit residues: 277.2937 Evaluate side-chains 375 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 335 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 310 ARG Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 929 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 147 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 204 optimal weight: 30.0000 chunk 183 optimal weight: 6.9990 chunk 304 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 338 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 265 optimal weight: 0.3980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 741 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.125183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.087229 restraints weight = 67635.914| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.76 r_work: 0.3215 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31192 Z= 0.148 Angle : 0.654 13.789 42260 Z= 0.341 Chirality : 0.041 0.172 4708 Planarity : 0.004 0.087 5280 Dihedral : 5.052 43.405 4024 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.53 % Allowed : 20.34 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.86 (0.14), residues: 3656 helix: 1.72 (0.10), residues: 2456 sheet: -1.54 (0.37), residues: 188 loop : -1.95 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 197 TYR 0.017 0.001 TYR A 191 PHE 0.041 0.001 PHE B1021 TRP 0.032 0.002 TRP B 786 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (31188) covalent geometry : angle 0.65146 / 0.34 (42252) SS BOND : bond 0.00587 / 0.27 ( 4) SS BOND : angle 4.02660 / 2.29 ( 8) hydrogen bonds : bond 0.04073 / 2.73 ( 1784) hydrogen bonds : angle 4.02213 / 2.84 ( 5292) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 348 time to evaluate : 1.176 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 162 ARG cc_start: 0.8575 (ttp-110) cc_final: 0.8359 (mtm-85) REVERT: A 189 MET cc_start: 0.7681 (mpp) cc_final: 0.7451 (mtm) REVERT: A 353 MET cc_start: 0.7655 (mpp) cc_final: 0.7327 (pmm) REVERT: A 731 PHE cc_start: 0.8117 (m-10) cc_final: 0.7558 (t80) REVERT: A 985 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8462 (mp) REVERT: A 1023 MET cc_start: 0.7641 (mmp) cc_final: 0.6583 (ttp) REVERT: A 1059 MET cc_start: 0.7848 (mpp) cc_final: 0.7151 (pmm) REVERT: B 179 ILE cc_start: 0.8765 (pt) cc_final: 0.8537 (pp) REVERT: B 189 MET cc_start: 0.7676 (mpp) cc_final: 0.7346 (mtm) REVERT: B 191 TYR cc_start: 0.8480 (t80) cc_final: 0.8250 (t80) REVERT: B 353 MET cc_start: 0.7628 (mpp) cc_final: 0.7310 (pmm) REVERT: B 462 MET cc_start: 0.8891 (tmm) cc_final: 0.8567 (tmm) REVERT: B 689 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8017 (p0) REVERT: B 731 PHE cc_start: 0.8122 (m-10) cc_final: 0.7545 (t80) REVERT: B 985 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8458 (mp) REVERT: B 1023 MET cc_start: 0.7434 (mmp) cc_final: 0.6352 (ttp) REVERT: B 1059 MET cc_start: 0.7842 (mpp) cc_final: 0.7143 (pmm) REVERT: C 179 ILE cc_start: 0.8769 (pt) cc_final: 0.8532 (pp) REVERT: C 189 MET cc_start: 0.7710 (mpp) cc_final: 0.7346 (mtm) REVERT: C 191 TYR cc_start: 0.8452 (t80) cc_final: 0.8249 (t80) REVERT: C 353 MET cc_start: 0.7786 (mpp) cc_final: 0.7456 (pmm) REVERT: C 689 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8037 (p0) REVERT: C 731 PHE cc_start: 0.8130 (m-10) cc_final: 0.7541 (t80) REVERT: C 985 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8444 (mp) REVERT: C 1023 MET cc_start: 0.7640 (mmp) cc_final: 0.6568 (ttp) REVERT: C 1059 MET cc_start: 0.7830 (mpp) cc_final: 0.7124 (pmm) REVERT: C 1076 GLU cc_start: 0.8955 (pp20) cc_final: 0.8610 (pm20) REVERT: D 189 MET cc_start: 0.7431 (mtm) cc_final: 0.7086 (mtt) REVERT: D 353 MET cc_start: 0.7738 (mpp) cc_final: 0.7342 (pmm) REVERT: D 495 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8695 (tm-30) REVERT: D 689 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8049 (p0) REVERT: D 731 PHE cc_start: 0.8095 (m-10) cc_final: 0.7507 (t80) REVERT: D 788 MET cc_start: 0.8144 (tmm) cc_final: 0.7665 (tmm) REVERT: D 863 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8470 (mmt) REVERT: D 985 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8452 (mp) REVERT: D 1023 MET cc_start: 0.7639 (mmp) cc_final: 0.6566 (ttp) REVERT: D 1059 MET cc_start: 0.7824 (mpp) cc_final: 0.7113 (pmm) outliers start: 51 outliers final: 32 residues processed: 392 average time/residue: 0.5675 time to fit residues: 265.5447 Evaluate side-chains 370 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 330 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 985 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 167 optimal weight: 0.5980 chunk 325 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 353 optimal weight: 0.9990 chunk 364 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.125339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.087427 restraints weight = 67962.216| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.80 r_work: 0.3220 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31192 Z= 0.140 Angle : 0.659 15.457 42260 Z= 0.342 Chirality : 0.041 0.169 4708 Planarity : 0.005 0.098 5280 Dihedral : 5.049 43.973 4024 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.44 % Allowed : 20.79 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.81 (0.14), residues: 3656 helix: 1.69 (0.10), residues: 2472 sheet: -1.54 (0.36), residues: 188 loop : -2.06 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 197 TYR 0.013 0.001 TYR D 186 PHE 0.042 0.001 PHE A1021 TRP 0.032 0.002 TRP C 786 HIS 0.004 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (31188) covalent geometry : angle 0.65645 / 0.34 (42252) SS BOND : bond 0.00558 / 0.26 ( 4) SS BOND : angle 3.89606 / 2.21 ( 8) hydrogen bonds : bond 0.04014 / 2.69 ( 1784) hydrogen bonds : angle 4.01507 / 2.83 ( 5292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11887.19 seconds wall clock time: 202 minutes 29.95 seconds (12149.95 seconds total)