Starting phenix.real_space_refine on Fri Mar 6 10:54:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wre_32724/03_2026/7wre_32724.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wre_32724/03_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_32724/03_2026/7wre_32724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wre_32724/03_2026/7wre_32724.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wre_32724/03_2026/7wre_32724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wre_32724/03_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.16, per 1000 atoms: 0.20 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: 2.48 Conformation dependent library (CDL) restraints added in 1.4 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: 0.84 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: 4.99 Time building geometry restraints manager: 3.42 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: 0.08 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: 1.050 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: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.640 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.090 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 covalent geometry : bond 0.01264 (31188) covalent geometry : angle 1.17886 (42252) SS BOND : bond 0.35249 ( 4) SS BOND : angle 19.71736 ( 8) hydrogen bonds : bond 0.17052 ( 1784) hydrogen bonds : angle 6.96062 ( 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 : 1.238 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: 0.7929 (mtt) REVERT: D 189 MET cc_start: 0.8253 (mpp) cc_final: 0.7918 (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: 0.7604 time to fit residues: 581.9774 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 : 1.238 ------------------------------------------------------------------------------- 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: 3.9990 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: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 257 HIS A 259 HIS A 270 HIS A 294 ASN A 438 GLN A 667 HIS A 671 GLN A 675 GLN B 136 HIS B 154 ASN B 257 HIS B 259 HIS B 270 HIS B 294 ASN B 438 GLN B 572 ASN 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 572 ASN 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 572 ASN D 667 HIS D 671 GLN D 675 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.123022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.085152 restraints weight = 69563.489| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.80 r_work: 0.3174 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 31192 Z= 0.220 Angle : 0.727 8.120 42260 Z= 0.386 Chirality : 0.044 0.148 4708 Planarity : 0.005 0.059 5280 Dihedral : 6.229 55.371 4032 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.70 % Allowed : 11.66 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.13), residues: 3656 helix: -0.12 (0.10), residues: 2436 sheet: -2.21 (0.33), residues: 204 loop : -2.81 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1079 TYR 0.016 0.002 TYR A 772 PHE 0.019 0.002 PHE B 874 TRP 0.026 0.002 TRP A 453 HIS 0.006 0.001 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00514 (31188) covalent geometry : angle 0.72589 (42252) SS BOND : bond 0.00506 ( 4) SS BOND : angle 3.04967 ( 8) hydrogen bonds : bond 0.05993 ( 1784) hydrogen bonds : angle 4.74405 ( 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 518 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 428 time to evaluate : 0.803 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: 0.7858 (mpp) cc_final: 0.7537 (mtm) REVERT: A 353 MET cc_start: 0.7781 (mpp) cc_final: 0.7503 (pmm) REVERT: A 401 ASP cc_start: 0.9060 (t0) cc_final: 0.8827 (t0) REVERT: A 462 MET cc_start: 0.8900 (tmm) cc_final: 0.8669 (tmm) REVERT: A 518 ASP cc_start: 0.8494 (t0) cc_final: 0.8121 (t0) REVERT: A 800 VAL cc_start: 0.9395 (t) cc_final: 0.9073 (m) REVERT: A 942 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8746 (pt0) REVERT: A 1059 MET cc_start: 0.8011 (mpp) cc_final: 0.7169 (pmm) REVERT: B 189 MET cc_start: 0.7879 (mpp) cc_final: 0.7573 (mtm) REVERT: B 282 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7994 (pp20) REVERT: B 353 MET cc_start: 0.7762 (mpp) cc_final: 0.7523 (pmm) REVERT: B 401 ASP cc_start: 0.9059 (t0) cc_final: 0.8827 (t0) REVERT: B 457 ASP cc_start: 0.7857 (t0) cc_final: 0.7621 (t0) REVERT: B 518 ASP cc_start: 0.8488 (t0) cc_final: 0.8091 (t0) REVERT: B 689 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8228 (p0) REVERT: B 800 VAL cc_start: 0.9392 (t) cc_final: 0.9067 (m) REVERT: B 942 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8773 (pt0) REVERT: B 1059 MET cc_start: 0.8003 (mpp) cc_final: 0.7151 (pmm) REVERT: C 189 MET cc_start: 0.7864 (mpp) cc_final: 0.7548 (mtm) REVERT: C 282 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7978 (pp20) REVERT: C 353 MET cc_start: 0.7764 (mpp) cc_final: 0.7527 (pmm) REVERT: C 401 ASP cc_start: 0.9068 (t0) cc_final: 0.8832 (t0) REVERT: C 462 MET cc_start: 0.8893 (tmm) cc_final: 0.8661 (tmm) REVERT: C 518 ASP cc_start: 0.8465 (t0) cc_final: 0.8076 (t0) REVERT: C 689 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8207 (p0) REVERT: C 800 VAL cc_start: 0.9398 (t) cc_final: 0.9077 (m) REVERT: C 942 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8770 (pt0) REVERT: C 1059 MET cc_start: 0.8016 (mpp) cc_final: 0.7156 (pmm) REVERT: D 189 MET cc_start: 0.7872 (mpp) cc_final: 0.7551 (mtm) REVERT: D 353 MET cc_start: 0.7764 (mpp) cc_final: 0.7488 (pmm) REVERT: D 401 ASP cc_start: 0.9057 (t0) cc_final: 0.8829 (t0) REVERT: D 457 ASP cc_start: 0.7810 (t0) cc_final: 0.7441 (t0) REVERT: D 462 MET cc_start: 0.8902 (tmm) cc_final: 0.8672 (tmm) REVERT: D 518 ASP cc_start: 0.8469 (t0) cc_final: 0.8076 (t0) REVERT: D 689 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8163 (p0) REVERT: D 800 VAL cc_start: 0.9398 (t) cc_final: 0.9079 (m) REVERT: D 942 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8743 (pt0) REVERT: D 1059 MET cc_start: 0.8005 (mpp) cc_final: 0.7147 (pmm) REVERT: D 1078 MET cc_start: 0.7080 (mmt) cc_final: 0.6879 (mmt) outliers start: 90 outliers final: 25 residues processed: 491 average time/residue: 0.6948 time to fit residues: 396.7763 Evaluate side-chains 374 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 340 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 282 GLU 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 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: 4.9990 chunk 63 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 278 optimal weight: 40.0000 chunk 223 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 217 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN A 609 ASN A 741 ASN A 761 HIS B 154 ASN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 ASN B 761 HIS ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN C 761 HIS D 609 ASN D 761 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.121653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.083407 restraints weight = 69535.007| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.81 r_work: 0.3145 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 31192 Z= 0.260 Angle : 0.711 8.307 42260 Z= 0.374 Chirality : 0.045 0.146 4708 Planarity : 0.005 0.058 5280 Dihedral : 5.917 50.430 4024 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.40 % Allowed : 13.43 % Favored : 83.17 % 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: -0.66 (0.13), residues: 3656 helix: 0.59 (0.10), residues: 2452 sheet: -1.99 (0.36), residues: 188 loop : -2.60 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1083 TYR 0.018 0.002 TYR C 191 PHE 0.024 0.002 PHE C1021 TRP 0.028 0.002 TRP B 453 HIS 0.007 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00615 (31188) covalent geometry : angle 0.70800 (42252) SS BOND : bond 0.01505 ( 4) SS BOND : angle 4.39283 ( 8) hydrogen bonds : bond 0.05815 ( 1784) hydrogen bonds : angle 4.60406 ( 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 484 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 371 time to evaluate : 1.270 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: A 141 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8548 (p) REVERT: A 189 MET cc_start: 0.7796 (mpp) cc_final: 0.7500 (mtm) REVERT: A 462 MET cc_start: 0.8921 (tmm) cc_final: 0.8650 (tmm) REVERT: A 942 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8749 (pt0) REVERT: A 985 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8506 (mp) REVERT: A 1023 MET cc_start: 0.7534 (mmp) cc_final: 0.6321 (ttm) REVERT: B 141 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8535 (p) REVERT: B 189 MET cc_start: 0.7790 (mpp) cc_final: 0.7480 (mtm) REVERT: B 282 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8035 (pp20) REVERT: B 689 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8215 (p0) REVERT: B 942 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8746 (pt0) REVERT: B 985 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8496 (mp) REVERT: B 1023 MET cc_start: 0.7522 (mmp) cc_final: 0.6316 (ttm) REVERT: C 141 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8545 (p) REVERT: C 189 MET cc_start: 0.7806 (mpp) cc_final: 0.7488 (mtm) REVERT: C 191 TYR cc_start: 0.8325 (t80) cc_final: 0.8078 (t80) REVERT: C 194 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8796 (mt-10) REVERT: C 282 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.8025 (pp20) REVERT: C 462 MET cc_start: 0.8918 (tmm) cc_final: 0.8648 (tmm) REVERT: C 689 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8203 (p0) REVERT: C 801 MET cc_start: 0.8321 (ppp) cc_final: 0.8027 (ppp) REVERT: C 942 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8780 (pt0) REVERT: C 985 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8495 (mp) REVERT: C 1023 MET cc_start: 0.7534 (mmp) cc_final: 0.6355 (ttm) REVERT: D 141 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8553 (p) REVERT: D 189 MET cc_start: 0.7814 (mpp) cc_final: 0.7528 (mtm) REVERT: D 360 ARG cc_start: 0.8440 (ppp-140) cc_final: 0.8213 (ppp80) REVERT: D 457 ASP cc_start: 0.7989 (t0) cc_final: 0.7617 (t0) REVERT: D 462 MET cc_start: 0.8921 (tmm) cc_final: 0.8652 (tmm) REVERT: D 637 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7772 (mp0) REVERT: D 689 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8194 (p0) REVERT: D 942 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8785 (pt0) REVERT: D 985 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8506 (mp) REVERT: D 1023 MET cc_start: 0.7532 (mmp) cc_final: 0.6313 (ttm) outliers start: 113 outliers final: 39 residues processed: 459 average time/residue: 0.6272 time to fit residues: 339.3132 Evaluate side-chains 372 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 316 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 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 282 GLU 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 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 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 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 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: 0.0980 chunk 40 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 333 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 271 optimal weight: 4.9990 chunk 297 optimal weight: 20.0000 chunk 223 optimal weight: 9.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3988 r_free = 0.3988 target = 0.122977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.085070 restraints weight = 68465.812| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.78 r_work: 0.3171 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31192 Z= 0.179 Angle : 0.646 8.808 42260 Z= 0.337 Chirality : 0.042 0.137 4708 Planarity : 0.004 0.039 5280 Dihedral : 5.709 54.175 4024 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.09 % Allowed : 14.90 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3656 helix: 0.97 (0.10), residues: 2448 sheet: -2.05 (0.38), residues: 176 loop : -2.33 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 197 TYR 0.015 0.002 TYR C 191 PHE 0.025 0.001 PHE B 779 TRP 0.026 0.002 TRP D 453 HIS 0.005 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00421 (31188) covalent geometry : angle 0.64362 (42252) SS BOND : bond 0.00889 ( 4) SS BOND : angle 4.37556 ( 8) hydrogen bonds : bond 0.04986 ( 1784) hydrogen bonds : angle 4.37367 ( 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 463 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 360 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8801 (OUTLIER) cc_final: 0.8488 (p) REVERT: A 157 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8082 (tm) REVERT: A 189 MET cc_start: 0.7736 (mpp) cc_final: 0.7435 (mtm) REVERT: A 191 TYR cc_start: 0.8235 (t80) cc_final: 0.7953 (t80) REVERT: A 194 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8790 (mt-10) REVERT: A 353 MET cc_start: 0.7691 (mpp) cc_final: 0.7350 (pmm) REVERT: A 457 ASP cc_start: 0.7909 (t0) cc_final: 0.7612 (t0) REVERT: A 462 MET cc_start: 0.8938 (tmm) cc_final: 0.8707 (tmm) REVERT: A 731 PHE cc_start: 0.8227 (m-10) cc_final: 0.7518 (t80) REVERT: A 788 MET cc_start: 0.8277 (tmm) cc_final: 0.7948 (tmm) REVERT: A 942 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8726 (pt0) REVERT: A 985 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8529 (mp) REVERT: A 1059 MET cc_start: 0.8034 (mpp) cc_final: 0.7249 (pmm) REVERT: B 141 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8481 (p) REVERT: B 189 MET cc_start: 0.7739 (mpp) cc_final: 0.7430 (mtm) REVERT: B 191 TYR cc_start: 0.8231 (t80) cc_final: 0.7940 (t80) REVERT: B 194 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8794 (mt-10) REVERT: B 353 MET cc_start: 0.7692 (mpp) cc_final: 0.7356 (pmm) REVERT: B 457 ASP cc_start: 0.7915 (t0) cc_final: 0.7628 (t0) REVERT: B 518 ASP cc_start: 0.8336 (t0) cc_final: 0.7999 (t0) REVERT: B 689 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8160 (p0) REVERT: B 731 PHE cc_start: 0.8099 (m-10) cc_final: 0.7542 (t80) REVERT: B 788 MET cc_start: 0.8279 (tmm) cc_final: 0.7941 (tmm) REVERT: B 942 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8765 (pt0) REVERT: B 985 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8516 (mp) REVERT: B 1023 MET cc_start: 0.7460 (mmp) cc_final: 0.6284 (ttm) REVERT: B 1059 MET cc_start: 0.8039 (mpp) cc_final: 0.7223 (pmm) REVERT: C 141 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8486 (p) REVERT: C 157 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8086 (tm) REVERT: C 189 MET cc_start: 0.7760 (mpp) cc_final: 0.7453 (mtm) REVERT: C 194 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8808 (mt-10) REVERT: C 353 MET cc_start: 0.7696 (mpp) cc_final: 0.7361 (pmm) REVERT: C 457 ASP cc_start: 0.7923 (t0) cc_final: 0.7640 (t0) REVERT: C 462 MET cc_start: 0.8932 (tmm) cc_final: 0.8698 (tmm) REVERT: C 518 ASP cc_start: 0.8321 (t0) cc_final: 0.7998 (t0) REVERT: C 689 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8131 (p0) REVERT: C 731 PHE cc_start: 0.8100 (m-10) cc_final: 0.7553 (t80) REVERT: C 788 MET cc_start: 0.8296 (tmm) cc_final: 0.7961 (tmm) REVERT: C 942 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8742 (pt0) REVERT: C 985 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8499 (mp) REVERT: C 1023 MET cc_start: 0.7467 (mmp) cc_final: 0.6285 (ttm) REVERT: C 1059 MET cc_start: 0.8018 (mpp) cc_final: 0.7266 (pmm) REVERT: D 141 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8493 (p) REVERT: D 157 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8086 (tm) REVERT: D 189 MET cc_start: 0.7760 (mpp) cc_final: 0.7469 (mtm) REVERT: D 191 TYR cc_start: 0.8262 (t80) cc_final: 0.7981 (t80) REVERT: D 194 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8828 (mt-10) REVERT: D 353 MET cc_start: 0.7788 (mpp) cc_final: 0.7432 (pmm) REVERT: D 457 ASP cc_start: 0.7894 (t0) cc_final: 0.7606 (t0) REVERT: D 462 MET cc_start: 0.8937 (tmm) cc_final: 0.8698 (tmm) REVERT: D 518 ASP cc_start: 0.8298 (t0) cc_final: 0.8039 (t0) REVERT: D 689 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8152 (p0) REVERT: D 731 PHE cc_start: 0.8217 (m-10) cc_final: 0.7496 (t80) REVERT: D 942 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8739 (pt0) REVERT: D 985 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8529 (mp) REVERT: D 1059 MET cc_start: 0.8039 (mpp) cc_final: 0.7226 (pmm) outliers start: 103 outliers final: 51 residues processed: 436 average time/residue: 0.5925 time to fit residues: 307.3824 Evaluate side-chains 392 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 323 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 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 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 1047 ASN 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 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 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 1047 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 157 LEU 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 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 758 MET 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 1015 PHE Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 157 LEU 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 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 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 Chi-restraints excluded: chain D residue 1047 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 134 optimal weight: 2.9990 chunk 349 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 348 optimal weight: 3.9990 chunk 340 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 chunk 336 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 973 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.122404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.084340 restraints weight = 68794.934| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.79 r_work: 0.3156 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 31192 Z= 0.202 Angle : 0.650 10.291 42260 Z= 0.341 Chirality : 0.043 0.157 4708 Planarity : 0.004 0.048 5280 Dihedral : 5.590 53.282 4024 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.28 % Allowed : 15.96 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3656 helix: 1.12 (0.10), residues: 2452 sheet: -1.97 (0.35), residues: 188 loop : -2.20 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1083 TYR 0.014 0.002 TYR A 727 PHE 0.030 0.002 PHE C1021 TRP 0.022 0.002 TRP B 898 HIS 0.005 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00478 (31188) covalent geometry : angle 0.64860 (42252) SS BOND : bond 0.00734 ( 4) SS BOND : angle 3.61685 ( 8) hydrogen bonds : bond 0.05143 ( 1784) hydrogen bonds : angle 4.35337 ( 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 462 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 353 time to evaluate : 1.086 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 141 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8562 (p) REVERT: A 191 TYR cc_start: 0.8301 (t80) cc_final: 0.8040 (t80) REVERT: A 194 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8721 (mt-10) REVERT: A 353 MET cc_start: 0.7765 (mpp) cc_final: 0.7404 (pmm) REVERT: A 462 MET cc_start: 0.8929 (tmm) cc_final: 0.8641 (tmm) REVERT: A 731 PHE cc_start: 0.8199 (m-10) cc_final: 0.7556 (t80) REVERT: A 788 MET cc_start: 0.8206 (tmm) cc_final: 0.7782 (tmm) REVERT: A 942 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8719 (pt0) REVERT: A 985 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8518 (mp) REVERT: A 1023 MET cc_start: 0.7409 (mmp) cc_final: 0.6255 (ttm) REVERT: B 141 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8534 (p) REVERT: B 189 MET cc_start: 0.7759 (mpp) cc_final: 0.7546 (mtm) REVERT: B 353 MET cc_start: 0.7765 (mpp) cc_final: 0.7401 (pmm) REVERT: B 518 ASP cc_start: 0.8377 (t0) cc_final: 0.8039 (t0) REVERT: B 689 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8145 (p0) REVERT: B 731 PHE cc_start: 0.8222 (m-10) cc_final: 0.7531 (t80) REVERT: B 788 MET cc_start: 0.8199 (tmm) cc_final: 0.7789 (tmm) REVERT: B 942 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8724 (pt0) REVERT: B 985 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8521 (mp) REVERT: C 141 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8573 (p) REVERT: C 189 MET cc_start: 0.7779 (mpp) cc_final: 0.7563 (mtm) REVERT: C 353 MET cc_start: 0.7744 (mpp) cc_final: 0.7386 (pmm) REVERT: C 462 MET cc_start: 0.8929 (tmm) cc_final: 0.8642 (tmm) REVERT: C 518 ASP cc_start: 0.8373 (t0) cc_final: 0.8031 (t0) REVERT: C 689 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8125 (p0) REVERT: C 731 PHE cc_start: 0.8227 (m-10) cc_final: 0.7533 (t80) REVERT: C 788 MET cc_start: 0.8228 (tmm) cc_final: 0.7815 (tmm) REVERT: C 942 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8722 (pt0) REVERT: C 985 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8499 (mp) REVERT: C 1023 MET cc_start: 0.7607 (mmp) cc_final: 0.6524 (ttp) REVERT: D 141 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8581 (p) REVERT: D 189 MET cc_start: 0.7798 (mpp) cc_final: 0.7558 (mtm) REVERT: D 191 TYR cc_start: 0.8294 (t80) cc_final: 0.8040 (t80) REVERT: D 194 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8792 (mt-10) REVERT: D 353 MET cc_start: 0.7831 (mpp) cc_final: 0.7576 (pmm) REVERT: D 457 ASP cc_start: 0.7933 (t0) cc_final: 0.7614 (t0) REVERT: D 462 MET cc_start: 0.8934 (tmm) cc_final: 0.8645 (tmm) REVERT: D 518 ASP cc_start: 0.8325 (t0) cc_final: 0.8034 (t0) REVERT: D 689 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8134 (p0) REVERT: D 731 PHE cc_start: 0.8244 (m-10) cc_final: 0.7551 (t80) REVERT: D 942 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8720 (pt0) REVERT: D 985 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8533 (mp) REVERT: D 1023 MET cc_start: 0.7412 (mmp) cc_final: 0.6249 (ttm) outliers start: 109 outliers final: 48 residues processed: 438 average time/residue: 0.5824 time to fit residues: 304.3336 Evaluate side-chains 389 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 326 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 942 GLU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1095 LEU 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 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 B residue 1047 ASN 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 758 MET 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 985 ILE Chi-restraints excluded: chain C residue 1015 PHE Chi-restraints excluded: chain C residue 1047 ASN 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 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 985 ILE Chi-restraints excluded: chain D residue 1047 ASN Chi-restraints excluded: chain D residue 1095 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 323 optimal weight: 2.9990 chunk 344 optimal weight: 0.8980 chunk 182 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 303 optimal weight: 1.9990 chunk 360 optimal weight: 0.9990 chunk 187 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 973 ASN B 973 ASN D 973 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.123447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.085505 restraints weight = 68759.131| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.79 r_work: 0.3182 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31192 Z= 0.157 Angle : 0.627 10.521 42260 Z= 0.329 Chirality : 0.042 0.160 4708 Planarity : 0.004 0.042 5280 Dihedral : 5.405 49.659 4024 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.52 % Allowed : 17.16 % Favored : 80.32 % 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: 0.38 (0.14), residues: 3656 helix: 1.32 (0.10), residues: 2456 sheet: -1.86 (0.36), residues: 188 loop : -2.02 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 162 TYR 0.020 0.002 TYR B 191 PHE 0.028 0.001 PHE B1021 TRP 0.021 0.002 TRP B 898 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00368 (31188) covalent geometry : angle 0.62588 (42252) SS BOND : bond 0.00639 ( 4) SS BOND : angle 2.73192 ( 8) hydrogen bonds : bond 0.04622 ( 1784) hydrogen bonds : angle 4.25527 ( 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 450 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 366 time to evaluate : 1.186 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 141 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8529 (p) REVERT: A 179 ILE cc_start: 0.8692 (pt) cc_final: 0.8444 (pp) REVERT: A 189 MET cc_start: 0.7347 (mtm) cc_final: 0.6883 (mtt) REVERT: A 194 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8743 (mt-10) REVERT: A 353 MET cc_start: 0.7721 (mpp) cc_final: 0.7401 (pmm) REVERT: A 731 PHE cc_start: 0.8122 (m-10) cc_final: 0.7551 (t80) REVERT: A 788 MET cc_start: 0.8186 (tmm) cc_final: 0.7970 (tmm) REVERT: A 942 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8691 (pt0) REVERT: A 985 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8525 (mp) REVERT: A 1023 MET cc_start: 0.7368 (mmp) cc_final: 0.6298 (ttp) REVERT: A 1059 MET cc_start: 0.8026 (mpp) cc_final: 0.7353 (pmm) REVERT: B 141 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8537 (p) REVERT: B 179 ILE cc_start: 0.8699 (pt) cc_final: 0.8425 (pp) REVERT: B 189 MET cc_start: 0.7699 (mpp) cc_final: 0.7401 (mtm) REVERT: B 194 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8821 (mt-10) REVERT: B 353 MET cc_start: 0.7719 (mpp) cc_final: 0.7396 (pmm) REVERT: B 462 MET cc_start: 0.8749 (tmm) cc_final: 0.8542 (tmm) REVERT: B 518 ASP cc_start: 0.8362 (t0) cc_final: 0.7941 (t0) REVERT: B 689 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8090 (p0) REVERT: B 731 PHE cc_start: 0.8124 (m-10) cc_final: 0.7533 (t80) REVERT: B 788 MET cc_start: 0.8151 (tmm) cc_final: 0.7940 (tmm) REVERT: B 942 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8696 (pt0) REVERT: B 985 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8521 (mp) REVERT: B 1023 MET cc_start: 0.7372 (mmp) cc_final: 0.6309 (ttp) REVERT: B 1059 MET cc_start: 0.8029 (mpp) cc_final: 0.7199 (pmm) REVERT: C 141 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8522 (p) REVERT: C 179 ILE cc_start: 0.8698 (pt) cc_final: 0.8446 (pp) REVERT: C 189 MET cc_start: 0.7723 (mpp) cc_final: 0.7428 (mtm) REVERT: C 191 TYR cc_start: 0.8307 (t80) cc_final: 0.8091 (t80) REVERT: C 194 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8811 (mt-10) REVERT: C 353 MET cc_start: 0.7722 (mpp) cc_final: 0.7401 (pmm) REVERT: C 518 ASP cc_start: 0.8340 (t0) cc_final: 0.7909 (t0) REVERT: C 689 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8073 (p0) REVERT: C 731 PHE cc_start: 0.8113 (m-10) cc_final: 0.7510 (t80) REVERT: C 788 MET cc_start: 0.8192 (tmm) cc_final: 0.7985 (tmm) REVERT: C 942 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8729 (pt0) REVERT: C 985 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8508 (mp) REVERT: C 1023 MET cc_start: 0.7473 (mmp) cc_final: 0.6391 (ttp) REVERT: C 1059 MET cc_start: 0.8025 (mpp) cc_final: 0.7338 (pmm) REVERT: D 141 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8526 (p) REVERT: D 179 ILE cc_start: 0.8709 (pt) cc_final: 0.8436 (pp) REVERT: D 189 MET cc_start: 0.7722 (mpp) cc_final: 0.7490 (mtm) REVERT: D 194 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8736 (mt-10) REVERT: D 353 MET cc_start: 0.7831 (mpp) cc_final: 0.7536 (pmm) REVERT: D 457 ASP cc_start: 0.7837 (t0) cc_final: 0.7541 (t0) REVERT: D 518 ASP cc_start: 0.8371 (t0) cc_final: 0.8042 (t0) REVERT: D 689 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8065 (p0) REVERT: D 731 PHE cc_start: 0.8110 (m-10) cc_final: 0.7521 (t80) REVERT: D 942 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8713 (pt0) REVERT: D 985 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8535 (mp) REVERT: D 1023 MET cc_start: 0.7396 (mmp) cc_final: 0.6333 (ttp) REVERT: D 1059 MET cc_start: 0.8024 (mpp) cc_final: 0.7202 (pmm) outliers start: 84 outliers final: 39 residues processed: 427 average time/residue: 0.5947 time to fit residues: 302.4893 Evaluate side-chains 386 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 332 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 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 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 304 PHE 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 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 C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 338 VAL 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 929 CYS 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 146 ILE 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 864 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 98 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 351 optimal weight: 2.9990 chunk 246 optimal weight: 7.9990 chunk 341 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 295 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 973 ASN D 741 ASN D 973 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.121209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.082889 restraints weight = 68732.980| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.80 r_work: 0.3131 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 31192 Z= 0.258 Angle : 0.698 9.900 42260 Z= 0.367 Chirality : 0.045 0.181 4708 Planarity : 0.005 0.063 5280 Dihedral : 5.453 51.837 4024 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.31 % Allowed : 17.01 % 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: 0.31 (0.14), residues: 3656 helix: 1.28 (0.10), residues: 2456 sheet: -1.86 (0.36), residues: 188 loop : -2.08 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 162 TYR 0.023 0.002 TYR D 191 PHE 0.027 0.002 PHE C 779 TRP 0.023 0.002 TRP A 898 HIS 0.006 0.001 HIS B 765 Details of bonding type rmsd covalent geometry : bond 0.00615 (31188) covalent geometry : angle 0.69635 (42252) SS BOND : bond 0.00700 ( 4) SS BOND : angle 3.26517 ( 8) hydrogen bonds : bond 0.05460 ( 1784) hydrogen bonds : angle 4.40662 ( 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 448 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 338 time to evaluate : 1.083 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: A 141 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8559 (p) REVERT: A 189 MET cc_start: 0.7444 (mtm) cc_final: 0.6927 (mtt) REVERT: A 191 TYR cc_start: 0.8349 (t80) cc_final: 0.8130 (t80) REVERT: A 194 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8703 (mt-10) REVERT: A 353 MET cc_start: 0.7665 (mpp) cc_final: 0.7287 (pmm) REVERT: A 462 MET cc_start: 0.8879 (tmm) cc_final: 0.8606 (tmm) REVERT: A 731 PHE cc_start: 0.8169 (m-10) cc_final: 0.7532 (t80) REVERT: A 788 MET cc_start: 0.8213 (tmm) cc_final: 0.7997 (tmm) REVERT: A 942 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8734 (pt0) REVERT: A 985 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8507 (mp) REVERT: A 1023 MET cc_start: 0.7444 (mmp) cc_final: 0.6354 (ttp) REVERT: A 1059 MET cc_start: 0.8013 (mpp) cc_final: 0.7327 (pmm) REVERT: B 141 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8586 (p) REVERT: B 189 MET cc_start: 0.7863 (mpp) cc_final: 0.7603 (mtm) REVERT: B 353 MET cc_start: 0.7707 (mpp) cc_final: 0.7336 (pmm) REVERT: B 451 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7076 (pmt-80) REVERT: B 462 MET cc_start: 0.8773 (tmm) cc_final: 0.8516 (tmm) REVERT: B 689 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8083 (p0) REVERT: B 731 PHE cc_start: 0.8157 (m-10) cc_final: 0.7517 (t80) REVERT: B 788 MET cc_start: 0.8225 (tmm) cc_final: 0.8018 (tmm) REVERT: B 942 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8717 (pt0) REVERT: B 985 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8493 (mp) REVERT: B 1023 MET cc_start: 0.7449 (mmp) cc_final: 0.6362 (ttp) REVERT: B 1059 MET cc_start: 0.7846 (mpp) cc_final: 0.7210 (pmm) REVERT: C 141 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8599 (p) REVERT: C 162 ARG cc_start: 0.8432 (ttp-110) cc_final: 0.8215 (mtm-85) REVERT: C 189 MET cc_start: 0.7875 (mpp) cc_final: 0.7617 (mtm) REVERT: C 194 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8745 (mt-10) REVERT: C 255 ASN cc_start: 0.8771 (m110) cc_final: 0.8561 (p0) REVERT: C 353 MET cc_start: 0.7670 (mpp) cc_final: 0.7292 (pmm) REVERT: C 451 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7080 (pmt-80) REVERT: C 462 MET cc_start: 0.8862 (tmm) cc_final: 0.8593 (tmm) REVERT: C 689 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8109 (p0) REVERT: C 731 PHE cc_start: 0.8159 (m-10) cc_final: 0.7519 (t80) REVERT: C 788 MET cc_start: 0.8259 (tmm) cc_final: 0.8056 (tmm) REVERT: C 942 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8773 (pt0) REVERT: C 985 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8505 (mp) REVERT: C 1021 PHE cc_start: 0.8086 (m-80) cc_final: 0.7799 (m-80) REVERT: C 1023 MET cc_start: 0.7544 (mmp) cc_final: 0.6503 (ttp) REVERT: C 1059 MET cc_start: 0.7984 (mpp) cc_final: 0.7333 (pmm) REVERT: D 141 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8584 (p) REVERT: D 189 MET cc_start: 0.7918 (mpp) cc_final: 0.7637 (mtm) REVERT: D 194 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8692 (mt-10) REVERT: D 353 MET cc_start: 0.7854 (mpp) cc_final: 0.7571 (pmm) REVERT: D 457 ASP cc_start: 0.7880 (t0) cc_final: 0.7619 (t0) REVERT: D 518 ASP cc_start: 0.8411 (t0) cc_final: 0.8053 (t0) REVERT: D 689 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8097 (p0) REVERT: D 731 PHE cc_start: 0.8176 (m-10) cc_final: 0.7534 (t80) REVERT: D 942 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8825 (pt0) REVERT: D 985 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8507 (mp) REVERT: D 1023 MET cc_start: 0.7442 (mmp) cc_final: 0.6344 (ttp) REVERT: D 1059 MET cc_start: 0.7873 (mpp) cc_final: 0.7208 (pmm) outliers start: 110 outliers final: 53 residues processed: 416 average time/residue: 0.5672 time to fit residues: 282.0727 Evaluate side-chains 388 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 318 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 985 ILE 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 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 566 ILE 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 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 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 451 ARG Chi-restraints excluded: chain C residue 499 THR 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 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 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 608 ILE 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 1015 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 339 optimal weight: 4.9990 chunk 241 optimal weight: 0.8980 chunk 197 optimal weight: 20.0000 chunk 326 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 265 optimal weight: 0.9980 chunk 255 optimal weight: 0.6980 chunk 295 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.123569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.085774 restraints weight = 68266.677| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.77 r_work: 0.3189 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4068 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= 0.144 Angle : 0.636 11.655 42260 Z= 0.335 Chirality : 0.042 0.158 4708 Planarity : 0.004 0.056 5280 Dihedral : 5.335 48.920 4024 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.19 % Allowed : 18.39 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.66 (0.14), residues: 3656 helix: 1.57 (0.10), residues: 2452 sheet: -1.74 (0.36), residues: 188 loop : -1.98 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 162 TYR 0.016 0.002 TYR A 191 PHE 0.038 0.001 PHE B1021 TRP 0.021 0.002 TRP D 898 HIS 0.004 0.001 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00331 (31188) covalent geometry : angle 0.63396 (42252) SS BOND : bond 0.00353 ( 4) SS BOND : angle 4.03426 ( 8) hydrogen bonds : bond 0.04432 ( 1784) hydrogen bonds : angle 4.13528 ( 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 421 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 348 time to evaluate : 1.106 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: 0.8728 (OUTLIER) cc_final: 0.8527 (p) REVERT: A 179 ILE cc_start: 0.8724 (pt) cc_final: 0.8488 (pp) REVERT: A 189 MET cc_start: 0.7372 (mtm) cc_final: 0.6863 (mtt) REVERT: A 194 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8704 (mt-10) REVERT: A 353 MET cc_start: 0.7787 (mpp) cc_final: 0.7427 (pmm) REVERT: A 462 MET cc_start: 0.8853 (tmm) cc_final: 0.8571 (tmm) REVERT: A 731 PHE cc_start: 0.8136 (m-10) cc_final: 0.7555 (t80) REVERT: A 788 MET cc_start: 0.8143 (tmm) cc_final: 0.7930 (tmm) REVERT: A 942 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8689 (pt0) REVERT: A 985 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8514 (mp) REVERT: A 1023 MET cc_start: 0.7433 (mmp) cc_final: 0.6340 (ttp) REVERT: B 179 ILE cc_start: 0.8762 (pt) cc_final: 0.8506 (pp) REVERT: B 189 MET cc_start: 0.7727 (mpp) cc_final: 0.7410 (mtm) REVERT: B 194 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8860 (mt-10) REVERT: B 353 MET cc_start: 0.7783 (mpp) cc_final: 0.7418 (pmm) REVERT: B 451 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7307 (pmt-80) REVERT: B 462 MET cc_start: 0.8797 (tmm) cc_final: 0.8533 (tmm) REVERT: B 689 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8028 (p0) REVERT: B 731 PHE cc_start: 0.8121 (m-10) cc_final: 0.7538 (t80) REVERT: B 942 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8699 (pt0) REVERT: B 985 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8514 (mp) REVERT: B 1023 MET cc_start: 0.7406 (mmp) cc_final: 0.6295 (ttp) REVERT: C 141 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8567 (p) REVERT: C 162 ARG cc_start: 0.8451 (ttp-110) cc_final: 0.8209 (mtm-85) REVERT: C 179 ILE cc_start: 0.8765 (pt) cc_final: 0.8511 (pp) REVERT: C 189 MET cc_start: 0.7732 (mpp) cc_final: 0.7471 (mtm) REVERT: C 194 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8822 (mt-10) REVERT: C 353 MET cc_start: 0.7787 (mpp) cc_final: 0.7426 (pmm) REVERT: C 451 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7294 (pmt-80) REVERT: C 462 MET cc_start: 0.8842 (tmm) cc_final: 0.8545 (tmm) REVERT: C 689 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8046 (p0) REVERT: C 731 PHE cc_start: 0.8118 (m-10) cc_final: 0.7543 (t80) REVERT: C 942 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8699 (pt0) REVERT: C 985 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8490 (mp) REVERT: C 1021 PHE cc_start: 0.8170 (m-80) cc_final: 0.7948 (m-80) REVERT: C 1023 MET cc_start: 0.7582 (mmp) cc_final: 0.6490 (ttp) REVERT: C 1066 LYS cc_start: 0.9180 (mtpp) cc_final: 0.8956 (mtmm) REVERT: D 179 ILE cc_start: 0.8765 (pt) cc_final: 0.8502 (pp) REVERT: D 194 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8746 (mt-10) REVERT: D 353 MET cc_start: 0.7771 (mpp) cc_final: 0.7473 (pmm) REVERT: D 457 ASP cc_start: 0.7902 (t0) cc_final: 0.7620 (t0) REVERT: D 518 ASP cc_start: 0.8335 (t0) cc_final: 0.7975 (t0) REVERT: D 689 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8034 (p0) REVERT: D 731 PHE cc_start: 0.8112 (m-10) cc_final: 0.7534 (t80) REVERT: D 942 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8702 (pt0) REVERT: D 985 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8518 (mp) REVERT: D 1023 MET cc_start: 0.7409 (mmp) cc_final: 0.6308 (ttp) outliers start: 73 outliers final: 39 residues processed: 409 average time/residue: 0.6031 time to fit residues: 293.9269 Evaluate side-chains 377 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 323 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 310 ARG 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 864 LEU 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 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 451 ARG 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 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 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 469 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 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 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 864 LEU 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: 3.9990 chunk 174 optimal weight: 2.9990 chunk 279 optimal weight: 20.0000 chunk 356 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 227 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.124618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.086850 restraints weight = 68246.207| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.77 r_work: 0.3210 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31192 Z= 0.132 Angle : 0.644 12.994 42260 Z= 0.336 Chirality : 0.041 0.178 4708 Planarity : 0.004 0.079 5280 Dihedral : 5.216 45.106 4024 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.07 % Allowed : 18.99 % Favored : 78.94 % 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: 0.81 (0.14), residues: 3656 helix: 1.66 (0.10), residues: 2452 sheet: -1.61 (0.37), residues: 188 loop : -1.89 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 197 TYR 0.020 0.002 TYR C 186 PHE 0.029 0.001 PHE D 779 TRP 0.018 0.001 TRP B 898 HIS 0.008 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00295 (31188) covalent geometry : angle 0.64243 (42252) SS BOND : bond 0.00542 ( 4) SS BOND : angle 3.75826 ( 8) hydrogen bonds : bond 0.04147 ( 1784) hydrogen bonds : angle 4.04327 ( 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 415 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 346 time to evaluate : 0.780 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 179 ILE cc_start: 0.8739 (pt) cc_final: 0.8488 (pp) REVERT: A 189 MET cc_start: 0.7314 (mtm) cc_final: 0.6826 (mtt) REVERT: A 194 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8829 (mt-10) REVERT: A 353 MET cc_start: 0.7845 (mpp) cc_final: 0.7459 (pmm) REVERT: A 462 MET cc_start: 0.8901 (tmm) cc_final: 0.8619 (tmm) REVERT: A 731 PHE cc_start: 0.8142 (m-10) cc_final: 0.7550 (t80) REVERT: A 788 MET cc_start: 0.8141 (tmm) cc_final: 0.7613 (tmm) REVERT: A 942 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8643 (pt0) REVERT: A 985 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8501 (mp) REVERT: A 1023 MET cc_start: 0.7393 (mmp) cc_final: 0.6317 (ttp) REVERT: A 1059 MET cc_start: 0.8180 (mpp) cc_final: 0.7595 (pmm) REVERT: B 189 MET cc_start: 0.7695 (mpp) cc_final: 0.7394 (mtm) REVERT: B 353 MET cc_start: 0.7843 (mpp) cc_final: 0.7451 (pmm) REVERT: B 462 MET cc_start: 0.8800 (tmm) cc_final: 0.8533 (tmm) REVERT: B 627 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8849 (mt-10) REVERT: B 689 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8041 (p0) REVERT: B 731 PHE cc_start: 0.8129 (m-10) cc_final: 0.7507 (t80) REVERT: B 942 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8611 (pt0) REVERT: B 985 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8514 (mp) REVERT: B 1001 LEU cc_start: 0.9128 (pp) cc_final: 0.8733 (tm) REVERT: B 1023 MET cc_start: 0.7377 (mmp) cc_final: 0.6285 (ttp) REVERT: B 1059 MET cc_start: 0.8056 (mpp) cc_final: 0.7468 (pmm) REVERT: C 162 ARG cc_start: 0.8480 (ttp-110) cc_final: 0.8224 (mtm-85) REVERT: C 179 ILE cc_start: 0.8773 (pt) cc_final: 0.8549 (pp) REVERT: C 189 MET cc_start: 0.7695 (mpp) cc_final: 0.7395 (mtm) REVERT: C 353 MET cc_start: 0.7849 (mpp) cc_final: 0.7460 (pmm) REVERT: C 462 MET cc_start: 0.8842 (tmm) cc_final: 0.8574 (tmm) REVERT: C 627 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8843 (mt-10) REVERT: C 689 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8042 (p0) REVERT: C 731 PHE cc_start: 0.8115 (m-10) cc_final: 0.7533 (t80) REVERT: C 788 MET cc_start: 0.8209 (tmm) cc_final: 0.7851 (tmm) REVERT: C 942 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8637 (pt0) REVERT: C 985 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8472 (mp) REVERT: C 1021 PHE cc_start: 0.8140 (m-80) cc_final: 0.7908 (m-80) REVERT: C 1023 MET cc_start: 0.7581 (mmp) cc_final: 0.6508 (ttp) REVERT: C 1059 MET cc_start: 0.8159 (mpp) cc_final: 0.7424 (pmm) REVERT: D 189 MET cc_start: 0.7462 (mtm) cc_final: 0.7113 (mtt) REVERT: D 194 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8869 (mt-10) REVERT: D 353 MET cc_start: 0.7705 (mpp) cc_final: 0.7424 (pmm) REVERT: D 457 ASP cc_start: 0.7931 (t0) cc_final: 0.7533 (t0) REVERT: D 689 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8036 (p0) REVERT: D 731 PHE cc_start: 0.8129 (m-10) cc_final: 0.7568 (t80) REVERT: D 942 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8636 (pt0) REVERT: D 985 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8506 (mp) REVERT: D 1023 MET cc_start: 0.7397 (mmp) cc_final: 0.6308 (ttp) REVERT: D 1059 MET cc_start: 0.8060 (mpp) cc_final: 0.7486 (pmm) outliers start: 69 outliers final: 42 residues processed: 405 average time/residue: 0.6155 time to fit residues: 295.5502 Evaluate side-chains 364 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 311 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 310 ARG 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 864 LEU 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 B residue 146 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 637 GLU 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 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 499 THR 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 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 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 637 GLU 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 929 CYS Chi-restraints excluded: chain D residue 942 GLU 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 147 optimal weight: 0.0470 chunk 176 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 204 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 304 optimal weight: 0.4980 chunk 1 optimal weight: 5.9990 chunk 338 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 265 optimal weight: 1.9990 overall best weight: 2.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.124077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.085772 restraints weight = 68623.002| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.77 r_work: 0.3191 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31192 Z= 0.155 Angle : 0.653 12.495 42260 Z= 0.341 Chirality : 0.042 0.168 4708 Planarity : 0.004 0.065 5280 Dihedral : 5.169 44.545 4024 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.77 % Allowed : 20.04 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.84 (0.14), residues: 3656 helix: 1.69 (0.10), residues: 2452 sheet: -1.58 (0.37), residues: 188 loop : -1.88 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 197 TYR 0.019 0.002 TYR A 191 PHE 0.042 0.001 PHE A1021 TRP 0.031 0.002 TRP C 786 HIS 0.004 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00362 (31188) covalent geometry : angle 0.65045 (42252) SS BOND : bond 0.00608 ( 4) SS BOND : angle 3.88544 ( 8) hydrogen bonds : bond 0.04353 ( 1784) hydrogen bonds : angle 4.05817 ( 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 396 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 337 time to evaluate : 1.034 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: A 179 ILE cc_start: 0.8705 (pt) cc_final: 0.8486 (pp) REVERT: A 189 MET cc_start: 0.7354 (mtm) cc_final: 0.6837 (mtt) REVERT: A 194 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8841 (mt-10) REVERT: A 353 MET cc_start: 0.7774 (mpp) cc_final: 0.7389 (pmm) REVERT: A 440 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8038 (p0) REVERT: A 462 MET cc_start: 0.8919 (tmm) cc_final: 0.8616 (tmm) REVERT: A 731 PHE cc_start: 0.8156 (m-10) cc_final: 0.7540 (t80) REVERT: A 788 MET cc_start: 0.8185 (tmm) cc_final: 0.7694 (tmm) REVERT: A 942 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8660 (pt0) REVERT: A 985 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8468 (mp) REVERT: A 1023 MET cc_start: 0.7417 (mmp) cc_final: 0.6312 (ttp) REVERT: A 1059 MET cc_start: 0.8140 (mpp) cc_final: 0.7346 (pmm) REVERT: B 353 MET cc_start: 0.7841 (mpp) cc_final: 0.7458 (pmm) REVERT: B 462 MET cc_start: 0.8827 (tmm) cc_final: 0.8551 (tmm) REVERT: B 627 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8867 (mt-10) REVERT: B 689 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8069 (p0) REVERT: B 731 PHE cc_start: 0.8156 (m-10) cc_final: 0.7545 (t80) REVERT: B 788 MET cc_start: 0.8232 (ttp) cc_final: 0.7762 (tmm) REVERT: B 942 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8661 (pt0) REVERT: B 985 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8471 (mp) REVERT: B 1023 MET cc_start: 0.7329 (mmp) cc_final: 0.6246 (ttp) REVERT: B 1059 MET cc_start: 0.8013 (mpp) cc_final: 0.7356 (pmm) REVERT: B 1078 MET cc_start: 0.7669 (mmt) cc_final: 0.7305 (mmt) REVERT: C 162 ARG cc_start: 0.8499 (ttp-110) cc_final: 0.8237 (mtm-85) REVERT: C 353 MET cc_start: 0.7780 (mpp) cc_final: 0.7393 (pmm) REVERT: C 440 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8048 (p0) REVERT: C 462 MET cc_start: 0.8845 (tmm) cc_final: 0.8538 (tmm) REVERT: C 627 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8855 (mt-10) REVERT: C 689 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8036 (p0) REVERT: C 731 PHE cc_start: 0.8132 (m-10) cc_final: 0.7528 (t80) REVERT: C 788 MET cc_start: 0.8162 (tmm) cc_final: 0.7784 (tmm) REVERT: C 942 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8672 (pt0) REVERT: C 985 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8443 (mp) REVERT: C 1021 PHE cc_start: 0.8121 (m-80) cc_final: 0.7892 (m-80) REVERT: C 1023 MET cc_start: 0.7641 (mmp) cc_final: 0.6561 (ttp) REVERT: C 1059 MET cc_start: 0.7991 (mpp) cc_final: 0.7423 (pmm) REVERT: C 1076 GLU cc_start: 0.8954 (pp20) cc_final: 0.8607 (pm20) REVERT: D 189 MET cc_start: 0.7434 (mtm) cc_final: 0.7065 (mtt) REVERT: D 191 TYR cc_start: 0.8389 (t80) cc_final: 0.8175 (t80) REVERT: D 194 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8871 (mt-10) REVERT: D 353 MET cc_start: 0.7690 (mpp) cc_final: 0.7405 (pmm) REVERT: D 689 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8048 (p0) REVERT: D 731 PHE cc_start: 0.8146 (m-10) cc_final: 0.7571 (t80) REVERT: D 942 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8653 (pt0) REVERT: D 985 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8469 (mp) REVERT: D 1023 MET cc_start: 0.7357 (mmp) cc_final: 0.6286 (ttp) REVERT: D 1059 MET cc_start: 0.8002 (mpp) cc_final: 0.7356 (pmm) outliers start: 59 outliers final: 36 residues processed: 385 average time/residue: 0.6004 time to fit residues: 275.4712 Evaluate side-chains 371 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 322 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 310 ARG 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 864 LEU 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 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 452 ARG Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 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 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 499 THR 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 985 ILE 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 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 929 CYS Chi-restraints excluded: chain D residue 942 GLU 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: 0.9990 chunk 325 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 353 optimal weight: 0.5980 chunk 364 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.125618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.087551 restraints weight = 68777.509| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.80 r_work: 0.3223 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31192 Z= 0.129 Angle : 0.635 12.354 42260 Z= 0.333 Chirality : 0.041 0.175 4708 Planarity : 0.004 0.056 5280 Dihedral : 5.045 43.966 4024 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.65 % Allowed : 20.34 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.14), residues: 3656 helix: 1.73 (0.10), residues: 2464 sheet: -1.58 (0.36), residues: 188 loop : -1.95 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 197 TYR 0.019 0.001 TYR C 191 PHE 0.031 0.001 PHE D 779 TRP 0.026 0.001 TRP C 786 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00287 (31188) covalent geometry : angle 0.63341 (42252) SS BOND : bond 0.00522 ( 4) SS BOND : angle 3.47647 ( 8) hydrogen bonds : bond 0.03938 ( 1784) hydrogen bonds : angle 3.96239 ( 5292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13093.74 seconds wall clock time: 222 minutes 37.74 seconds (13357.74 seconds total)