Starting phenix.real_space_refine on Fri Dec 15 01:18:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/12_2023/7wk9_32563.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/12_2023/7wk9_32563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/12_2023/7wk9_32563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/12_2023/7wk9_32563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/12_2023/7wk9_32563.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/12_2023/7wk9_32563.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 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: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 18997 2.51 5 N 4964 2.21 5 O 5651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 29745 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8165 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 54, 'TRANS': 987} Chain breaks: 7 Chain: "C" Number of atoms: 8239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8239 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 54, 'TRANS': 996} Chain breaks: 7 Chain: "c" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "d" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 8239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8239 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 54, 'TRANS': 996} Chain breaks: 7 Chain: "a" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "b" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 14.20, per 1000 atoms: 0.48 Number of scatterers: 29745 At special positions: 0 Unit cell: (185.81, 137.718, 196.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 133 16.00 O 5651 8.00 N 4964 7.00 C 18997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 96 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 92 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS a 147 " - pdb=" SG CYS a 202 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 92 " distance=2.03 Simple disulfide: pdb=" SG CYS b 138 " - pdb=" SG CYS b 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 11.46 Conformation dependent library (CDL) restraints added in 5.8 seconds 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7136 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 67 sheets defined 18.3% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.736A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.628A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.856A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.622A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.827A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 4.026A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 removed outlier: 3.503A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 909 removed outlier: 3.719A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.735A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 919' Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.613A pdb=" N ALA A 924 " --> pdb=" O GLN A 920 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 960 removed outlier: 3.710A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 965 removed outlier: 3.745A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.553A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 982' Processing helix chain 'A' and resid 988 through 1031 removed outlier: 3.993A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.673A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.378A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.694A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.958A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.790A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.892A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 746 through 752' Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.913A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.511A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.879A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.601A pdb=" N ALA C 876 " --> pdb=" O GLN C 872 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 906 removed outlier: 3.913A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.814A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.609A pdb=" N ALA C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 963 removed outlier: 3.820A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.571A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.871A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.812A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 56 No H-bonds generated for 'chain 'd' and resid 54 through 56' Processing helix chain 'd' and resid 83 through 87 removed outlier: 4.106A pdb=" N ALA d 87 " --> pdb=" O GLU d 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.617A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.262A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 410' Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.527A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.813A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.763A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.932A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 824 removed outlier: 3.860A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.814A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.601A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.676A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.661A pdb=" N ALA B 924 " --> pdb=" O GLN B 920 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 963 removed outlier: 3.799A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.660A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 3.644A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET B1029 " --> pdb=" O ALA B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.901A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 32 removed outlier: 3.581A pdb=" N ARG a 31 " --> pdb=" O SER a 28 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE a 32 " --> pdb=" O PHE a 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 28 through 32' Processing helix chain 'a' and resid 87 through 91 removed outlier: 3.879A pdb=" N SER a 91 " --> pdb=" O SER a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 198 removed outlier: 4.014A pdb=" N SER a 197 " --> pdb=" O SER a 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 87 removed outlier: 4.245A pdb=" N ALA b 87 " --> pdb=" O GLU b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 132 removed outlier: 3.560A pdb=" N LEU b 129 " --> pdb=" O SER b 125 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER b 131 " --> pdb=" O GLU b 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 187 through 192 removed outlier: 3.892A pdb=" N ARG b 192 " --> pdb=" O ASP b 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.524A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.780A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.525A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.534A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 removed outlier: 5.853A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.507A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 511 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.590A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 8.209A pdb=" N ASN A 450 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N ARG A 493 " --> pdb=" O ASN A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.075A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.765A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.456A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.634A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A1060 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.613A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.923A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.506A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 48 through 52 removed outlier: 3.745A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.633A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.633A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.005A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.684A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.566A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.514A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.952A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.720A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AD4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.721A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.663A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.972A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'c' and resid 9 through 11 removed outlier: 3.757A pdb=" N TYR c 95 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL c 37 " --> pdb=" O TYR c 95 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N MET c 34 " --> pdb=" O MET c 50 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N MET c 50 " --> pdb=" O MET c 34 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP c 36 " --> pdb=" O ILE c 48 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG c 40 " --> pdb=" O GLY c 44 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY c 44 " --> pdb=" O ARG c 40 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU c 57 " --> pdb=" O HIS c 52 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 9 through 11 removed outlier: 6.667A pdb=" N CYS c 96 " --> pdb=" O TRP c 110 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TRP c 110 " --> pdb=" O CYS c 96 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG c 98 " --> pdb=" O ALA c 108 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP c 106 " --> pdb=" O ASP c 100 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'c' and resid 17 through 23 removed outlier: 3.827A pdb=" N MET c 81 " --> pdb=" O LEU c 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR c 71 " --> pdb=" O TYR c 80 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 4 through 7 removed outlier: 3.812A pdb=" N SER d 7 " --> pdb=" O SER d 22 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER d 22 " --> pdb=" O SER d 7 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS d 23 " --> pdb=" O PHE d 75 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE d 75 " --> pdb=" O CYS d 23 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP d 74 " --> pdb=" O SER d 71 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER d 71 " --> pdb=" O ASP d 74 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 10 through 14 removed outlier: 6.628A pdb=" N LEU d 11 " --> pdb=" O GLU d 109 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS d 111 " --> pdb=" O LEU d 11 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL d 13 " --> pdb=" O LYS d 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'd' and resid 52 through 53 Processing sheet with id=AE6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.595A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.629A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.762A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 244 through 245 Processing sheet with id=AF1, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.393A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.882A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.879A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.678A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.749A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AF8, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.681A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AG1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.841A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AG3, first strand: chain 'a' and resid 9 through 12 removed outlier: 3.709A pdb=" N VAL a 12 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA a 92 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS a 99 " --> pdb=" O TRP a 33 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TRP a 33 " --> pdb=" O LYS a 99 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N MET a 34 " --> pdb=" O MET a 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TRP a 36 " --> pdb=" O ILE a 48 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG a 40 " --> pdb=" O GLY a 44 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 9 through 12 removed outlier: 3.709A pdb=" N VAL a 12 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA a 92 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG a 98 " --> pdb=" O TYR a 109 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR a 109 " --> pdb=" O ARG a 98 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 17 through 23 removed outlier: 3.757A pdb=" N THR a 71 " --> pdb=" O TYR a 80 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 127 through 131 removed outlier: 6.402A pdb=" N TYR a 182 " --> pdb=" O GLY a 151 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER a 187 " --> pdb=" O HIS a 171 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a' and resid 127 through 131 removed outlier: 6.402A pdb=" N TYR a 182 " --> pdb=" O GLY a 151 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 158 through 161 removed outlier: 3.539A pdb=" N THR a 211 " --> pdb=" O HIS a 206 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 5 through 7 removed outlier: 3.701A pdb=" N SER b 7 " --> pdb=" O SER b 22 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER b 22 " --> pdb=" O SER b 7 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS b 23 " --> pdb=" O PHE b 75 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE b 75 " --> pdb=" O CYS b 23 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP b 74 " --> pdb=" O SER b 71 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 10 through 13 removed outlier: 6.256A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP b 39 " --> pdb=" O LEU b 51 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN b 41 " --> pdb=" O LYS b 49 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 10 through 13 removed outlier: 6.256A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS b 94 " --> pdb=" O ALA b 101 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA b 101 " --> pdb=" O HIS b 94 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 118 through 122 removed outlier: 3.540A pdb=" N VAL b 137 " --> pdb=" O PHE b 122 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR b 177 " --> pdb=" O ASN b 142 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 157 through 158 removed outlier: 3.829A pdb=" N TYR b 196 " --> pdb=" O PHE b 213 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE b 213 " --> pdb=" O TYR b 196 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA b 200 " --> pdb=" O ILE b 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE b 209 " --> pdb=" O ALA b 200 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2418 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: 16.49 Time building geometry restraints manager: 12.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9136 1.34 - 1.46: 6545 1.46 - 1.58: 14606 1.58 - 1.70: 0 1.70 - 1.82: 170 Bond restraints: 30457 Sorted by residual: bond pdb=" N LEU C 24 " pdb=" CA LEU C 24 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.87e+01 bond pdb=" N LEU B 24 " pdb=" CA LEU B 24 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.85e+01 bond pdb=" C GLY B 526 " pdb=" N PRO B 527 " ideal model delta sigma weight residual 1.334 1.433 -0.099 2.34e-02 1.83e+03 1.78e+01 bond pdb=" N GLN C 271 " pdb=" CA GLN C 271 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.43e+01 bond pdb=" N LEU A 24 " pdb=" CA LEU A 24 " ideal model delta sigma weight residual 1.452 1.489 -0.036 1.11e-02 8.12e+03 1.07e+01 ... (remaining 30452 not shown) Histogram of bond angle deviations from ideal: 99.92 - 107.07: 1019 107.07 - 114.22: 17020 114.22 - 121.37: 15000 121.37 - 128.52: 8208 128.52 - 135.67: 186 Bond angle restraints: 41433 Sorted by residual: angle pdb=" C ASN B 122 " pdb=" N ALA B 123 " pdb=" CA ALA B 123 " ideal model delta sigma weight residual 121.54 132.51 -10.97 1.91e+00 2.74e-01 3.30e+01 angle pdb=" C GLY B 639 " pdb=" N SER B 640 " pdb=" CA SER B 640 " ideal model delta sigma weight residual 121.54 132.00 -10.46 1.91e+00 2.74e-01 3.00e+01 angle pdb=" C GLY C 639 " pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 121.54 131.61 -10.07 1.91e+00 2.74e-01 2.78e+01 angle pdb=" C CYS B 525 " pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sigma weight residual 117.23 110.67 6.56 1.36e+00 5.41e-01 2.33e+01 angle pdb=" N GLY A 504 " pdb=" CA GLY A 504 " pdb=" C GLY A 504 " ideal model delta sigma weight residual 113.37 119.37 -6.00 1.34e+00 5.57e-01 2.00e+01 ... (remaining 41428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 17711 17.42 - 34.84: 341 34.84 - 52.27: 110 52.27 - 69.69: 15 69.69 - 87.11: 2 Dihedral angle restraints: 18179 sinusoidal: 7093 harmonic: 11086 Sorted by residual: dihedral pdb=" CA LYS B 795 " pdb=" C LYS B 795 " pdb=" N TYR B 796 " pdb=" CA TYR B 796 " ideal model delta harmonic sigma weight residual 180.00 155.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA TYR a 101 " pdb=" C TYR a 101 " pdb=" N ASP a 102 " pdb=" CA ASP a 102 " ideal model delta harmonic sigma weight residual 180.00 156.26 23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ARG C 634 " pdb=" C ARG C 634 " pdb=" N VAL C 635 " pdb=" CA VAL C 635 " ideal model delta harmonic sigma weight residual -180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 18176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3570 0.056 - 0.112: 863 0.112 - 0.169: 199 0.169 - 0.225: 31 0.225 - 0.281: 8 Chirality restraints: 4671 Sorted by residual: chirality pdb=" CB ILE C 312 " pdb=" CA ILE C 312 " pdb=" CG1 ILE C 312 " pdb=" CG2 ILE C 312 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE B 312 " pdb=" CA ILE B 312 " pdb=" CG1 ILE B 312 " pdb=" CG2 ILE B 312 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE b 121 " pdb=" CA ILE b 121 " pdb=" CG1 ILE b 121 " pdb=" CG2 ILE b 121 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 4668 not shown) Planarity restraints: 5342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 295 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 445 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" C VAL A 445 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL A 445 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 446 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.047 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO B 987 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.040 5.00e-02 4.00e+02 ... (remaining 5339 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 9257 2.85 - 3.37: 22275 3.37 - 3.88: 47980 3.88 - 4.39: 50056 4.39 - 4.90: 90211 Nonbonded interactions: 219779 Sorted by model distance: nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.342 2.440 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.345 2.440 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.351 2.440 nonbonded pdb=" O ALA A 879 " pdb=" OG1 THR A 883 " model vdw 2.351 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.352 2.440 ... (remaining 219774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 631 or resid 641 through 1147)) selection = (chain 'C' and (resid 14 through 631 or resid 641 through 1147)) } 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.130 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 81.900 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.130 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 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 : 0.005 0.099 30457 Z= 0.301 Angle : 0.785 10.974 41433 Z= 0.459 Chirality : 0.053 0.281 4671 Planarity : 0.006 0.082 5342 Dihedral : 8.279 87.110 10914 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.89 % Favored : 95.95 % Rotamer: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.11), residues: 3749 helix: -4.92 (0.05), residues: 574 sheet: -0.20 (0.16), residues: 750 loop : -1.57 (0.10), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 33 HIS 0.012 0.001 HIS B 954 PHE 0.026 0.003 PHE B 490 TYR 0.032 0.002 TYR d 53 ARG 0.006 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 930 time to evaluate : 3.206 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 outliers start: 12 outliers final: 6 residues processed: 940 average time/residue: 0.4530 time to fit residues: 657.1249 Evaluate side-chains 669 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 663 time to evaluate : 3.435 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3712 time to fit residues: 8.5436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 0.9990 chunk 286 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 296 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 220 optimal weight: 20.0000 chunk 343 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 66 HIS A 196 ASN A 414 GLN A 703 ASN A 755 GLN A 895 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 239 GLN C 360 ASN C 409 GLN C 519 HIS C 717 ASN C 762 GLN C 895 GLN C 901 GLN C1101 HIS ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 207 HIS ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 717 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN B1083 HIS B1106 GLN B1113 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 GLN b 93 HIS b 194 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30457 Z= 0.252 Angle : 0.637 9.841 41433 Z= 0.334 Chirality : 0.046 0.219 4671 Planarity : 0.005 0.058 5342 Dihedral : 4.677 29.857 4084 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.84 % Favored : 98.13 % Rotamer: Outliers : 2.65 % Allowed : 9.28 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.12), residues: 3749 helix: -2.75 (0.15), residues: 599 sheet: 0.24 (0.15), residues: 873 loop : -1.13 (0.11), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 104 HIS 0.007 0.001 HIS C 207 PHE 0.024 0.002 PHE B 377 TYR 0.017 0.002 TYR b 36 ARG 0.017 0.001 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 710 time to evaluate : 3.378 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 outliers start: 88 outliers final: 44 residues processed: 760 average time/residue: 0.4276 time to fit residues: 512.4192 Evaluate side-chains 665 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 621 time to evaluate : 3.264 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.2628 time to fit residues: 26.4618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 343 optimal weight: 8.9990 chunk 371 optimal weight: 8.9990 chunk 306 optimal weight: 1.9990 chunk 341 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 414 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 965 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 360 ASN ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 895 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** a 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 GLN ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.138 30457 Z= 0.426 Angle : 0.747 11.620 41433 Z= 0.394 Chirality : 0.049 0.235 4671 Planarity : 0.005 0.058 5342 Dihedral : 5.100 22.498 4084 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 3.53 % Allowed : 11.21 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.12), residues: 3749 helix: -0.92 (0.19), residues: 606 sheet: 0.52 (0.17), residues: 840 loop : -1.10 (0.12), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 886 HIS 0.010 0.002 HIS C1058 PHE 0.034 0.003 PHE C 543 TYR 0.028 0.002 TYR A1110 ARG 0.008 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 694 time to evaluate : 3.299 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 outliers start: 117 outliers final: 59 residues processed: 748 average time/residue: 0.4440 time to fit residues: 519.0830 Evaluate side-chains 677 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 618 time to evaluate : 3.322 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.2996 time to fit residues: 37.2056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 2.9990 chunk 258 optimal weight: 0.4980 chunk 178 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 164 optimal weight: 0.5980 chunk 230 optimal weight: 6.9990 chunk 345 optimal weight: 5.9990 chunk 365 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 chunk 327 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 409 GLN C 658 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C 919 ASN C 949 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 955 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN a 35 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 170 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30457 Z= 0.194 Angle : 0.594 9.044 41433 Z= 0.305 Chirality : 0.045 0.224 4671 Planarity : 0.004 0.059 5342 Dihedral : 4.627 22.730 4084 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.63 % Rotamer: Outliers : 1.78 % Allowed : 14.58 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 3749 helix: 0.20 (0.21), residues: 611 sheet: 0.51 (0.16), residues: 877 loop : -0.98 (0.12), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 104 HIS 0.009 0.001 HIS C 954 PHE 0.037 0.002 PHE C 342 TYR 0.025 0.001 TYR A1110 ARG 0.010 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 626 time to evaluate : 3.269 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 outliers start: 59 outliers final: 33 residues processed: 649 average time/residue: 0.4698 time to fit residues: 475.0831 Evaluate side-chains 618 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 585 time to evaluate : 3.347 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3710 time to fit residues: 25.8408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 0.0970 chunk 207 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 272 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 311 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 327 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 409 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN a 35 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30457 Z= 0.222 Angle : 0.594 9.202 41433 Z= 0.306 Chirality : 0.044 0.193 4671 Planarity : 0.004 0.057 5342 Dihedral : 4.467 22.161 4084 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 1.69 % Allowed : 16.06 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 3749 helix: 0.66 (0.22), residues: 613 sheet: 0.49 (0.16), residues: 891 loop : -0.92 (0.12), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 104 HIS 0.011 0.001 HIS C 245 PHE 0.037 0.002 PHE C 55 TYR 0.016 0.001 TYR A1110 ARG 0.006 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 626 time to evaluate : 3.362 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 outliers start: 56 outliers final: 35 residues processed: 644 average time/residue: 0.4626 time to fit residues: 460.5376 Evaluate side-chains 622 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 587 time to evaluate : 3.042 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3017 time to fit residues: 23.3470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 1.9990 chunk 329 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 214 optimal weight: 0.0010 chunk 90 optimal weight: 0.5980 chunk 365 optimal weight: 8.9990 chunk 303 optimal weight: 0.4980 chunk 169 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 120 optimal weight: 0.7980 chunk 192 optimal weight: 0.9980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 271 GLN A 955 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 207 HIS C 245 HIS C 409 GLN C 505 HIS C 762 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN a 35 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30457 Z= 0.184 Angle : 0.580 10.359 41433 Z= 0.296 Chirality : 0.044 0.187 4671 Planarity : 0.004 0.064 5342 Dihedral : 4.373 22.714 4084 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.63 % Allowed : 16.27 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 3749 helix: 0.71 (0.22), residues: 651 sheet: 0.48 (0.17), residues: 894 loop : -0.88 (0.12), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 104 HIS 0.010 0.001 HIS C 245 PHE 0.028 0.001 PHE C 55 TYR 0.029 0.001 TYR C 365 ARG 0.008 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 616 time to evaluate : 3.196 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 outliers start: 54 outliers final: 26 residues processed: 639 average time/residue: 0.4641 time to fit residues: 461.6046 Evaluate side-chains 616 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 590 time to evaluate : 3.360 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3346 time to fit residues: 20.1589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 0.0370 chunk 41 optimal weight: 10.0000 chunk 208 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 206 optimal weight: 0.5980 chunk 307 optimal weight: 0.0170 chunk 204 optimal weight: 3.9990 chunk 364 optimal weight: 6.9990 chunk 228 optimal weight: 0.0010 chunk 222 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 245 HIS ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1113 GLN a 35 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.6817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30457 Z= 0.163 Angle : 0.585 11.472 41433 Z= 0.294 Chirality : 0.043 0.189 4671 Planarity : 0.004 0.047 5342 Dihedral : 4.261 23.367 4084 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.96 % Allowed : 18.02 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 3749 helix: 0.85 (0.22), residues: 663 sheet: 0.53 (0.16), residues: 913 loop : -0.84 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP a 36 HIS 0.008 0.001 HIS C 245 PHE 0.024 0.001 PHE C 55 TYR 0.037 0.001 TYR b 90 ARG 0.006 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 603 time to evaluate : 3.341 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 outliers start: 32 outliers final: 23 residues processed: 616 average time/residue: 0.4887 time to fit residues: 471.6415 Evaluate side-chains 599 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 576 time to evaluate : 3.423 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3201 time to fit residues: 18.5412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 217 optimal weight: 30.0000 chunk 109 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 70 optimal weight: 1.9990 chunk 231 optimal weight: 10.0000 chunk 248 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 245 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN ** a 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.7100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30457 Z= 0.236 Angle : 0.625 10.819 41433 Z= 0.316 Chirality : 0.044 0.179 4671 Planarity : 0.004 0.062 5342 Dihedral : 4.349 22.661 4084 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.18 % Allowed : 18.44 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 3749 helix: 0.85 (0.22), residues: 657 sheet: 0.57 (0.17), residues: 883 loop : -0.88 (0.12), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP a 36 HIS 0.010 0.001 HIS C 245 PHE 0.035 0.002 PHE B 981 TYR 0.027 0.001 TYR B 707 ARG 0.008 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 593 time to evaluate : 3.334 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 outliers start: 39 outliers final: 18 residues processed: 610 average time/residue: 0.4617 time to fit residues: 435.6871 Evaluate side-chains 586 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 568 time to evaluate : 3.364 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2855 time to fit residues: 13.9250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 1.9990 chunk 349 optimal weight: 2.9990 chunk 318 optimal weight: 0.0970 chunk 339 optimal weight: 3.9990 chunk 348 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 306 optimal weight: 2.9990 chunk 321 optimal weight: 0.5980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 422 ASN A 564 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C 544 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1125 ASN ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 170 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.7605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 30457 Z= 0.294 Angle : 0.676 11.828 41433 Z= 0.345 Chirality : 0.046 0.191 4671 Planarity : 0.004 0.057 5342 Dihedral : 4.677 24.233 4084 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.19 % Rotamer: Outliers : 1.11 % Allowed : 18.77 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 3749 helix: 0.75 (0.22), residues: 655 sheet: 0.48 (0.17), residues: 902 loop : -0.97 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP a 36 HIS 0.009 0.002 HIS b 38 PHE 0.026 0.002 PHE B 543 TYR 0.025 0.002 TYR C 380 ARG 0.011 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 615 time to evaluate : 3.401 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 outliers start: 37 outliers final: 23 residues processed: 628 average time/residue: 0.4670 time to fit residues: 455.9130 Evaluate side-chains 600 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 577 time to evaluate : 3.270 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2975 time to fit residues: 16.8004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 359 optimal weight: 20.0000 chunk 219 optimal weight: 20.0000 chunk 170 optimal weight: 2.9990 chunk 249 optimal weight: 0.3980 chunk 376 optimal weight: 4.9990 chunk 346 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN C 49 HIS ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 314 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 GLN ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.8045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 30457 Z= 0.388 Angle : 0.740 11.816 41433 Z= 0.382 Chirality : 0.048 0.231 4671 Planarity : 0.005 0.067 5342 Dihedral : 5.034 26.990 4084 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.32 % Favored : 95.65 % Rotamer: Outliers : 0.93 % Allowed : 19.92 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 3749 helix: 0.50 (0.21), residues: 653 sheet: 0.33 (0.17), residues: 893 loop : -1.13 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 104 HIS 0.008 0.002 HIS B1064 PHE 0.043 0.002 PHE C 562 TYR 0.022 0.002 TYR A 660 ARG 0.011 0.001 ARG C 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 600 time to evaluate : 3.471 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 outliers start: 31 outliers final: 20 residues processed: 611 average time/residue: 0.4691 time to fit residues: 445.1323 Evaluate side-chains 604 residues out of total 3319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 584 time to evaluate : 3.146 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2787 time to fit residues: 14.9044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 0.9990 chunk 238 optimal weight: 5.9990 chunk 319 optimal weight: 0.0470 chunk 91 optimal weight: 2.9990 chunk 276 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 300 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 308 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B1083 HIS ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.172476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132692 restraints weight = 66385.038| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 4.22 r_work: 0.3593 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.8105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30457 Z= 0.226 Angle : 0.674 12.344 41433 Z= 0.342 Chirality : 0.046 0.260 4671 Planarity : 0.004 0.065 5342 Dihedral : 4.804 28.550 4084 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 0.57 % Allowed : 20.94 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 3749 helix: 0.81 (0.22), residues: 641 sheet: 0.32 (0.17), residues: 870 loop : -1.04 (0.12), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP a 36 HIS 0.007 0.001 HIS c 52 PHE 0.037 0.002 PHE B 543 TYR 0.037 0.001 TYR C 365 ARG 0.009 0.001 ARG C 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9021.37 seconds wall clock time: 162 minutes 37.38 seconds (9757.38 seconds total)