Starting phenix.real_space_refine on Sat Mar 23 03:29:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd7_32433/03_2024/7wd7_32433.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd7_32433/03_2024/7wd7_32433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd7_32433/03_2024/7wd7_32433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd7_32433/03_2024/7wd7_32433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd7_32433/03_2024/7wd7_32433.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd7_32433/03_2024/7wd7_32433.pdb" } resolution = 3.5 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= 0.006 sd= 0.106 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 156 5.16 5 C 22467 2.51 5 N 5850 2.21 5 O 6849 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 18": "NH1" <-> "NH2" Residue "b TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35322 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1025} Chain breaks: 6 Chain: "a" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1627 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "b" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1693 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Chain: "B" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 50, 'TRANS': 1022} Chain breaks: 6 Chain: "c" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1627 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "d" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1693 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Chain: "C" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 2, 'PTRANS': 52, 'TRANS': 1024} Chain breaks: 6 Chain: "e" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1627 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "f" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1693 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Time building chain proxies: 18.34, per 1000 atoms: 0.52 Number of scatterers: 35322 At special positions: 0 Unit cell: (160.671, 161.764, 281.994, 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 156 16.00 O 6849 8.00 N 5850 7.00 C 22467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, 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=2.04 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 a 22 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 199 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 94 " distance=2.03 Simple disulfide: pdb=" SG CYS b 139 " - pdb=" SG CYS b 199 " distance=2.03 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 c 22 " - pdb=" SG CYS c 96 " distance=2.03 Simple disulfide: pdb=" SG CYS c 144 " - pdb=" SG CYS c 199 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 94 " distance=2.03 Simple disulfide: pdb=" SG CYS d 139 " - pdb=" SG CYS d 199 " 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 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " 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 e 22 " - pdb=" SG CYS e 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 144 " - pdb=" SG CYS e 199 " distance=2.03 Simple disulfide: pdb=" SG CYS f 23 " - pdb=" SG CYS f 94 " distance=2.03 Simple disulfide: pdb=" SG CYS f 139 " - pdb=" SG CYS f 199 " 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: 12.79 Conformation dependent library (CDL) restraints added in 6.3 seconds 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8496 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 77 sheets defined 17.6% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.555A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.792A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.433A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 390' Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.653A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.616A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.517A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 780 removed outlier: 3.590A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 removed outlier: 3.955A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.532A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.584A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.951A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.648A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.922A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.679A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.429A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 4.164A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A1156 " --> pdb=" O LEU A1152 " (cutoff:3.500A) Processing helix chain 'a' and resid 87 through 91 removed outlier: 4.136A pdb=" N SER a 91 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'b' and resid 128 through 132 Processing helix chain 'b' and resid 188 through 193 removed outlier: 3.604A pdb=" N GLU b 192 " --> pdb=" O LYS b 188 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG b 193 " --> pdb=" O ASP b 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 188 through 193' Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.592A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.683A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.687A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.683A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.523A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 780 removed outlier: 3.616A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 removed outlier: 3.962A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 854 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.570A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.582A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.972A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.627A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (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 965 removed outlier: 3.952A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.661A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.441A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 4.170A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B1155 " --> pdb=" O GLU B1151 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B1156 " --> pdb=" O LEU B1152 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'c' and resid 87 through 91 removed outlier: 3.965A pdb=" N SER c 91 " --> pdb=" O PHE c 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 132 removed outlier: 3.800A pdb=" N LEU d 130 " --> pdb=" O SER d 126 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 193 removed outlier: 3.511A pdb=" N GLU d 192 " --> pdb=" O LYS d 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.603A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.694A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.692A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.504A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 780 removed outlier: 3.596A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 removed outlier: 3.985A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 854 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.505A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.569A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.970A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.637A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.678A 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 965 removed outlier: 3.964A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.683A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.503A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.172A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR C1155 " --> pdb=" O GLU C1151 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C1156 " --> pdb=" O LEU C1152 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing helix chain 'e' and resid 87 through 91 removed outlier: 3.794A pdb=" N SER e 91 " --> pdb=" O PHE e 88 " (cutoff:3.500A) Processing helix chain 'f' and resid 85 through 89 removed outlier: 4.084A pdb=" N LEU f 89 " --> pdb=" O ALA f 86 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 132 removed outlier: 3.792A pdb=" N LEU f 130 " --> pdb=" O SER f 126 " (cutoff:3.500A) Processing helix chain 'f' and resid 188 through 193 removed outlier: 3.500A pdb=" N GLU f 192 " --> pdb=" O LYS f 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.199A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.764A 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: 4.515A 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: 3.520A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.529A pdb=" N GLY A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.523A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.694A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.940A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.793A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.540A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 653 through 655 removed outlier: 5.813A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.538A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.593A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.675A 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 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'a' and resid 5 through 6 removed outlier: 3.521A pdb=" N GLU a 82 " --> pdb=" O THR a 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'a' and resid 10 through 12 removed outlier: 3.677A pdb=" N GLU a 10 " --> pdb=" O LEU a 112 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR a 114 " --> pdb=" O GLU a 10 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL a 12 " --> pdb=" O THR a 114 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL a 113 " --> pdb=" O ALA a 92 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N MET a 34 " --> pdb=" O GLY a 50 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP a 36 " --> pdb=" O ILE a 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP a 57 " --> pdb=" O ASN a 52 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 10 through 12 removed outlier: 3.677A pdb=" N GLU a 10 " --> pdb=" O LEU a 112 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR a 114 " --> pdb=" O GLU a 10 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL a 12 " --> pdb=" O THR a 114 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL a 113 " --> pdb=" O ALA a 92 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE a 106 " --> pdb=" O ARG a 98 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'a' and resid 124 through 128 removed outlier: 3.916A pdb=" N GLY a 143 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL a 185 " --> pdb=" O LEU a 142 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS a 144 " --> pdb=" O SER a 183 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER a 183 " --> pdb=" O CYS a 144 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY a 148 " --> pdb=" O TYR a 179 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER a 184 " --> pdb=" O HIS a 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'a' and resid 124 through 128 removed outlier: 3.916A pdb=" N GLY a 143 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL a 185 " --> pdb=" O LEU a 142 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS a 144 " --> pdb=" O SER a 183 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER a 183 " --> pdb=" O CYS a 144 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY a 148 " --> pdb=" O TYR a 179 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 155 through 158 removed outlier: 3.591A pdb=" N THR a 155 " --> pdb=" O ALA a 202 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN a 200 " --> pdb=" O THR a 157 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL a 197 " --> pdb=" O ILE a 214 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS a 212 " --> pdb=" O CYS a 199 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL a 201 " --> pdb=" O VAL a 210 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL a 210 " --> pdb=" O VAL a 201 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR a 208 " --> pdb=" O HIS a 203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'b' and resid 4 through 7 removed outlier: 3.729A pdb=" N SER b 7 " --> pdb=" O THR b 22 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR b 22 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b' and resid 10 through 12 removed outlier: 7.073A pdb=" N LEU b 11 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP b 41 " --> pdb=" O LEU b 53 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER b 59 " --> pdb=" O TYR b 55 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b' and resid 30 through 31 removed outlier: 3.744A pdb=" N LYS b 36 " --> pdb=" O TYR b 31 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 134 through 144 removed outlier: 6.389A pdb=" N TYR b 178 " --> pdb=" O ASN b 143 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 158 through 159 removed outlier: 3.874A pdb=" N ASN b 150 " --> pdb=" O THR b 202 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS b 212 " --> pdb=" O CYS b 199 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA b 201 " --> pdb=" O ILE b 210 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE b 210 " --> pdb=" O ALA b 201 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.166A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.471A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.514A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.549A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.540A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 325 through 326 removed outlier: 4.966A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 355 through 356 removed outlier: 4.069A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 448 through 453 removed outlier: 7.118A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR B 495 " --> pdb=" O TYR B 451 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 653 through 655 removed outlier: 5.793A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.543A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.570A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE6, first strand: chain 'c' and resid 5 through 6 removed outlier: 3.655A pdb=" N VAL c 18 " --> pdb=" O PHE c 83 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 10 through 12 removed outlier: 6.404A pdb=" N GLU c 10 " --> pdb=" O THR c 114 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL c 93 " --> pdb=" O GLN c 39 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N MET c 34 " --> pdb=" O GLY c 50 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY c 50 " --> pdb=" O MET c 34 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TRP c 36 " --> pdb=" O ILE c 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'c' and resid 10 through 12 removed outlier: 6.404A pdb=" N GLU c 10 " --> pdb=" O THR c 114 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'c' and resid 124 through 128 removed outlier: 3.865A pdb=" N GLY c 143 " --> pdb=" O LEU c 128 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY c 148 " --> pdb=" O TYR c 179 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR c 179 " --> pdb=" O GLY c 148 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'c' and resid 124 through 128 removed outlier: 3.865A pdb=" N GLY c 143 " --> pdb=" O LEU c 128 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY c 148 " --> pdb=" O TYR c 179 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR c 179 " --> pdb=" O GLY c 148 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'c' and resid 155 through 158 removed outlier: 3.922A pdb=" N VAL c 197 " --> pdb=" O ILE c 214 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 4 through 7 removed outlier: 3.646A pdb=" N SER d 7 " --> pdb=" O THR d 22 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR d 22 " --> pdb=" O SER d 7 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'd' and resid 10 through 12 removed outlier: 7.128A pdb=" N LEU d 11 " --> pdb=" O GLU d 111 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP d 41 " --> pdb=" O LEU d 53 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'd' and resid 30 through 31 removed outlier: 3.745A pdb=" N TYR d 31 " --> pdb=" O LYS d 36 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS d 36 " --> pdb=" O TYR d 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'd' and resid 119 through 123 removed outlier: 3.819A pdb=" N THR d 119 " --> pdb=" O ASN d 142 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN d 142 " --> pdb=" O THR d 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER d 121 " --> pdb=" O PHE d 140 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL d 138 " --> pdb=" O PHE d 123 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS d 139 " --> pdb=" O SER d 182 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER d 182 " --> pdb=" O CYS d 139 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR d 178 " --> pdb=" O ASN d 143 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'd' and resid 158 through 159 removed outlier: 3.675A pdb=" N ASN d 150 " --> pdb=" O THR d 202 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR d 197 " --> pdb=" O PHE d 214 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE d 214 " --> pdb=" O TYR d 197 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS d 199 " --> pdb=" O LYS d 212 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS d 212 " --> pdb=" O CYS d 199 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA d 201 " --> pdb=" O ILE d 210 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE d 210 " --> pdb=" O ALA d 201 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.167A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.504A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.502A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.593A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.527A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 325 through 327 removed outlier: 4.243A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 354 through 356 removed outlier: 4.341A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 448 through 453 removed outlier: 7.096A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR C 495 " --> pdb=" O TYR C 451 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 653 through 655 removed outlier: 5.797A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.521A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.611A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AH2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AH3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AH4, first strand: chain 'e' and resid 5 through 6 removed outlier: 3.654A pdb=" N VAL e 18 " --> pdb=" O PHE e 83 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'e' and resid 10 through 12 removed outlier: 6.411A pdb=" N GLU e 10 " --> pdb=" O THR e 114 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL e 93 " --> pdb=" O GLN e 39 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET e 34 " --> pdb=" O GLY e 50 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLY e 50 " --> pdb=" O MET e 34 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TRP e 36 " --> pdb=" O ILE e 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'e' and resid 10 through 12 removed outlier: 6.411A pdb=" N GLU e 10 " --> pdb=" O THR e 114 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'e' and resid 124 through 128 removed outlier: 3.954A pdb=" N GLY e 143 " --> pdb=" O LEU e 128 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY e 148 " --> pdb=" O TYR e 179 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR e 179 " --> pdb=" O GLY e 148 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'e' and resid 124 through 128 removed outlier: 3.954A pdb=" N GLY e 143 " --> pdb=" O LEU e 128 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY e 148 " --> pdb=" O TYR e 179 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR e 179 " --> pdb=" O GLY e 148 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'e' and resid 155 through 158 removed outlier: 3.866A pdb=" N VAL e 197 " --> pdb=" O ILE e 214 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL e 201 " --> pdb=" O VAL e 210 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL e 210 " --> pdb=" O VAL e 201 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR e 208 " --> pdb=" O HIS e 203 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'f' and resid 4 through 7 removed outlier: 3.691A pdb=" N SER f 7 " --> pdb=" O THR f 22 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR f 22 " --> pdb=" O SER f 7 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'f' and resid 10 through 12 removed outlier: 7.172A pdb=" N LEU f 11 " --> pdb=" O GLU f 111 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU f 39 " --> pdb=" O TYR f 55 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR f 55 " --> pdb=" O LEU f 39 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP f 41 " --> pdb=" O LEU f 53 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR f 55 " --> pdb=" O SER f 59 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER f 59 " --> pdb=" O TYR f 55 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'f' and resid 30 through 31 removed outlier: 3.752A pdb=" N TYR f 31 " --> pdb=" O LYS f 36 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS f 36 " --> pdb=" O TYR f 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'f' and resid 119 through 123 removed outlier: 3.824A pdb=" N THR f 119 " --> pdb=" O ASN f 142 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN f 142 " --> pdb=" O THR f 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER f 121 " --> pdb=" O PHE f 140 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL f 138 " --> pdb=" O PHE f 123 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS f 139 " --> pdb=" O SER f 182 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER f 182 " --> pdb=" O CYS f 139 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR f 178 " --> pdb=" O ASN f 143 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'f' and resid 158 through 159 removed outlier: 3.702A pdb=" N ASN f 150 " --> pdb=" O THR f 202 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR f 197 " --> pdb=" O PHE f 214 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE f 214 " --> pdb=" O TYR f 197 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS f 199 " --> pdb=" O LYS f 212 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS f 212 " --> pdb=" O CYS f 199 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA f 201 " --> pdb=" O ILE f 210 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE f 210 " --> pdb=" O ALA f 201 " (cutoff:3.500A) 1221 hydrogen bonds defined for protein. 3312 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: 19.72 Time building geometry restraints manager: 13.93 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: 11312 1.34 - 1.46: 8961 1.46 - 1.58: 15685 1.58 - 1.70: 0 1.70 - 1.82: 201 Bond restraints: 36159 Sorted by residual: bond pdb=" C LEU C 229 " pdb=" N PRO C 230 " ideal model delta sigma weight residual 1.334 1.419 -0.085 2.34e-02 1.83e+03 1.32e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.34e-02 1.83e+03 1.17e+01 bond pdb=" C LYS B 424 " pdb=" N LEU B 425 " ideal model delta sigma weight residual 1.332 1.391 -0.060 1.92e-02 2.71e+03 9.65e+00 bond pdb=" CA CYS C 336 " pdb=" C CYS C 336 " ideal model delta sigma weight residual 1.524 1.560 -0.036 1.26e-02 6.30e+03 8.24e+00 bond pdb=" C LYS C 424 " pdb=" N LEU C 425 " ideal model delta sigma weight residual 1.332 1.386 -0.054 1.92e-02 2.71e+03 7.98e+00 ... (remaining 36154 not shown) Histogram of bond angle deviations from ideal: 99.97 - 108.85: 2189 108.85 - 117.74: 24537 117.74 - 126.62: 22014 126.62 - 135.51: 474 135.51 - 144.39: 1 Bond angle restraints: 49215 Sorted by residual: angle pdb=" N LEU C 335 " pdb=" CA LEU C 335 " pdb=" C LEU C 335 " ideal model delta sigma weight residual 110.30 125.46 -15.16 1.50e+00 4.44e-01 1.02e+02 angle pdb=" C PHE B 329 " pdb=" N PRO B 330 " pdb=" CA PRO B 330 " ideal model delta sigma weight residual 127.00 144.39 -17.39 2.40e+00 1.74e-01 5.25e+01 angle pdb=" C PHE B 329 " pdb=" N PRO B 330 " pdb=" CD PRO B 330 " ideal model delta sigma weight residual 120.60 105.09 15.51 2.20e+00 2.07e-01 4.97e+01 angle pdb=" N PHE B 329 " pdb=" CA PHE B 329 " pdb=" C PHE B 329 " ideal model delta sigma weight residual 108.82 120.09 -11.27 1.65e+00 3.67e-01 4.67e+01 angle pdb=" N SER B 530 " pdb=" CA SER B 530 " pdb=" C SER B 530 " ideal model delta sigma weight residual 108.75 117.15 -8.40 1.71e+00 3.42e-01 2.41e+01 ... (remaining 49210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.85: 21327 25.85 - 51.70: 172 51.70 - 77.55: 24 77.55 - 103.41: 22 103.41 - 129.26: 1 Dihedral angle restraints: 21546 sinusoidal: 8334 harmonic: 13212 Sorted by residual: dihedral pdb=" CA LEU C 335 " pdb=" C LEU C 335 " pdb=" N CYS C 336 " pdb=" CA CYS C 336 " ideal model delta harmonic sigma weight residual -180.00 -50.74 -129.26 0 5.00e+00 4.00e-02 6.68e+02 dihedral pdb=" CA CYS B 291 " pdb=" C CYS B 291 " pdb=" N ALA B 292 " pdb=" CA ALA B 292 " ideal model delta harmonic sigma weight residual 180.00 126.26 53.74 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA CYS C 291 " pdb=" C CYS C 291 " pdb=" N ALA C 292 " pdb=" CA ALA C 292 " ideal model delta harmonic sigma weight residual 180.00 126.41 53.59 0 5.00e+00 4.00e-02 1.15e+02 ... (remaining 21543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4677 0.054 - 0.108: 739 0.108 - 0.162: 137 0.162 - 0.216: 2 0.216 - 0.271: 1 Chirality restraints: 5556 Sorted by residual: chirality pdb=" CA LEU C 335 " pdb=" N LEU C 335 " pdb=" C LEU C 335 " pdb=" CB LEU C 335 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA PHE B 329 " pdb=" N PHE B 329 " pdb=" C PHE B 329 " pdb=" CB PHE B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CA ALA b 114 " pdb=" N ALA b 114 " pdb=" C ALA b 114 " pdb=" CB ALA b 114 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 5553 not shown) Planarity restraints: 6348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " -0.072 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO C 337 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA a 117 " 0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C ALA a 117 " -0.076 2.00e-02 2.50e+03 pdb=" O ALA a 117 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA a 118 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 291 " 0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C CYS A 291 " -0.075 2.00e-02 2.50e+03 pdb=" O CYS A 291 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA A 292 " 0.025 2.00e-02 2.50e+03 ... (remaining 6345 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1030 2.71 - 3.25: 32574 3.25 - 3.80: 52693 3.80 - 4.35: 67017 4.35 - 4.90: 114177 Nonbonded interactions: 267491 Sorted by model distance: nonbonded pdb=" O ASN C 448 " pdb=" OG SER C 494 " model vdw 2.158 2.440 nonbonded pdb=" OH TYR b 42 " pdb=" OE1 GLN b 95 " model vdw 2.158 2.440 nonbonded pdb=" O ASN B 448 " pdb=" OG SER B 494 " model vdw 2.162 2.440 nonbonded pdb=" OG1 THR A 912 " pdb=" NE2 GLN A1106 " model vdw 2.232 2.520 nonbonded pdb=" O GLY A 215 " pdb=" OH TYR A 266 " model vdw 2.238 2.440 ... (remaining 267486 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' selection = chain 'C' } ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' } 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 group one per residue 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: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 14.850 Check model and map are aligned: 0.550 Set scattering table: 0.340 Process input model: 96.150 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.290 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:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5435 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 : 0.002 0.085 36159 Z= 0.148 Angle : 0.601 17.389 49215 Z= 0.365 Chirality : 0.042 0.271 5556 Planarity : 0.004 0.110 6348 Dihedral : 8.226 129.257 12903 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 0.03 % Allowed : 0.18 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.14 % 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: -1.98 (0.10), residues: 4476 helix: -2.88 (0.12), residues: 650 sheet: -0.19 (0.14), residues: 1129 loop : -1.42 (0.10), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.004 0.001 HIS d 203 PHE 0.017 0.001 PHE B 329 TYR 0.015 0.001 TYR C 145 ARG 0.003 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 916 time to evaluate : 4.163 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: A 146 HIS cc_start: -0.1350 (m-70) cc_final: -0.3114 (p-80) REVERT: A 177 MET cc_start: 0.0269 (ttm) cc_final: -0.0171 (mtm) REVERT: A 203 ILE cc_start: 0.8191 (mt) cc_final: 0.7945 (mt) REVERT: A 387 LEU cc_start: 0.7780 (tp) cc_final: 0.7577 (tp) REVERT: A 462 LYS cc_start: 0.7463 (mttt) cc_final: 0.7175 (pttp) REVERT: A 693 ILE cc_start: 0.8200 (pt) cc_final: 0.7978 (pt) REVERT: A 979 ASP cc_start: 0.6730 (t0) cc_final: 0.6361 (t0) REVERT: a 98 ARG cc_start: 0.3755 (ttp80) cc_final: 0.2468 (mmp80) REVERT: b 211 VAL cc_start: 0.3175 (m) cc_final: 0.2562 (p) REVERT: B 608 VAL cc_start: 0.8839 (t) cc_final: 0.8618 (m) REVERT: d 4 MET cc_start: -0.0387 (mtm) cc_final: -0.3271 (ppp) REVERT: C 357 ARG cc_start: 0.4801 (ttm-80) cc_final: 0.4470 (tpm170) REVERT: C 588 THR cc_start: 0.8603 (m) cc_final: 0.8326 (p) REVERT: e 127 PRO cc_start: 0.0326 (Cg_endo) cc_final: -0.0191 (Cg_exo) REVERT: f 4 MET cc_start: -0.0010 (mtm) cc_final: -0.2149 (ptm) outliers start: 1 outliers final: 0 residues processed: 917 average time/residue: 0.4778 time to fit residues: 703.1874 Evaluate side-chains 420 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 3.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 377 optimal weight: 2.9990 chunk 338 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 350 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 213 optimal weight: 0.6980 chunk 260 optimal weight: 0.8980 chunk 405 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 394 ASN A 498 GLN A 644 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1010 GLN A1083 HIS A1106 GLN A1159 HIS a 3 GLN a 159 ASN a 168 HIS b 171 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 506 GLN B 641 ASN B 690 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 955 ASN B1048 HIS B1159 HIS d 34 ASN ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 334 ASN C 506 GLN C 563 GLN C 580 GLN C 613 GLN C 655 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 955 ASN C1048 HIS C1159 HIS ** e 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 168 HIS f 34 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 36159 Z= 0.255 Angle : 0.640 10.162 49215 Z= 0.335 Chirality : 0.046 0.220 5556 Planarity : 0.005 0.094 6348 Dihedral : 4.535 72.255 4854 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 2.64 % Allowed : 8.13 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.93 (0.11), residues: 4476 helix: 0.10 (0.19), residues: 643 sheet: 0.18 (0.13), residues: 1206 loop : -1.21 (0.11), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 886 HIS 0.010 0.001 HIS C 655 PHE 0.024 0.002 PHE B 329 TYR 0.025 0.002 TYR e 32 ARG 0.012 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 464 time to evaluate : 3.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: -0.1206 (m90) cc_final: -0.2937 (p90) REVERT: A 170 TYR cc_start: 0.5136 (t80) cc_final: 0.4784 (t80) REVERT: A 571 ASP cc_start: 0.7505 (t70) cc_final: 0.7154 (t0) REVERT: A 979 ASP cc_start: 0.7146 (t0) cc_final: 0.6875 (t0) REVERT: a 81 MET cc_start: 0.0039 (tpp) cc_final: -0.0477 (ppp) REVERT: a 98 ARG cc_start: 0.3328 (ttp80) cc_final: 0.2227 (mmp80) REVERT: a 139 MET cc_start: -0.0379 (OUTLIER) cc_final: -0.1283 (mpp) REVERT: B 177 MET cc_start: 0.1637 (OUTLIER) cc_final: 0.1171 (mtp) REVERT: B 571 ASP cc_start: 0.7018 (t0) cc_final: 0.6737 (t0) REVERT: B 1092 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6674 (mt-10) REVERT: B 1111 GLU cc_start: 0.7438 (tp30) cc_final: 0.7163 (tp30) REVERT: c 81 MET cc_start: -0.1934 (ttt) cc_final: -0.4379 (ptm) REVERT: C 357 ARG cc_start: 0.5510 (ttm-80) cc_final: 0.4538 (tpm170) REVERT: C 817 PHE cc_start: 0.8511 (t80) cc_final: 0.8105 (t80) REVERT: C 1019 ARG cc_start: 0.8116 (tpt170) cc_final: 0.7851 (ttp80) REVERT: f 4 MET cc_start: 0.0608 (mtm) cc_final: -0.1857 (ttp) outliers start: 105 outliers final: 67 residues processed: 537 average time/residue: 0.4340 time to fit residues: 387.6988 Evaluate side-chains 412 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 343 time to evaluate : 3.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 139 MET Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain d residue 196 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 76 ASP Chi-restraints excluded: chain f residue 198 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 225 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 337 optimal weight: 7.9990 chunk 276 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 406 optimal weight: 0.6980 chunk 439 optimal weight: 6.9990 chunk 362 optimal weight: 2.9990 chunk 403 optimal weight: 0.9990 chunk 138 optimal weight: 0.0980 chunk 326 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 394 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN B1005 GLN B1106 GLN d 44 GLN ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 762 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** e 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36159 Z= 0.207 Angle : 0.565 9.230 49215 Z= 0.294 Chirality : 0.044 0.192 5556 Planarity : 0.004 0.087 6348 Dihedral : 4.396 54.451 4854 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.02 % Favored : 96.94 % Rotamer: Outliers : 2.95 % Allowed : 9.89 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.02 % 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: -0.48 (0.11), residues: 4476 helix: 1.11 (0.20), residues: 655 sheet: 0.30 (0.13), residues: 1222 loop : -1.02 (0.11), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 56 HIS 0.004 0.001 HIS B 655 PHE 0.028 0.002 PHE C 643 TYR 0.023 0.001 TYR e 35 ARG 0.010 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 374 time to evaluate : 4.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: -0.0762 (m90) cc_final: -0.2887 (p90) REVERT: A 571 ASP cc_start: 0.7783 (t70) cc_final: 0.7338 (t0) REVERT: A 979 ASP cc_start: 0.7240 (t0) cc_final: 0.6984 (t0) REVERT: a 81 MET cc_start: 0.0063 (tpp) cc_final: -0.0671 (ppp) REVERT: a 98 ARG cc_start: 0.3591 (ttp80) cc_final: 0.2479 (mmp80) REVERT: a 139 MET cc_start: 0.0005 (OUTLIER) cc_final: -0.0861 (mpp) REVERT: B 571 ASP cc_start: 0.7126 (t0) cc_final: 0.6882 (t0) REVERT: B 975 SER cc_start: 0.9036 (p) cc_final: 0.8767 (m) REVERT: B 996 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8641 (mp) REVERT: B 1031 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: c 81 MET cc_start: -0.1806 (ttt) cc_final: -0.4191 (ptm) REVERT: c 98 ARG cc_start: 0.0842 (tpt-90) cc_final: 0.0349 (mmt180) REVERT: d 186 LEU cc_start: 0.4567 (OUTLIER) cc_final: 0.3844 (mt) REVERT: C 154 GLU cc_start: 0.3491 (OUTLIER) cc_final: 0.3082 (tm-30) REVERT: C 357 ARG cc_start: 0.5732 (ttm-80) cc_final: 0.4632 (tpm170) REVERT: C 730 SER cc_start: 0.9346 (t) cc_final: 0.8837 (p) REVERT: C 817 PHE cc_start: 0.8537 (t80) cc_final: 0.7962 (t80) REVERT: C 856 ASN cc_start: 0.8062 (t0) cc_final: 0.7777 (t0) REVERT: C 1019 ARG cc_start: 0.8200 (tpt170) cc_final: 0.7928 (ttp80) REVERT: f 4 MET cc_start: 0.0841 (mtm) cc_final: -0.1189 (ptp) outliers start: 117 outliers final: 71 residues processed: 454 average time/residue: 0.4205 time to fit residues: 322.2647 Evaluate side-chains 382 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 306 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain a residue 139 MET Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 20 THR Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 76 ASP Chi-restraints excluded: chain f residue 102 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 401 optimal weight: 2.9990 chunk 305 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 194 optimal weight: 0.6980 chunk 273 optimal weight: 8.9990 chunk 408 optimal weight: 1.9990 chunk 432 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 chunk 386 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 751 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 762 GLN C 774 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** e 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 34 ASN f 96 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 36159 Z= 0.259 Angle : 0.604 7.803 49215 Z= 0.313 Chirality : 0.044 0.222 5556 Planarity : 0.005 0.077 6348 Dihedral : 4.664 44.177 4854 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.57 % Favored : 96.38 % Rotamer: Outliers : 3.35 % Allowed : 10.98 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.02 % 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 (0.12), residues: 4476 helix: 1.41 (0.20), residues: 663 sheet: 0.28 (0.14), residues: 1278 loop : -1.02 (0.11), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP f 56 HIS 0.006 0.001 HIS A1058 PHE 0.025 0.002 PHE B 329 TYR 0.021 0.002 TYR A 369 ARG 0.010 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 351 time to evaluate : 4.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: -0.0296 (m90) cc_final: -0.2006 (p-80) REVERT: A 571 ASP cc_start: 0.7780 (t70) cc_final: 0.7219 (t0) REVERT: a 81 MET cc_start: -0.0222 (tpp) cc_final: -0.0515 (ppp) REVERT: a 139 MET cc_start: -0.0672 (OUTLIER) cc_final: -0.1709 (mpp) REVERT: B 661 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7175 (tt0) REVERT: B 918 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: B 975 SER cc_start: 0.9026 (p) cc_final: 0.8735 (m) REVERT: B 996 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8537 (mp) REVERT: B 1031 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: B 1040 VAL cc_start: 0.9335 (OUTLIER) cc_final: 0.9017 (m) REVERT: c 98 ARG cc_start: 0.1218 (tpt-90) cc_final: 0.0528 (mmt180) REVERT: d 186 LEU cc_start: 0.4464 (OUTLIER) cc_final: 0.3737 (mt) REVERT: C 137 ASN cc_start: 0.6458 (OUTLIER) cc_final: 0.6177 (m-40) REVERT: C 336 CYS cc_start: 0.1111 (OUTLIER) cc_final: 0.0640 (p) REVERT: C 730 SER cc_start: 0.9427 (t) cc_final: 0.9060 (p) REVERT: C 884 SER cc_start: 0.9099 (m) cc_final: 0.8741 (p) REVERT: C 935 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: C 1019 ARG cc_start: 0.8204 (tpt170) cc_final: 0.7948 (ttp80) REVERT: e 81 MET cc_start: 0.1835 (ppp) cc_final: 0.1370 (ppp) REVERT: f 4 MET cc_start: 0.1074 (mtm) cc_final: -0.1441 (ttp) outliers start: 133 outliers final: 93 residues processed: 446 average time/residue: 0.4185 time to fit residues: 318.8300 Evaluate side-chains 401 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 299 time to evaluate : 4.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain a residue 139 MET Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain f residue 198 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 359 optimal weight: 0.4980 chunk 245 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 321 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 368 optimal weight: 4.9990 chunk 298 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 chunk 387 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS B 99 ASN B 409 GLN c 43 GLN ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1101 HIS e 61 ASN f 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36159 Z= 0.211 Angle : 0.555 9.737 49215 Z= 0.287 Chirality : 0.043 0.201 5556 Planarity : 0.004 0.068 6348 Dihedral : 4.523 46.037 4854 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.71 % Favored : 96.27 % Rotamer: Outliers : 3.02 % Allowed : 12.06 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.02 % 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: -0.30 (0.12), residues: 4476 helix: 1.70 (0.20), residues: 658 sheet: 0.24 (0.14), residues: 1278 loop : -0.96 (0.12), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP f 56 HIS 0.008 0.001 HIS A 146 PHE 0.032 0.002 PHE B 329 TYR 0.021 0.001 TYR C 741 ARG 0.010 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 312 time to evaluate : 3.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: 0.0043 (m90) cc_final: -0.2377 (p-80) REVERT: A 429 PHE cc_start: 0.0390 (t80) cc_final: 0.0104 (t80) REVERT: A 571 ASP cc_start: 0.7839 (t70) cc_final: 0.7292 (t0) REVERT: A 869 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7336 (mtt) REVERT: A 974 SER cc_start: 0.9071 (p) cc_final: 0.8539 (p) REVERT: A 983 ARG cc_start: 0.7597 (ttm110) cc_final: 0.7318 (ttm-80) REVERT: a 81 MET cc_start: -0.0213 (tpp) cc_final: -0.0492 (ppp) REVERT: B 918 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: B 975 SER cc_start: 0.9015 (p) cc_final: 0.8774 (m) REVERT: B 996 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8514 (mp) REVERT: B 1031 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: B 1041 ASP cc_start: 0.7763 (t0) cc_final: 0.7529 (t0) REVERT: d 186 LEU cc_start: 0.4503 (OUTLIER) cc_final: 0.3766 (mt) REVERT: C 730 SER cc_start: 0.9373 (t) cc_final: 0.9079 (p) REVERT: C 884 SER cc_start: 0.8941 (m) cc_final: 0.8541 (p) REVERT: e 81 MET cc_start: 0.1896 (ppp) cc_final: 0.1483 (ppp) REVERT: f 4 MET cc_start: 0.1000 (mtm) cc_final: -0.1335 (ptm) outliers start: 120 outliers final: 87 residues processed: 404 average time/residue: 0.4298 time to fit residues: 296.7179 Evaluate side-chains 383 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 291 time to evaluate : 4.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 196 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain e residue 75 SER Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 76 ASP Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain f residue 198 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 145 optimal weight: 9.9990 chunk 389 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 432 optimal weight: 6.9990 chunk 359 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** d 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 203 HIS C 149 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1106 GLN e 61 ASN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.6418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 36159 Z= 0.302 Angle : 0.642 10.708 49215 Z= 0.333 Chirality : 0.045 0.259 5556 Planarity : 0.005 0.091 6348 Dihedral : 4.982 48.604 4854 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.76 % Favored : 95.22 % Rotamer: Outliers : 3.90 % Allowed : 11.76 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.02 % 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: -0.53 (0.12), residues: 4476 helix: 1.48 (0.20), residues: 662 sheet: 0.11 (0.14), residues: 1255 loop : -1.10 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A 886 HIS 0.008 0.001 HIS A 146 PHE 0.033 0.002 PHE C 456 TYR 0.023 0.002 TYR C 741 ARG 0.008 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 323 time to evaluate : 4.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: 0.0007 (m90) cc_final: -0.2574 (p-80) REVERT: A 571 ASP cc_start: 0.7922 (t70) cc_final: 0.7534 (t0) REVERT: A 869 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7602 (mtt) REVERT: a 209 LYS cc_start: 0.4017 (mttm) cc_final: 0.3506 (tttm) REVERT: B 509 ARG cc_start: 0.2942 (OUTLIER) cc_final: 0.0668 (mtm180) REVERT: B 596 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8721 (p) REVERT: B 737 ASP cc_start: 0.8133 (t0) cc_final: 0.7780 (t70) REVERT: B 918 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: B 975 SER cc_start: 0.8959 (p) cc_final: 0.8698 (m) REVERT: B 996 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8498 (mp) REVERT: B 1031 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: B 1041 ASP cc_start: 0.7943 (t0) cc_final: 0.7524 (t0) REVERT: d 149 ILE cc_start: 0.0843 (mp) cc_final: 0.0627 (tt) REVERT: C 884 SER cc_start: 0.8976 (m) cc_final: 0.8592 (p) REVERT: e 34 MET cc_start: 0.3978 (mpp) cc_final: 0.2693 (tpp) REVERT: f 4 MET cc_start: 0.0551 (mtm) cc_final: -0.1663 (ptm) outliers start: 155 outliers final: 114 residues processed: 440 average time/residue: 0.4188 time to fit residues: 315.0092 Evaluate side-chains 411 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 291 time to evaluate : 4.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain b residue 21 LEU Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 423 TYR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain e residue 75 SER Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 211 ASP Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 30 LEU Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 76 ASP Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain f residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 416 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 246 optimal weight: 0.9990 chunk 315 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 364 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 430 optimal weight: 0.0050 chunk 269 optimal weight: 0.0770 chunk 262 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 overall best weight: 1.0158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 49 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A 920 GLN ** a 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 39 GLN ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN e 61 ASN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.6558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36159 Z= 0.191 Angle : 0.557 10.560 49215 Z= 0.286 Chirality : 0.043 0.217 5556 Planarity : 0.004 0.122 6348 Dihedral : 4.667 48.484 4854 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.71 % Favored : 96.27 % Rotamer: Outliers : 2.97 % Allowed : 13.12 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.02 % 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: -0.41 (0.12), residues: 4476 helix: 1.79 (0.20), residues: 656 sheet: 0.10 (0.14), residues: 1289 loop : -1.05 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP c 47 HIS 0.007 0.001 HIS A 146 PHE 0.037 0.001 PHE A 429 TYR 0.024 0.001 TYR C 904 ARG 0.007 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 313 time to evaluate : 4.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: -0.0203 (m90) cc_final: -0.2726 (p-80) REVERT: A 571 ASP cc_start: 0.7947 (t70) cc_final: 0.7599 (t0) REVERT: A 740 MET cc_start: 0.7579 (ttp) cc_final: 0.7364 (ttp) REVERT: A 869 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7565 (mtt) REVERT: a 209 LYS cc_start: 0.3829 (mttm) cc_final: 0.3350 (tttm) REVERT: B 596 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8670 (p) REVERT: B 737 ASP cc_start: 0.8060 (t0) cc_final: 0.7663 (t70) REVERT: B 796 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7212 (p0) REVERT: B 918 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: B 975 SER cc_start: 0.8925 (p) cc_final: 0.8680 (m) REVERT: B 996 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8511 (mp) REVERT: B 1031 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: B 1040 VAL cc_start: 0.9276 (m) cc_final: 0.9027 (p) REVERT: C 884 SER cc_start: 0.8900 (m) cc_final: 0.8482 (p) REVERT: e 66 ASP cc_start: 0.4965 (p0) cc_final: 0.4631 (t0) REVERT: f 4 MET cc_start: 0.0342 (mtm) cc_final: -0.1829 (ptm) outliers start: 118 outliers final: 90 residues processed: 403 average time/residue: 0.4137 time to fit residues: 287.2929 Evaluate side-chains 381 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 285 time to evaluate : 3.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain d residue 196 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain e residue 75 SER Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 30 LEU Chi-restraints excluded: chain f residue 42 TYR Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain f residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 266 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 257 optimal weight: 0.7980 chunk 129 optimal weight: 0.0040 chunk 84 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 273 optimal weight: 6.9990 chunk 293 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 338 optimal weight: 6.9990 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** a 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 61 ASN f 34 ASN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.6996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36159 Z= 0.247 Angle : 0.602 9.538 49215 Z= 0.311 Chirality : 0.044 0.214 5556 Planarity : 0.005 0.117 6348 Dihedral : 4.820 48.369 4854 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.35 % Allowed : 13.37 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.02 % 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: -0.50 (0.12), residues: 4476 helix: 1.65 (0.20), residues: 663 sheet: -0.02 (0.14), residues: 1306 loop : -1.06 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP c 47 HIS 0.008 0.001 HIS A 146 PHE 0.033 0.002 PHE A 429 TYR 0.030 0.002 TYR C 904 ARG 0.006 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 304 time to evaluate : 4.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: -0.0274 (m90) cc_final: -0.2927 (p-80) REVERT: A 571 ASP cc_start: 0.7908 (t70) cc_final: 0.7629 (t0) REVERT: A 869 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7671 (mtt) REVERT: a 98 ARG cc_start: 0.3375 (ttp80) cc_final: 0.2984 (mmp80) REVERT: a 209 LYS cc_start: 0.3702 (mttm) cc_final: 0.3258 (tttm) REVERT: B 596 SER cc_start: 0.9177 (OUTLIER) cc_final: 0.8712 (p) REVERT: B 737 ASP cc_start: 0.8100 (t0) cc_final: 0.7853 (t70) REVERT: B 796 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7186 (p0) REVERT: B 918 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: B 975 SER cc_start: 0.8949 (p) cc_final: 0.8684 (m) REVERT: B 996 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8530 (mp) REVERT: B 1031 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: B 1040 VAL cc_start: 0.9278 (m) cc_final: 0.9020 (p) REVERT: B 1041 ASP cc_start: 0.7883 (t0) cc_final: 0.7674 (t0) REVERT: d 196 SER cc_start: 0.4519 (OUTLIER) cc_final: 0.4215 (m) REVERT: C 177 MET cc_start: 0.1981 (ptt) cc_final: 0.1712 (ptt) REVERT: C 884 SER cc_start: 0.8921 (m) cc_final: 0.8533 (p) REVERT: e 66 ASP cc_start: 0.5153 (p0) cc_final: 0.4826 (t0) REVERT: f 4 MET cc_start: 0.0430 (mtm) cc_final: -0.1736 (ptm) outliers start: 133 outliers final: 107 residues processed: 406 average time/residue: 0.4179 time to fit residues: 294.2137 Evaluate side-chains 400 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 286 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain a residue 81 MET Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain b residue 21 LEU Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 423 TYR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain d residue 196 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain e residue 75 SER Chi-restraints excluded: chain e residue 87 THR Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 30 LEU Chi-restraints excluded: chain f residue 42 TYR Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain f residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 391 optimal weight: 2.9990 chunk 412 optimal weight: 6.9990 chunk 376 optimal weight: 0.9990 chunk 401 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 315 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 362 optimal weight: 2.9990 chunk 379 optimal weight: 0.2980 chunk 400 optimal weight: 0.7980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 394 ASN A 493 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 641 ASN d 35 GLN ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.7310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 36159 Z= 0.233 Angle : 0.595 9.727 49215 Z= 0.305 Chirality : 0.044 0.221 5556 Planarity : 0.004 0.113 6348 Dihedral : 4.795 47.266 4854 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.17 % Allowed : 13.72 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.02 % 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: -0.53 (0.12), residues: 4476 helix: 1.75 (0.20), residues: 663 sheet: -0.00 (0.14), residues: 1294 loop : -1.14 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP c 47 HIS 0.007 0.001 HIS A 146 PHE 0.034 0.002 PHE A 429 TYR 0.020 0.001 TYR C 904 ARG 0.005 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 313 time to evaluate : 4.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.5159 (t70) cc_final: 0.4942 (t70) REVERT: A 146 HIS cc_start: -0.0338 (m90) cc_final: -0.2960 (p-80) REVERT: A 177 MET cc_start: 0.2503 (ttm) cc_final: 0.2243 (ttp) REVERT: A 571 ASP cc_start: 0.7984 (t70) cc_final: 0.7727 (t0) REVERT: A 869 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7690 (mtt) REVERT: a 209 LYS cc_start: 0.3671 (mttm) cc_final: 0.3216 (tttm) REVERT: B 596 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8717 (p) REVERT: B 737 ASP cc_start: 0.8153 (t0) cc_final: 0.7662 (t70) REVERT: B 796 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7069 (p0) REVERT: B 975 SER cc_start: 0.9018 (p) cc_final: 0.8731 (m) REVERT: B 996 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8545 (mp) REVERT: B 1031 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: B 1040 VAL cc_start: 0.9291 (m) cc_final: 0.9042 (p) REVERT: B 1041 ASP cc_start: 0.8022 (t0) cc_final: 0.7736 (t0) REVERT: c 98 ARG cc_start: 0.2086 (tpt-90) cc_final: 0.0809 (mmm160) REVERT: d 4 MET cc_start: 0.2286 (mpp) cc_final: 0.1709 (mtp) REVERT: d 196 SER cc_start: 0.4548 (OUTLIER) cc_final: 0.4282 (m) REVERT: C 779 GLN cc_start: 0.8299 (tm-30) cc_final: 0.8052 (tm-30) REVERT: C 884 SER cc_start: 0.8949 (m) cc_final: 0.8536 (p) REVERT: f 4 MET cc_start: 0.0618 (mtm) cc_final: -0.1515 (ptm) outliers start: 126 outliers final: 111 residues processed: 412 average time/residue: 0.4276 time to fit residues: 305.4477 Evaluate side-chains 409 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 292 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain b residue 21 LEU Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 423 TYR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain c residue 89 ASP Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain d residue 196 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain e residue 75 SER Chi-restraints excluded: chain e residue 87 THR Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 30 LEU Chi-restraints excluded: chain f residue 42 TYR Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 76 ASP Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain f residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 263 optimal weight: 6.9990 chunk 424 optimal weight: 7.9990 chunk 259 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 295 optimal weight: 1.9990 chunk 445 optimal weight: 8.9990 chunk 409 optimal weight: 8.9990 chunk 354 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 273 optimal weight: 20.0000 chunk 217 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 370 ASN A 394 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.7479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36159 Z= 0.227 Angle : 0.595 9.786 49215 Z= 0.306 Chirality : 0.043 0.224 5556 Planarity : 0.004 0.112 6348 Dihedral : 4.802 47.097 4854 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.12 % Allowed : 13.97 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % 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: -0.52 (0.12), residues: 4476 helix: 1.87 (0.20), residues: 651 sheet: -0.05 (0.14), residues: 1287 loop : -1.12 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.003 TRP c 47 HIS 0.008 0.001 HIS A 146 PHE 0.033 0.002 PHE A 429 TYR 0.026 0.001 TYR C 904 ARG 0.005 0.000 ARG e 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 299 time to evaluate : 4.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.5164 (t70) cc_final: 0.4917 (t70) REVERT: A 146 HIS cc_start: -0.0192 (m90) cc_final: -0.2853 (p-80) REVERT: A 177 MET cc_start: 0.2873 (ttm) cc_final: 0.1626 (ttt) REVERT: A 571 ASP cc_start: 0.7971 (t70) cc_final: 0.7727 (t0) REVERT: A 869 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7691 (mtt) REVERT: a 209 LYS cc_start: 0.3798 (mttm) cc_final: 0.3299 (tttm) REVERT: b 50 PRO cc_start: 0.2132 (Cg_exo) cc_final: 0.1864 (Cg_endo) REVERT: B 596 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8717 (p) REVERT: B 737 ASP cc_start: 0.8148 (t0) cc_final: 0.7646 (t70) REVERT: B 796 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7103 (p0) REVERT: B 975 SER cc_start: 0.9022 (p) cc_final: 0.8756 (m) REVERT: B 996 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8540 (mp) REVERT: B 1031 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: B 1041 ASP cc_start: 0.8022 (t0) cc_final: 0.7747 (t0) REVERT: d 4 MET cc_start: 0.2118 (mpp) cc_final: 0.1737 (mtp) REVERT: d 196 SER cc_start: 0.4436 (OUTLIER) cc_final: 0.4171 (m) REVERT: C 177 MET cc_start: 0.2008 (ptt) cc_final: 0.1726 (ptt) REVERT: C 779 GLN cc_start: 0.8246 (tm-30) cc_final: 0.8022 (tm-30) REVERT: C 884 SER cc_start: 0.8933 (m) cc_final: 0.8522 (p) REVERT: f 4 MET cc_start: 0.0646 (mtm) cc_final: -0.1497 (ptm) outliers start: 124 outliers final: 108 residues processed: 396 average time/residue: 0.4166 time to fit residues: 284.1279 Evaluate side-chains 404 residues out of total 3972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 290 time to evaluate : 4.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain b residue 21 LEU Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 423 TYR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain c residue 89 ASP Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain d residue 196 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain e residue 75 SER Chi-restraints excluded: chain e residue 87 THR Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 42 TYR Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 76 ASP Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain f residue 170 ASP Chi-restraints excluded: chain f residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9018 > 50: distance: 4 - 8: 13.507 distance: 8 - 9: 12.304 distance: 8 - 191: 10.381 distance: 9 - 10: 17.473 distance: 9 - 12: 7.577 distance: 10 - 11: 14.095 distance: 10 - 16: 20.756 distance: 11 - 188: 26.284 distance: 12 - 13: 28.300 distance: 12 - 14: 25.244 distance: 13 - 15: 13.698 distance: 16 - 17: 3.251 distance: 17 - 20: 17.540 distance: 18 - 19: 6.969 distance: 18 - 21: 19.230 distance: 21 - 22: 20.288 distance: 21 - 181: 12.807 distance: 22 - 23: 22.554 distance: 22 - 25: 23.985 distance: 23 - 24: 21.041 distance: 23 - 29: 36.202 distance: 25 - 26: 20.707 distance: 25 - 27: 10.151 distance: 26 - 28: 17.065 distance: 29 - 30: 26.986 distance: 29 - 35: 16.210 distance: 30 - 31: 29.063 distance: 30 - 33: 8.922 distance: 31 - 32: 15.888 distance: 31 - 36: 31.254 distance: 33 - 34: 15.377 distance: 34 - 35: 21.230 distance: 36 - 37: 5.110 distance: 37 - 38: 15.179 distance: 37 - 40: 12.280 distance: 38 - 39: 24.657 distance: 38 - 43: 33.236 distance: 40 - 41: 25.939 distance: 40 - 42: 43.604 distance: 43 - 44: 17.389 distance: 44 - 45: 31.501 distance: 44 - 47: 6.889 distance: 45 - 46: 9.219 distance: 45 - 51: 35.577 distance: 47 - 48: 9.515 distance: 48 - 49: 7.916 distance: 48 - 50: 18.326 distance: 51 - 52: 11.809 distance: 52 - 53: 9.390 distance: 52 - 55: 25.358 distance: 53 - 54: 9.418 distance: 55 - 56: 16.469 distance: 56 - 57: 31.071 distance: 56 - 58: 23.306 distance: 57 - 59: 22.927 distance: 58 - 60: 20.381 distance: 59 - 61: 4.603 distance: 60 - 61: 4.710 distance: 62 - 63: 24.649 distance: 62 - 150: 29.443 distance: 63 - 64: 10.506 distance: 63 - 66: 18.870 distance: 64 - 65: 22.823 distance: 64 - 69: 13.511 distance: 65 - 147: 30.749 distance: 66 - 67: 21.528 distance: 66 - 68: 20.015 distance: 69 - 70: 26.972 distance: 70 - 71: 27.262 distance: 70 - 73: 23.891 distance: 71 - 72: 22.058 distance: 71 - 77: 57.696 distance: 73 - 74: 11.510 distance: 73 - 75: 14.931 distance: 74 - 76: 22.378 distance: 78 - 79: 54.990 distance: 79 - 80: 13.082 distance: 79 - 83: 23.931 distance: 80 - 129: 32.437 distance: 81 - 82: 41.097 distance: 90 - 122: 3.123