Starting phenix.real_space_refine (version: dev) on Mon May 16 05:34:27 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/05_2022/7wk9_32563.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/05_2022/7wk9_32563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/05_2022/7wk9_32563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/05_2022/7wk9_32563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/05_2022/7wk9_32563.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk9_32563/05_2022/7wk9_32563.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "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 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 29907 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "C" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 54, 'CIS': 2, 'TRANS': 1000} Chain breaks: 7 Chain: "c" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "d" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 102, 'PCIS': 3} Chain: "B" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 54, 'CIS': 2, 'TRANS': 1000} Chain breaks: 7 Chain: "a" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 201, 'PCIS': 2} Chain: "b" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 201, 'PCIS': 4} Time building chain proxies: 16.99, per 1000 atoms: 0.57 Number of scatterers: 29907 At special positions: 0 Unit cell: (185.81, 137.718, 196.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 5684 8.00 N 4991 7.00 C 19096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 96 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 92 " distance=2.03 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 a 22 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS a 147 " - pdb=" SG CYS a 202 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 92 " distance=2.03 Simple disulfide: pdb=" SG CYS b 138 " - pdb=" SG CYS b 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.61 Conformation dependent library (CDL) restraints added in 4.6 seconds 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7172 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 68 sheets defined 19.7% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.284A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.566A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 removed outlier: 4.394A pdb=" N ALA A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.878A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.511A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.830A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 removed outlier: 3.505A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 890 removed outlier: 4.058A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 4.204A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.319A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.783A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (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 966 removed outlier: 4.019A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.039A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.265A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.994A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 634 through 639 removed outlier: 4.104A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY C 639 " --> pdb=" O TYR C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.577A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.857A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.666A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.567A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.627A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.448A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (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: 3.942A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.811A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.777A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'c' and resid 87 through 91 removed outlier: 3.690A pdb=" N SER c 91 " --> pdb=" O SER c 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 83 through 87 removed outlier: 3.733A pdb=" N ALA d 87 " --> pdb=" O GLU d 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.678A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.162A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 410' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.674A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.986A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.534A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (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 782 removed outlier: 3.823A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 824 removed outlier: 4.007A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.608A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.606A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.535A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (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: 3.902A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.787A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'a' and resid 87 through 91 removed outlier: 3.570A pdb=" N SER a 91 " --> pdb=" O SER a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 198 removed outlier: 3.923A pdb=" N SER a 197 " --> pdb=" O SER a 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 87 removed outlier: 3.820A pdb=" N ALA b 87 " --> pdb=" O GLU b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 132 Processing helix chain 'b' and resid 187 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.149A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.682A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.252A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.636A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.445A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.055A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.775A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.171A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 454 removed outlier: 7.055A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 495 " --> pdb=" O TYR A 451 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.806A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.582A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.468A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.545A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.426A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.983A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.626A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.815A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.881A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 316 removed outlier: 3.608A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.054A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 354 through 359 removed outlier: 3.637A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.255A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AD3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.691A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.628A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.316A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.815A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'c' and resid 3 through 5 Processing sheet with id=AD8, first strand: chain 'c' and resid 9 through 11 removed outlier: 3.605A pdb=" N ALA c 92 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N MET c 34 " --> pdb=" O MET c 50 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N MET c 50 " --> pdb=" O MET c 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP c 36 " --> pdb=" O ILE c 48 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG c 40 " --> pdb=" O GLY c 44 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'c' and resid 9 through 11 removed outlier: 3.605A pdb=" N ALA c 92 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS c 96 " --> pdb=" O TRP c 110 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TRP c 110 " --> pdb=" O CYS c 96 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG c 98 " --> pdb=" O ALA c 108 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 4 through 7 removed outlier: 3.586A pdb=" N SER d 7 " --> pdb=" O SER d 22 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER d 22 " --> pdb=" O SER d 7 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'd' and resid 10 through 14 removed outlier: 6.496A pdb=" N LEU d 11 " --> pdb=" O GLU d 109 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS d 111 " --> pdb=" O LEU d 11 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL d 13 " --> pdb=" O LYS d 111 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE d 52 " --> pdb=" O TRP d 39 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLN d 41 " --> pdb=" O LEU d 50 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU d 50 " --> pdb=" O GLN d 41 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER d 57 " --> pdb=" O TYR d 53 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 10 through 14 removed outlier: 6.496A pdb=" N LEU d 11 " --> pdb=" O GLU d 109 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS d 111 " --> pdb=" O LEU d 11 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL d 13 " --> pdb=" O LYS d 111 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS d 94 " --> pdb=" O ALA d 101 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA d 101 " --> pdb=" O HIS d 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AE5, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.511A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.511A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.744A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.536A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU B 132 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.536A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 244 through 245 Processing sheet with id=AF2, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.360A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.836A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.907A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AF7, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.203A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AF9, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.604A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.541A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.829A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AG4, first strand: chain 'a' and resid 3 through 5 Processing sheet with id=AG5, first strand: chain 'a' and resid 9 through 12 removed outlier: 3.617A pdb=" N ALA a 92 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS a 99 " --> pdb=" O TRP a 33 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TRP a 33 " --> pdb=" O LYS a 99 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET a 34 " --> pdb=" O MET a 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP a 36 " --> pdb=" O ILE a 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 127 through 131 removed outlier: 6.208A pdb=" N TYR a 182 " --> pdb=" O GLY a 151 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a' and resid 127 through 131 removed outlier: 6.208A pdb=" N TYR a 182 " --> pdb=" O GLY a 151 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 158 through 161 Processing sheet with id=AG9, first strand: chain 'b' and resid 4 through 7 removed outlier: 3.587A pdb=" N SER b 7 " --> pdb=" O SER b 22 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER b 22 " --> pdb=" O SER b 7 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP b 74 " --> pdb=" O SER b 71 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 10 through 14 removed outlier: 6.360A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS b 111 " --> pdb=" O LEU b 11 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL b 13 " --> pdb=" O LYS b 111 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA b 88 " --> pdb=" O LEU b 108 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE b 52 " --> pdb=" O TRP b 39 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLN b 41 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU b 50 " --> pdb=" O GLN b 41 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 10 through 14 removed outlier: 6.360A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS b 111 " --> pdb=" O LEU b 11 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL b 13 " --> pdb=" O LYS b 111 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA b 88 " --> pdb=" O LEU b 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS b 94 " --> pdb=" O ALA b 101 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA b 101 " --> pdb=" O HIS b 94 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 30 through 31 Processing sheet with id=AH4, first strand: chain 'b' and resid 118 through 122 removed outlier: 6.218A pdb=" N TYR b 177 " --> pdb=" O ASN b 142 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 157 through 158 removed outlier: 6.215A pdb=" N HIS b 202 " --> pdb=" O SER b 207 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER b 207 " --> pdb=" O HIS b 202 " (cutoff:3.500A) 1153 hydrogen bonds defined for protein. 3114 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: 14.89 Time building geometry restraints manager: 12.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9589 1.34 - 1.46: 7463 1.46 - 1.58: 13394 1.58 - 1.70: 0 1.70 - 1.82: 176 Bond restraints: 30622 Sorted by residual: bond pdb=" C GLN C 271 " pdb=" N PRO C 272 " ideal model delta sigma weight residual 1.334 1.441 -0.107 2.34e-02 1.83e+03 2.10e+01 bond pdb=" C GLN A 271 " pdb=" N PRO A 272 " ideal model delta sigma weight residual 1.334 1.439 -0.105 2.34e-02 1.83e+03 2.03e+01 bond pdb=" C PRO B 25 " pdb=" N PRO B 26 " ideal model delta sigma weight residual 1.334 1.405 -0.071 2.34e-02 1.83e+03 9.30e+00 bond pdb=" C PRO C 25 " pdb=" N PRO C 26 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.76e+00 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 1.99e+00 ... (remaining 30617 not shown) Histogram of bond angle deviations from ideal: 100.26 - 107.01: 954 107.01 - 113.77: 16744 113.77 - 120.52: 11645 120.52 - 127.27: 11996 127.27 - 134.03: 310 Bond angle restraints: 41649 Sorted by residual: angle pdb=" C THR A 887 " pdb=" N PHE A 888 " pdb=" CA PHE A 888 " ideal model delta sigma weight residual 121.58 114.62 6.96 1.95e+00 2.63e-01 1.27e+01 angle pdb=" N GLY A 757 " pdb=" CA GLY A 757 " pdb=" C GLY A 757 " ideal model delta sigma weight residual 110.86 116.34 -5.48 1.84e+00 2.95e-01 8.88e+00 angle pdb=" N GLY B 757 " pdb=" CA GLY B 757 " pdb=" C GLY B 757 " ideal model delta sigma weight residual 110.86 116.11 -5.25 1.84e+00 2.95e-01 8.14e+00 angle pdb=" N ARG B 158 " pdb=" CA ARG B 158 " pdb=" C ARG B 158 " ideal model delta sigma weight residual 111.00 118.94 -7.94 2.80e+00 1.28e-01 8.03e+00 angle pdb=" C ASN B 122 " pdb=" N ALA B 123 " pdb=" CA ALA B 123 " ideal model delta sigma weight residual 121.54 126.76 -5.22 1.91e+00 2.74e-01 7.47e+00 ... (remaining 41644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 17883 15.89 - 31.78: 289 31.78 - 47.67: 95 47.67 - 63.56: 16 63.56 - 79.45: 1 Dihedral angle restraints: 18284 sinusoidal: 7144 harmonic: 11140 Sorted by residual: dihedral pdb=" CA TYR c 101 " pdb=" C TYR c 101 " pdb=" N ASP c 102 " pdb=" CA ASP c 102 " ideal model delta harmonic sigma weight residual 180.00 152.97 27.03 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA PHE B 157 " pdb=" C PHE B 157 " pdb=" N ARG B 158 " pdb=" CA ARG B 158 " ideal model delta harmonic sigma weight residual 0.00 21.21 -21.21 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA PHE C 157 " pdb=" C PHE C 157 " pdb=" N ARG C 158 " pdb=" CA ARG C 158 " ideal model delta harmonic sigma weight residual 0.00 20.04 -20.04 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 18281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2881 0.029 - 0.059: 1178 0.059 - 0.088: 275 0.088 - 0.117: 319 0.117 - 0.146: 36 Chirality restraints: 4689 Sorted by residual: chirality pdb=" CA ILE b 148 " pdb=" N ILE b 148 " pdb=" C ILE b 148 " pdb=" CB ILE b 148 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE B 95 " pdb=" N ILE B 95 " pdb=" C ILE B 95 " pdb=" CB ILE B 95 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE C 95 " pdb=" N ILE C 95 " pdb=" C ILE C 95 " pdb=" CB ILE C 95 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 4686 not shown) Planarity restraints: 5372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO A 295 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 25 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO A 26 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 578 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO B 579 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 579 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 579 " -0.023 5.00e-02 4.00e+02 ... (remaining 5369 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 695 2.70 - 3.25: 27772 3.25 - 3.80: 44676 3.80 - 4.35: 59615 4.35 - 4.90: 99337 Nonbonded interactions: 232095 Sorted by model distance: nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.151 2.440 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.166 2.440 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.185 2.440 nonbonded pdb=" OG SER A 968 " pdb=" O GLN C 755 " model vdw 2.207 2.440 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.217 2.440 ... (remaining 232090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 631 or resid 641 through 1147)) selection = (chain 'C' and (resid 14 through 631 or resid 641 through 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 19096 2.51 5 N 4991 2.21 5 O 5684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.980 Check model and map are aligned: 0.450 Convert atoms to be neutral: 0.280 Process input model: 79.600 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4833 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 0.107 30622 Z= 0.114 Angle : 0.467 8.801 41649 Z= 0.263 Chirality : 0.041 0.146 4689 Planarity : 0.003 0.054 5372 Dihedral : 7.124 79.452 10983 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.11), residues: 3767 helix: -3.37 (0.12), residues: 635 sheet: -0.27 (0.14), residues: 947 loop : -1.15 (0.11), residues: 2185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 938 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 938 average time/residue: 0.4495 time to fit residues: 649.3844 Evaluate side-chains 668 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 668 time to evaluate : 3.374 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 0.3980 chunk 286 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 296 optimal weight: 1.9990 chunk 114 optimal weight: 0.0000 chunk 180 optimal weight: 2.9990 chunk 220 optimal weight: 40.0000 chunk 343 optimal weight: 0.8980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 66 HIS A 207 HIS A 394 ASN A 606 ASN A 641 ASN A 787 GLN A 895 GLN A1048 HIS A1083 HIS A1134 ASN C 207 HIS C 245 HIS C 360 ASN C 519 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 717 ASN C 787 GLN C 895 GLN C 901 GLN C 954 HIS C 955 ASN C 965 GLN C1002 GLN C1083 HIS C1113 GLN B 14 GLN B 207 HIS B 317 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN B 895 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1002 GLN B1113 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 194 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5149 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 30622 Z= 0.215 Angle : 0.634 12.385 41649 Z= 0.328 Chirality : 0.045 0.220 4689 Planarity : 0.005 0.109 5372 Dihedral : 4.172 27.093 4105 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.90 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.12), residues: 3767 helix: -0.63 (0.18), residues: 681 sheet: 0.14 (0.14), residues: 1016 loop : -0.88 (0.12), residues: 2070 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 702 time to evaluate : 3.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 37 residues processed: 733 average time/residue: 0.4267 time to fit residues: 492.4901 Evaluate side-chains 645 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 608 time to evaluate : 3.392 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2909 time to fit residues: 25.8567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 343 optimal weight: 4.9990 chunk 371 optimal weight: 0.0060 chunk 306 optimal weight: 2.9990 chunk 341 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 275 optimal weight: 0.0570 overall best weight: 0.7716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 641 ASN A1036 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS C 66 HIS ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 703 ASN C 801 ASN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C1074 ASN C1088 HIS B 66 HIS B 121 ASN B 343 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 935 GLN B 955 ASN B1113 GLN B1119 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5296 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 30622 Z= 0.224 Angle : 0.597 10.725 41649 Z= 0.308 Chirality : 0.045 0.198 4689 Planarity : 0.005 0.100 5372 Dihedral : 4.176 25.178 4105 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.20 % Favored : 97.74 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.13), residues: 3767 helix: 0.36 (0.20), residues: 683 sheet: 0.24 (0.15), residues: 1014 loop : -0.79 (0.12), residues: 2070 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 648 time to evaluate : 3.451 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 outliers start: 62 outliers final: 35 residues processed: 675 average time/residue: 0.4351 time to fit residues: 461.0848 Evaluate side-chains 627 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 592 time to evaluate : 3.449 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3234 time to fit residues: 25.5944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 230 optimal weight: 30.0000 chunk 345 optimal weight: 0.9990 chunk 365 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 327 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 914 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 658 ASN C 703 ASN C 914 ASN C 955 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 314 GLN B 343 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** a 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5626 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.124 30622 Z= 0.450 Angle : 0.752 11.869 41649 Z= 0.394 Chirality : 0.049 0.307 4689 Planarity : 0.006 0.108 5372 Dihedral : 4.916 22.255 4105 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.81 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 3767 helix: 0.60 (0.20), residues: 652 sheet: 0.25 (0.15), residues: 1006 loop : -0.95 (0.12), residues: 2109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 663 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 58 residues processed: 706 average time/residue: 0.4594 time to fit residues: 511.4659 Evaluate side-chains 654 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 596 time to evaluate : 3.635 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.3091 time to fit residues: 37.6870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 0.4980 chunk 207 optimal weight: 0.6980 chunk 5 optimal weight: 0.0870 chunk 272 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 311 optimal weight: 0.5980 chunk 252 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 0.6980 chunk 327 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 914 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 173 GLN C 188 ASN C 207 HIS ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 314 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1074 ASN B1119 ASN ** a 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5531 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.089 30622 Z= 0.204 Angle : 0.623 11.069 41649 Z= 0.318 Chirality : 0.045 0.197 4689 Planarity : 0.005 0.103 5372 Dihedral : 4.546 23.143 4105 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.28 % Favored : 97.66 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.13), residues: 3767 helix: 1.14 (0.21), residues: 649 sheet: 0.28 (0.16), residues: 993 loop : -0.90 (0.12), residues: 2125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 618 time to evaluate : 3.706 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 outliers start: 60 outliers final: 34 residues processed: 648 average time/residue: 0.4653 time to fit residues: 474.5717 Evaluate side-chains 598 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 564 time to evaluate : 3.630 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3184 time to fit residues: 24.8585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 1.9990 chunk 329 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 214 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 365 optimal weight: 6.9990 chunk 303 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 965 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B1106 GLN B1119 ASN ** a 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5588 moved from start: 0.6324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.099 30622 Z= 0.257 Angle : 0.642 11.266 41649 Z= 0.327 Chirality : 0.045 0.190 4689 Planarity : 0.005 0.102 5372 Dihedral : 4.459 20.266 4105 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.81 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 3767 helix: 1.14 (0.21), residues: 655 sheet: 0.32 (0.16), residues: 1005 loop : -0.92 (0.13), residues: 2107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 600 time to evaluate : 3.534 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 outliers start: 54 outliers final: 31 residues processed: 624 average time/residue: 0.4486 time to fit residues: 435.1580 Evaluate side-chains 599 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 568 time to evaluate : 3.533 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3183 time to fit residues: 22.1317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 208 optimal weight: 0.8980 chunk 267 optimal weight: 5.9990 chunk 206 optimal weight: 0.6980 chunk 307 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 364 optimal weight: 10.0000 chunk 228 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 168 optimal weight: 0.1980 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 422 ASN A 914 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN C1113 GLN ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1119 ASN ** a 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5637 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 30622 Z= 0.277 Angle : 0.662 11.770 41649 Z= 0.339 Chirality : 0.045 0.197 4689 Planarity : 0.005 0.121 5372 Dihedral : 4.569 23.729 4105 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.66 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 3767 helix: 1.03 (0.21), residues: 674 sheet: 0.21 (0.16), residues: 1020 loop : -0.95 (0.13), residues: 2073 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 611 time to evaluate : 3.770 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 outliers start: 46 outliers final: 30 residues processed: 625 average time/residue: 0.4435 time to fit residues: 433.0317 Evaluate side-chains 616 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 586 time to evaluate : 3.078 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2715 time to fit residues: 19.0818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 0.0980 chunk 145 optimal weight: 9.9990 chunk 217 optimal weight: 30.0000 chunk 109 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 231 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 286 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5628 moved from start: 0.6869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.142 30622 Z= 0.263 Angle : 0.679 11.699 41649 Z= 0.346 Chirality : 0.045 0.196 4689 Planarity : 0.006 0.128 5372 Dihedral : 4.485 22.191 4105 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.63 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 3767 helix: 1.13 (0.21), residues: 666 sheet: 0.20 (0.16), residues: 1047 loop : -0.96 (0.13), residues: 2054 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 604 time to evaluate : 3.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 22 residues processed: 623 average time/residue: 0.4510 time to fit residues: 442.4710 Evaluate side-chains 599 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 577 time to evaluate : 3.452 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3007 time to fit residues: 16.6816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 0.9990 chunk 349 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 339 optimal weight: 3.9990 chunk 348 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 147 optimal weight: 8.9990 chunk 266 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 306 optimal weight: 2.9990 chunk 321 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 703 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN B1119 ASN ** a 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 35 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5697 moved from start: 0.7189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.127 30622 Z= 0.317 Angle : 0.712 12.881 41649 Z= 0.365 Chirality : 0.046 0.213 4689 Planarity : 0.006 0.134 5372 Dihedral : 4.659 21.793 4105 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.18 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.13), residues: 3767 helix: 0.94 (0.21), residues: 674 sheet: 0.18 (0.16), residues: 1020 loop : -1.03 (0.13), residues: 2073 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 596 time to evaluate : 3.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 23 residues processed: 604 average time/residue: 0.4497 time to fit residues: 426.0574 Evaluate side-chains 597 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 574 time to evaluate : 3.900 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3011 time to fit residues: 18.2115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 0.8980 chunk 222 optimal weight: 40.0000 chunk 359 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 170 optimal weight: 0.9990 chunk 249 optimal weight: 0.4980 chunk 376 optimal weight: 0.7980 chunk 346 optimal weight: 0.6980 chunk 299 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** a 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 35 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5656 moved from start: 0.7297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.149 30622 Z= 0.250 Angle : 0.706 17.192 41649 Z= 0.360 Chirality : 0.045 0.250 4689 Planarity : 0.006 0.145 5372 Dihedral : 4.584 22.196 4105 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.37 % Favored : 96.58 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 3767 helix: 1.11 (0.21), residues: 668 sheet: 0.22 (0.16), residues: 1030 loop : -1.04 (0.13), residues: 2069 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 584 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 590 average time/residue: 0.4436 time to fit residues: 410.9306 Evaluate side-chains 581 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 568 time to evaluate : 3.508 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3777 time to fit residues: 13.1059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 0.6980 chunk 238 optimal weight: 4.9990 chunk 319 optimal weight: 0.0470 chunk 91 optimal weight: 1.9990 chunk 276 optimal weight: 6.9990 chunk 44 optimal weight: 50.0000 chunk 83 optimal weight: 2.9990 chunk 300 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 308 optimal weight: 0.5980 chunk 38 optimal weight: 0.0970 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN C 173 GLN C 188 ASN C 207 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1119 ASN B1142 GLN ** a 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 35 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.174416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.136256 restraints weight = 69291.035| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 3.99 r_work: 0.3788 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work: 0.3764 rms_B_bonded: 3.73 restraints_weight: 0.1250 r_work: 0.3752 rms_B_bonded: 3.79 restraints_weight: 0.0625 r_work: 0.3739 rms_B_bonded: 3.88 restraints_weight: 0.0312 r_work: 0.3725 rms_B_bonded: 3.99 restraints_weight: 0.0156 r_work: 0.3711 rms_B_bonded: 4.12 restraints_weight: 0.0078 r_work: 0.3696 rms_B_bonded: 4.29 restraints_weight: 0.0039 r_work: 0.3681 rms_B_bonded: 4.47 restraints_weight: 0.0020 r_work: 0.3665 rms_B_bonded: 4.69 restraints_weight: 0.0010 r_work: 0.3647 rms_B_bonded: 4.93 restraints_weight: 0.0005 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.7350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.152 30622 Z= 0.213 Angle : 0.691 17.347 41649 Z= 0.351 Chirality : 0.045 0.194 4689 Planarity : 0.006 0.141 5372 Dihedral : 4.489 26.913 4105 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.37 % Favored : 96.58 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.13), residues: 3767 helix: 1.29 (0.21), residues: 660 sheet: 0.19 (0.15), residues: 1062 loop : -1.01 (0.13), residues: 2045 =============================================================================== Job complete usr+sys time: 8074.28 seconds wall clock time: 146 minutes 0.85 seconds (8760.85 seconds total)