Starting phenix.real_space_refine on Sun Dec 17 06:27:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu3_3958/12_2023/6eu3_3958_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu3_3958/12_2023/6eu3_3958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu3_3958/12_2023/6eu3_3958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu3_3958/12_2023/6eu3_3958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu3_3958/12_2023/6eu3_3958_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu3_3958/12_2023/6eu3_3958_neut.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 Mg 1 5.21 5 S 207 5.16 5 C 24312 2.51 5 N 6586 2.21 5 O 7218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A ARG 1187": "NH1" <-> "NH2" Residue "A ARG 1259": "NH1" <-> "NH2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B ARG 481": "NH1" <-> "NH2" Residue "B ARG 607": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 867": "NH1" <-> "NH2" Residue "B ARG 1048": "NH1" <-> "NH2" Residue "B ARG 1054": "NH1" <-> "NH2" Residue "B ARG 1056": "NH1" <-> "NH2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 277": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "M ARG 93": "NH1" <-> "NH2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 303": "NH1" <-> "NH2" Residue "N ARG 364": "NH1" <-> "NH2" Residue "N ARG 411": "NH1" <-> "NH2" Residue "O ARG 228": "NH1" <-> "NH2" Residue "O ARG 238": "NH1" <-> "NH2" Residue "O ARG 286": "NH1" <-> "NH2" Residue "O ARG 292": "NH1" <-> "NH2" Residue "O ARG 303": "NH1" <-> "NH2" Residue "O ARG 317": "NH1" <-> "NH2" Residue "O ARG 509": "NH1" <-> "NH2" Residue "O ARG 512": "NH1" <-> "NH2" Residue "O ARG 534": "NH1" <-> "NH2" Residue "O ARG 557": "NH1" <-> "NH2" Residue "O ARG 561": "NH1" <-> "NH2" Residue "O ARG 643": "NH1" <-> "NH2" Residue "P TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 38330 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 10980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1402, 10980 Classifications: {'peptide': 1402} Link IDs: {'PTRANS': 63, 'TRANS': 1338} Chain breaks: 3 Chain: "B" Number of atoms: 8788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8788 Classifications: {'peptide': 1114} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 1070} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 977 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 2 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1544 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 12, 'TRANS': 178} Chain breaks: 2 Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Chain: "I" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 321 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "J" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 558 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 1 Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Chain: "O" Number of atoms: 4316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4316 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 17, 'TRANS': 519} Chain breaks: 2 Chain: "P" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1024 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "Q" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 5, 'TRANS': 34} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 492 SG CYS A 67 74.419 65.509 80.944 1.00 71.80 S ATOM 510 SG CYS A 70 77.933 66.708 79.240 1.00 63.74 S ATOM 557 SG CYS A 77 78.581 64.324 81.979 1.00 54.56 S ATOM 795 SG CYS A 107 61.114 111.700 95.728 1.00 41.04 S ATOM 1184 SG CYS A 154 62.450 114.613 93.891 1.00 63.69 S ATOM 1208 SG CYS A 157 58.713 113.852 93.980 1.00 54.90 S ATOM 19341 SG CYS B1095 81.199 82.749 75.285 1.00 27.39 S ATOM 19364 SG CYS B1098 77.396 85.877 75.129 1.00 25.16 S ATOM 19430 SG CYS B1107 78.128 81.107 74.439 1.00 47.09 S ATOM 28892 SG CYS J 10 130.526 38.838 124.635 1.00 24.19 S ATOM 29172 SG CYS J 45 128.143 42.237 127.218 1.00 21.97 S ATOM 29178 SG CYS J 46 128.589 38.296 127.603 1.00 18.86 S ATOM 30215 SG CYS L 31 85.523 24.781 122.758 1.00 31.17 S ATOM 30235 SG CYS L 34 85.544 21.372 124.054 1.00 37.92 S ATOM 30339 SG CYS L 48 82.684 24.328 120.622 1.00 49.63 S ATOM 30362 SG CYS L 51 82.420 23.680 124.854 1.00 48.73 S Time building chain proxies: 20.14, per 1000 atoms: 0.53 Number of scatterers: 38330 At special positions: 0 Unit cell: (189, 159.6, 206.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 207 16.00 Mg 1 11.99 O 7218 8.00 N 6586 7.00 C 24312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 14.18 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 70 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 67 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 77 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 6 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9116 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 46 sheets defined 33.0% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 22 through 30 removed outlier: 3.768A pdb=" N VAL A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.821A pdb=" N GLY A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.518A pdb=" N ARG A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 150 removed outlier: 3.835A pdb=" N GLN A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 208 removed outlier: 4.337A pdb=" N ASP A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.662A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.844A pdb=" N GLU A 240 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 305 removed outlier: 4.024A pdb=" N VAL A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 327 removed outlier: 4.187A pdb=" N ILE A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 removed outlier: 4.227A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.857A pdb=" N ASN A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 456' Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 526 through 534 removed outlier: 3.555A pdb=" N GLU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 563 removed outlier: 3.549A pdb=" N THR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A 561 " --> pdb=" O PHE A 557 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 583 removed outlier: 3.781A pdb=" N THR A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLN A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 removed outlier: 4.066A pdb=" N PHE A 610 " --> pdb=" O GLY A 606 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 612 " --> pdb=" O GLN A 608 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 709 removed outlier: 3.564A pdb=" N THR A 680 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Proline residue: A 687 - end of helix removed outlier: 3.890A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 746 removed outlier: 3.607A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS A 736 " --> pdb=" O GLU A 732 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS A 737 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 740 " --> pdb=" O HIS A 736 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LEU A 741 " --> pdb=" O LYS A 737 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN A 746 " --> pdb=" O ILE A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.652A pdb=" N LYS A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 775 " --> pdb=" O SER A 771 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 777 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 797 removed outlier: 3.621A pdb=" N ALA A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 810 removed outlier: 3.500A pdb=" N VAL A 806 " --> pdb=" O SER A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 877 removed outlier: 3.706A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR A 875 " --> pdb=" O GLY A 871 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 882 removed outlier: 3.694A pdb=" N THR A 882 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 890 Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.543A pdb=" N ASP A 919 " --> pdb=" O TYR A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 946 removed outlier: 3.947A pdb=" N THR A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 963 removed outlier: 3.665A pdb=" N GLU A 961 " --> pdb=" O TYR A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 989 removed outlier: 3.705A pdb=" N ASP A 988 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 989 " --> pdb=" O ARG A 986 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 985 through 989' Processing helix chain 'A' and resid 999 through 1026 removed outlier: 3.869A pdb=" N LYS A1015 " --> pdb=" O TYR A1011 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A1016 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A1025 " --> pdb=" O ASN A1021 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1058 removed outlier: 3.629A pdb=" N SER A1055 " --> pdb=" O ASN A1051 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A1057 " --> pdb=" O LYS A1053 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN A1058 " --> pdb=" O THR A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1080 removed outlier: 3.535A pdb=" N VAL A1067 " --> pdb=" O SER A1063 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A1072 " --> pdb=" O ARG A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1099 removed outlier: 3.902A pdb=" N ILE A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A1099 " --> pdb=" O GLN A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1104 removed outlier: 3.682A pdb=" N GLN A1103 " --> pdb=" O PRO A1100 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET A1104 " --> pdb=" O GLY A1101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1100 through 1104' Processing helix chain 'A' and resid 1122 through 1131 Processing helix chain 'A' and resid 1151 through 1160 removed outlier: 3.553A pdb=" N ARG A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS A1158 " --> pdb=" O ALA A1154 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY A1159 " --> pdb=" O ARG A1155 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A1160 " --> pdb=" O VAL A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1170 removed outlier: 3.639A pdb=" N VAL A1169 " --> pdb=" O LEU A1165 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A1170 " --> pdb=" O LEU A1166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1170' Processing helix chain 'A' and resid 1190 through 1196 Processing helix chain 'A' and resid 1201 through 1211 Processing helix chain 'A' and resid 1255 through 1266 Processing helix chain 'A' and resid 1318 through 1326 removed outlier: 3.508A pdb=" N VAL A1325 " --> pdb=" O GLU A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1345 removed outlier: 3.566A pdb=" N TYR A1333 " --> pdb=" O GLU A1329 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A1334 " --> pdb=" O ALA A1330 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG A1337 " --> pdb=" O TYR A1333 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A1340 " --> pdb=" O ILE A1336 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A1343 " --> pdb=" O ILE A1339 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A1345 " --> pdb=" O TYR A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1362 removed outlier: 3.792A pdb=" N MET A1362 " --> pdb=" O LEU A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1387 Processing helix chain 'A' and resid 1394 through 1403 removed outlier: 4.047A pdb=" N ASP A1398 " --> pdb=" O ASP A1394 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1399 " --> pdb=" O HIS A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1457 removed outlier: 3.973A pdb=" N ALA A1456 " --> pdb=" O ASN A1453 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A1457 " --> pdb=" O GLU A1454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1453 through 1457' Processing helix chain 'B' and resid 42 through 45 removed outlier: 3.572A pdb=" N TRP B 45 " --> pdb=" O GLN B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.768A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 removed outlier: 4.322A pdb=" N SER B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 65 " --> pdb=" O HIS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 77 removed outlier: 4.284A pdb=" N ILE B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.602A pdb=" N LEU B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 279 through 289 removed outlier: 5.478A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 308 removed outlier: 3.524A pdb=" N TYR B 304 " --> pdb=" O GLN B 300 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.767A pdb=" N ARG B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 359 " --> pdb=" O ARG B 355 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 404 removed outlier: 3.898A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 440 removed outlier: 4.003A pdb=" N LEU B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.659A pdb=" N ALA B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 removed outlier: 3.631A pdb=" N GLN B 493 " --> pdb=" O GLN B 490 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B 494 " --> pdb=" O PRO B 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 490 through 494' Processing helix chain 'B' and resid 526 through 536 removed outlier: 4.219A pdb=" N LYS B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 580 Processing helix chain 'B' and resid 623 through 631 removed outlier: 3.778A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 629 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 630 " --> pdb=" O HIS B 626 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.842A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 643 " --> pdb=" O ASP B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 643' Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.849A pdb=" N THR B 679 " --> pdb=" O GLU B 676 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE B 680 " --> pdb=" O PRO B 677 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 681 " --> pdb=" O PHE B 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 676 through 681' Processing helix chain 'B' and resid 684 through 688 removed outlier: 3.910A pdb=" N ILE B 688 " --> pdb=" O ALA B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 removed outlier: 4.031A pdb=" N GLN B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS B 703 " --> pdb=" O ASN B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 893 removed outlier: 4.297A pdb=" N ASP B 892 " --> pdb=" O VAL B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 969 removed outlier: 3.607A pdb=" N LEU B 961 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY B 967 " --> pdb=" O SER B 963 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 969 " --> pdb=" O LYS B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 993 removed outlier: 3.668A pdb=" N ASP B 993 " --> pdb=" O LYS B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1074 removed outlier: 3.760A pdb=" N CYS B1069 " --> pdb=" O MET B1065 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B1072 " --> pdb=" O ASP B1068 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B1073 " --> pdb=" O CYS B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1084 removed outlier: 4.038A pdb=" N LEU B1079 " --> pdb=" O ALA B1075 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B1080 " --> pdb=" O SER B1076 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B1081 " --> pdb=" O GLN B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1088 Processing helix chain 'B' and resid 1123 through 1135 removed outlier: 3.746A pdb=" N MET B1135 " --> pdb=" O GLU B1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.586A pdb=" N LYS C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 removed outlier: 4.188A pdb=" N PHE C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 102 removed outlier: 3.541A pdb=" N ILE C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.524A pdb=" N MET C 112 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 109 through 113' Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.643A pdb=" N PHE C 219 " --> pdb=" O HIS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.661A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.680A pdb=" N LYS C 272 " --> pdb=" O ASP C 269 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP C 273 " --> pdb=" O ALA C 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 269 through 273' Processing helix chain 'C' and resid 309 through 327 removed outlier: 3.674A pdb=" N ILE C 313 " --> pdb=" O THR C 309 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 22 removed outlier: 3.989A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 removed outlier: 3.579A pdb=" N THR D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN D 64 " --> pdb=" O ARG D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 99 through 110 Processing helix chain 'D' and resid 117 through 125 removed outlier: 4.396A pdb=" N LEU D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 removed outlier: 3.516A pdb=" N TYR D 135 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.578A pdb=" N ILE D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 removed outlier: 3.860A pdb=" N GLU E 6 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 27 removed outlier: 3.639A pdb=" N ALA E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 47 removed outlier: 4.441A pdb=" N ALA E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.737A pdb=" N MET E 58 " --> pdb=" O ARG E 55 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 55 through 59' Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.652A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.789A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 103 removed outlier: 3.639A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 128 removed outlier: 3.513A pdb=" N MET F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.530A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.687A pdb=" N ASN G 32 " --> pdb=" O HIS G 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.765A pdb=" N ASP H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 88 through 92' Processing helix chain 'J' and resid 18 through 27 removed outlier: 3.586A pdb=" N GLU J 27 " --> pdb=" O ASN J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 38 Processing helix chain 'J' and resid 47 through 52 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'K' and resid 51 through 54 removed outlier: 3.746A pdb=" N THR K 54 " --> pdb=" O THR K 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 51 through 54' Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.843A pdb=" N GLY K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.940A pdb=" N GLN K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP K 123 " --> pdb=" O LYS K 119 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER K 133 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU K 137 " --> pdb=" O SER K 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS K 138 " --> pdb=" O LYS K 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 137 Processing helix chain 'M' and resid 184 through 193 Processing helix chain 'M' and resid 231 through 236 Processing helix chain 'N' and resid 277 through 282 removed outlier: 3.586A pdb=" N LEU N 282 " --> pdb=" O ALA N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 282 through 295 removed outlier: 3.739A pdb=" N HIS N 287 " --> pdb=" O LEU N 283 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN N 288 " --> pdb=" O ASN N 284 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS N 289 " --> pdb=" O ALA N 285 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS N 295 " --> pdb=" O LEU N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 55 removed outlier: 3.809A pdb=" N VAL O 53 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 72 removed outlier: 3.640A pdb=" N MET O 67 " --> pdb=" O SER O 63 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL O 69 " --> pdb=" O ILE O 65 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA O 70 " --> pdb=" O GLY O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 84 removed outlier: 3.521A pdb=" N LYS O 82 " --> pdb=" O GLU O 78 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP O 84 " --> pdb=" O VAL O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 101 removed outlier: 3.798A pdb=" N THR O 93 " --> pdb=" O ASP O 89 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR O 94 " --> pdb=" O SER O 90 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL O 96 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER O 97 " --> pdb=" O THR O 93 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 133 removed outlier: 3.668A pdb=" N ILE O 127 " --> pdb=" O ASN O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 135 through 140 Processing helix chain 'O' and resid 159 through 167 Processing helix chain 'O' and resid 185 through 195 removed outlier: 3.784A pdb=" N LEU O 190 " --> pdb=" O THR O 186 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS O 195 " --> pdb=" O PHE O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 222 removed outlier: 3.521A pdb=" N LEU O 214 " --> pdb=" O PRO O 210 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU O 218 " --> pdb=" O LEU O 214 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS O 222 " --> pdb=" O LEU O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 254 removed outlier: 5.238A pdb=" N LYS O 242 " --> pdb=" O ARG O 238 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS O 251 " --> pdb=" O THR O 247 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE O 252 " --> pdb=" O ASP O 248 " (cutoff:3.500A) Processing helix chain 'O' and resid 285 through 301 removed outlier: 3.856A pdb=" N LYS O 289 " --> pdb=" O ASP O 285 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER O 293 " --> pdb=" O LYS O 289 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS O 294 " --> pdb=" O GLY O 290 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN O 295 " --> pdb=" O ARG O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 318 Processing helix chain 'O' and resid 338 through 355 removed outlier: 4.150A pdb=" N GLN O 346 " --> pdb=" O ALA O 342 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP O 347 " --> pdb=" O LYS O 343 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU O 350 " --> pdb=" O GLN O 346 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 367 removed outlier: 3.610A pdb=" N LEU O 366 " --> pdb=" O ALA O 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA O 367 " --> pdb=" O ILE O 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 363 through 367' Processing helix chain 'O' and resid 451 through 462 Processing helix chain 'O' and resid 483 through 500 removed outlier: 3.671A pdb=" N VAL O 491 " --> pdb=" O LEU O 487 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR O 492 " --> pdb=" O LYS O 488 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR O 494 " --> pdb=" O SER O 490 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL O 495 " --> pdb=" O VAL O 491 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE O 496 " --> pdb=" O TYR O 492 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 514 removed outlier: 3.954A pdb=" N ARG O 512 " --> pdb=" O SER O 508 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN O 514 " --> pdb=" O CYS O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 532 through 542 removed outlier: 3.529A pdb=" N LEU O 537 " --> pdb=" O ILE O 533 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA O 538 " --> pdb=" O ARG O 534 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER O 539 " --> pdb=" O SER O 535 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) Processing helix chain 'O' and resid 572 through 593 removed outlier: 3.573A pdb=" N MET O 577 " --> pdb=" O SER O 573 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS O 592 " --> pdb=" O LEU O 588 " (cutoff:3.500A) Processing helix chain 'O' and resid 594 through 599 removed outlier: 3.518A pdb=" N GLU O 598 " --> pdb=" O LEU O 595 " (cutoff:3.500A) Processing helix chain 'O' and resid 626 through 649 removed outlier: 3.521A pdb=" N ASN O 631 " --> pdb=" O LEU O 627 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU O 632 " --> pdb=" O LYS O 628 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG O 633 " --> pdb=" O MET O 629 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL O 637 " --> pdb=" O ARG O 633 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE O 638 " --> pdb=" O GLU O 634 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG O 640 " --> pdb=" O ASN O 636 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG O 643 " --> pdb=" O ALA O 639 " (cutoff:3.500A) Processing helix chain 'O' and resid 650 through 653 removed outlier: 3.726A pdb=" N MET O 653 " --> pdb=" O VAL O 650 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 650 through 653' Processing helix chain 'P' and resid 172 through 190 removed outlier: 4.023A pdb=" N ASN P 176 " --> pdb=" O ILE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 209 Processing helix chain 'P' and resid 219 through 227 Processing helix chain 'P' and resid 239 through 248 Processing helix chain 'P' and resid 256 through 260 removed outlier: 3.936A pdb=" N CYS P 260 " --> pdb=" O THR P 257 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 271 removed outlier: 3.761A pdb=" N MET P 271 " --> pdb=" O SER P 267 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 67 removed outlier: 3.800A pdb=" N ALA Q 55 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 19 removed outlier: 5.062A pdb=" N ILE A 13 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU B1144 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 15 " --> pdb=" O ARG B1142 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B1142 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 3.556A pdb=" N LEU A 86 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG A 259 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 107 removed outlier: 3.756A pdb=" N ALA A 112 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 166 removed outlier: 4.232A pdb=" N HIS A 180 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP A 220 " --> pdb=" O HIS A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 372 removed outlier: 4.224A pdb=" N LYS A 371 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.583A pdb=" N LYS A 491 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 499 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N PHE A 498 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A 380 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU A 500 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N SER A 382 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 404 through 407 removed outlier: 4.059A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 628 removed outlier: 6.138A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 897 through 898 removed outlier: 7.532A pdb=" N VAL A 904 " --> pdb=" O VAL A 912 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1141 through 1142 Processing sheet with id=AB3, first strand: chain 'A' and resid 1176 through 1178 Processing sheet with id=AB4, first strand: chain 'A' and resid 1281 through 1285 Processing sheet with id=AB5, first strand: chain 'A' and resid 1429 through 1431 Processing sheet with id=AB6, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.980A pdb=" N LEU B 93 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR B 95 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU B 134 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP B 97 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY B 150 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL B 131 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLU B 148 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE B 133 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP B 146 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N TYR B 135 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS B 144 " --> pdb=" O TYR B 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB8, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.475A pdb=" N VAL B 196 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 205 through 208 removed outlier: 4.095A pdb=" N LYS B 228 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 241 through 242 removed outlier: 3.833A pdb=" N LEU B 242 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE B 251 " --> pdb=" O LEU B 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 441 through 442 removed outlier: 3.570A pdb=" N TRP B 442 " --> pdb=" O ARG B 451 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG B 451 " --> pdb=" O TRP B 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC4, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC5, first strand: chain 'B' and resid 560 through 561 Processing sheet with id=AC6, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.842A pdb=" N GLU B 786 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASN B 903 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N SER B 879 " --> pdb=" O ASN B 903 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.842A pdb=" N GLU B 786 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASN B 903 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N SER B 879 " --> pdb=" O ASN B 903 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1001 through 1002 removed outlier: 3.882A pdb=" N GLN B1025 " --> pdb=" O SER B 913 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU B 771 " --> pdb=" O ILE B 924 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL B 926 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU B 773 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 772 " --> pdb=" O ILE B 943 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 943 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 758 " --> pdb=" O ILE B 942 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 841 through 843 removed outlier: 4.369A pdb=" N ILE B 843 " --> pdb=" O VAL B 871 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 846 through 848 Processing sheet with id=AD2, first strand: chain 'B' and resid 1089 through 1095 Processing sheet with id=AD3, first strand: chain 'C' and resid 41 through 47 removed outlier: 3.766A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.683A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 83 " --> pdb=" O PHE L 67 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 106 through 107 removed outlier: 4.012A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.652A pdb=" N THR C 141 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 230 through 234 removed outlier: 4.127A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 2 through 5 removed outlier: 3.686A pdb=" N LYS D 2 " --> pdb=" O ALA G 8 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LYS G 6 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN G 69 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU G 52 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR G 71 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP G 50 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ARG G 73 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE G 48 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.523A pdb=" N GLU E 81 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL E 111 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY E 108 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.176A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE E 199 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 88 through 91 removed outlier: 7.317A pdb=" N LYS G 98 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE G 97 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE G 108 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 95 through 96 removed outlier: 5.340A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL H 107 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 13 through 16 removed outlier: 3.636A pdb=" N LEU I 13 " --> pdb=" O ALA I 25 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 47 through 49 removed outlier: 3.642A pdb=" N GLN K 64 " --> pdb=" O LYS K 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 76 through 77 removed outlier: 6.558A pdb=" N LYS M 77 " --> pdb=" O LEU M 170 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL N 306 " --> pdb=" O ILE N 416 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 84 through 87 removed outlier: 4.533A pdb=" N SER M 84 " --> pdb=" O ILE N 399 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE N 399 " --> pdb=" O SER M 84 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER N 398 " --> pdb=" O GLU N 407 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU N 407 " --> pdb=" O SER N 398 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 104 through 109 Processing sheet with id=AE9, first strand: chain 'O' and resid 200 through 202 Processing sheet with id=AF1, first strand: chain 'O' and resid 548 through 552 1079 hydrogen bonds defined for protein. 3045 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: 15.61 Time building geometry restraints manager: 15.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12474 1.34 - 1.46: 7862 1.46 - 1.58: 18342 1.58 - 1.70: 1 1.70 - 1.82: 337 Bond restraints: 39016 Sorted by residual: bond pdb=" CA VAL E 124 " pdb=" CB VAL E 124 " ideal model delta sigma weight residual 1.534 1.554 -0.020 6.80e-03 2.16e+04 8.38e+00 bond pdb=" C VAL E 124 " pdb=" N PRO E 125 " ideal model delta sigma weight residual 1.340 1.418 -0.078 2.76e-02 1.31e+03 7.96e+00 bond pdb=" C ALA P 209 " pdb=" N PRO P 210 " ideal model delta sigma weight residual 1.332 1.369 -0.037 1.33e-02 5.65e+03 7.86e+00 bond pdb=" C GLY P 201 " pdb=" N PRO P 202 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.20e-02 6.94e+03 7.65e+00 bond pdb=" C PRO E 128 " pdb=" N PRO E 129 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.80e+00 ... (remaining 39011 not shown) Histogram of bond angle deviations from ideal: 92.49 - 100.93: 76 100.93 - 109.37: 3743 109.37 - 117.81: 25080 117.81 - 126.25: 23224 126.25 - 134.69: 564 Bond angle restraints: 52687 Sorted by residual: angle pdb=" N LEU N 409 " pdb=" CA LEU N 409 " pdb=" C LEU N 409 " ideal model delta sigma weight residual 110.80 92.49 18.31 2.13e+00 2.20e-01 7.39e+01 angle pdb=" C GLN A 275 " pdb=" N ASP A 276 " pdb=" CA ASP A 276 " ideal model delta sigma weight residual 121.54 134.69 -13.15 1.91e+00 2.74e-01 4.74e+01 angle pdb=" C ILE Q 43 " pdb=" N ASN Q 44 " pdb=" CA ASN Q 44 " ideal model delta sigma weight residual 121.54 133.49 -11.95 1.91e+00 2.74e-01 3.91e+01 angle pdb=" C GLU P 308 " pdb=" N VAL P 309 " pdb=" CA VAL P 309 " ideal model delta sigma weight residual 121.97 132.97 -11.00 1.80e+00 3.09e-01 3.74e+01 angle pdb=" N ILE B 324 " pdb=" CA ILE B 324 " pdb=" C ILE B 324 " ideal model delta sigma weight residual 113.53 107.95 5.58 9.80e-01 1.04e+00 3.24e+01 ... (remaining 52682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 22318 15.97 - 31.94: 1225 31.94 - 47.91: 363 47.91 - 63.88: 23 63.88 - 79.85: 30 Dihedral angle restraints: 23959 sinusoidal: 9879 harmonic: 14080 Sorted by residual: dihedral pdb=" CA LYS P 307 " pdb=" C LYS P 307 " pdb=" N GLU P 308 " pdb=" CA GLU P 308 " ideal model delta harmonic sigma weight residual -180.00 -100.15 -79.85 0 5.00e+00 4.00e-02 2.55e+02 dihedral pdb=" CA GLU P 308 " pdb=" C GLU P 308 " pdb=" N VAL P 309 " pdb=" CA VAL P 309 " ideal model delta harmonic sigma weight residual -180.00 -110.89 -69.11 0 5.00e+00 4.00e-02 1.91e+02 dihedral pdb=" CA LYS B 583 " pdb=" C LYS B 583 " pdb=" N VAL B 584 " pdb=" CA VAL B 584 " ideal model delta harmonic sigma weight residual -180.00 -121.12 -58.88 0 5.00e+00 4.00e-02 1.39e+02 ... (remaining 23956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 5111 0.082 - 0.164: 770 0.164 - 0.246: 68 0.246 - 0.328: 8 0.328 - 0.410: 4 Chirality restraints: 5961 Sorted by residual: chirality pdb=" CB ILE A 551 " pdb=" CA ILE A 551 " pdb=" CG1 ILE A 551 " pdb=" CG2 ILE A 551 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CB ILE A 712 " pdb=" CA ILE A 712 " pdb=" CG1 ILE A 712 " pdb=" CG2 ILE A 712 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB VAL B 888 " pdb=" CA VAL B 888 " pdb=" CG1 VAL B 888 " pdb=" CG2 VAL B 888 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 5958 not shown) Planarity restraints: 6778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER O 239 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C SER O 239 " -0.060 2.00e-02 2.50e+03 pdb=" O SER O 239 " 0.023 2.00e-02 2.50e+03 pdb=" N GLN O 240 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS O 236 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C LYS O 236 " 0.057 2.00e-02 2.50e+03 pdb=" O LYS O 236 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS O 237 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 28 " -0.015 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C LYS L 28 " 0.054 2.00e-02 2.50e+03 pdb=" O LYS L 28 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR L 29 " -0.018 2.00e-02 2.50e+03 ... (remaining 6775 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.91: 2 1.91 - 2.66: 501 2.66 - 3.41: 49828 3.41 - 4.15: 85268 4.15 - 4.90: 154247 Nonbonded interactions: 289846 Sorted by model distance: nonbonded pdb=" CZ PHE N 304 " pdb=" CD2 LEU N 409 " model vdw 1.167 3.760 nonbonded pdb=" CE2 PHE N 304 " pdb=" CD2 LEU N 409 " model vdw 1.635 3.760 nonbonded pdb=" CE1 PHE N 304 " pdb=" CD2 LEU N 409 " model vdw 2.133 3.760 nonbonded pdb=" OD1 ASP A 513 " pdb="MG MG A2002 " model vdw 2.143 2.170 nonbonded pdb=" O SER I 28 " pdb=" OH TYR M 185 " model vdw 2.245 2.440 ... (remaining 289841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 0.040 Extract box with map and model: 8.480 Check model and map are aligned: 0.590 Set scattering table: 0.320 Process input model: 103.660 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0373 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 : 0.004 0.078 39016 Z= 0.287 Angle : 1.064 18.313 52687 Z= 0.561 Chirality : 0.059 0.410 5961 Planarity : 0.007 0.072 6778 Dihedral : 11.408 79.855 14843 Min Nonbonded Distance : 1.167 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.89 % Favored : 86.61 % Rotamer: Outliers : 0.26 % Allowed : 6.52 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 1.92 % Twisted General : 0.70 % 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: -5.18 (0.09), residues: 4765 helix: -3.81 (0.08), residues: 1517 sheet: -2.12 (0.20), residues: 558 loop : -3.65 (0.09), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP O 583 HIS 0.015 0.002 HIS A 92 PHE 0.031 0.002 PHE B1018 TYR 0.030 0.002 TYR P 249 ARG 0.011 0.001 ARG B 915 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 563 time to evaluate : 4.197 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 outliers start: 11 outliers final: 2 residues processed: 574 average time/residue: 0.5335 time to fit residues: 497.2378 Evaluate side-chains 338 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 336 time to evaluate : 4.160 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3252 time to fit residues: 7.5391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 401 optimal weight: 7.9990 chunk 360 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 243 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 373 optimal weight: 0.0270 chunk 144 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 chunk 277 optimal weight: 10.0000 chunk 432 optimal weight: 0.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 161 ASN ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 HIS A 618 HIS A 643 ASN A 808 GLN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN A 948 ASN A 990 ASN A1021 ASN A1142 ASN A1218 GLN ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 ASN A1254 ASN A1354 HIS A1419 GLN A1453 ASN B 39 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN B 362 ASN B 626 HIS ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN B 800 ASN B 840 GLN B 861 ASN B 893 GLN ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 GLN B1049 GLN C 137 ASN C 143 ASN C 161 HIS D 71 ASN D 133 HIS E 5 ASN E 32 GLN E 54 GLN E 101 GLN E 113 GLN E 136 ASN G 36 ASN H 33 GLN H 128 ASN I 10 ASN K 95 HIS M 117 HIS ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 155 ASN M 158 GLN M 190 ASN N 298 ASN O 202 GLN O 244 ASN O 254 ASN O 298 ASN O 310 GLN O 346 GLN O 362 ASN O 369 HIS O 464 ASN ** O 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 572 HIS O 631 ASN O 652 GLN ** P 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1086 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 39016 Z= 0.266 Angle : 0.806 17.119 52687 Z= 0.414 Chirality : 0.047 0.292 5961 Planarity : 0.006 0.088 6778 Dihedral : 6.732 73.851 5227 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.09 % Favored : 87.51 % Rotamer: Outliers : 2.11 % Allowed : 9.56 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.48 % 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: -4.18 (0.10), residues: 4765 helix: -2.45 (0.11), residues: 1531 sheet: -1.77 (0.21), residues: 532 loop : -3.31 (0.10), residues: 2702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B1106 HIS 0.014 0.002 HIS B 244 PHE 0.027 0.002 PHE N 304 TYR 0.027 0.002 TYR P 249 ARG 0.011 0.001 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 393 time to evaluate : 4.413 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: 90 outliers final: 38 residues processed: 459 average time/residue: 0.5347 time to fit residues: 406.4350 Evaluate side-chains 374 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 336 time to evaluate : 4.269 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.3830 time to fit residues: 34.9284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 240 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 359 optimal weight: 9.9990 chunk 294 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 433 optimal weight: 0.9980 chunk 467 optimal weight: 6.9990 chunk 385 optimal weight: 3.9990 chunk 429 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 347 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS A 109 ASN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS A 523 GLN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 GLN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 GLN B 61 HIS ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN D 31 GLN E 101 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS M 89 GLN M 92 ASN M 155 ASN M 190 ASN N 284 ASN N 289 HIS O 152 HIS O 207 HIS O 240 GLN O 579 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2823 moved from start: 0.6979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.163 39016 Z= 0.461 Angle : 1.163 22.313 52687 Z= 0.600 Chirality : 0.061 0.373 5961 Planarity : 0.009 0.127 6778 Dihedral : 8.016 77.829 5227 Min Nonbonded Distance : 1.579 Molprobity Statistics. All-atom Clashscore : 24.31 Ramachandran Plot: Outliers : 0.42 % Allowed : 14.42 % Favored : 85.16 % Rotamer: Outliers : 3.98 % Allowed : 12.92 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 1.92 % Twisted General : 0.59 % 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: -4.19 (0.10), residues: 4765 helix: -2.36 (0.11), residues: 1509 sheet: -1.88 (0.21), residues: 530 loop : -3.36 (0.10), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP O 583 HIS 0.026 0.004 HIS A 80 PHE 0.048 0.004 PHE C 86 TYR 0.055 0.004 TYR B1073 ARG 0.020 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 485 time to evaluate : 4.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 170 outliers final: 56 residues processed: 611 average time/residue: 0.5093 time to fit residues: 515.3499 Evaluate side-chains 416 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 360 time to evaluate : 4.255 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.3550 time to fit residues: 43.8289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 427 optimal weight: 0.2980 chunk 325 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 206 optimal weight: 0.5980 chunk 290 optimal weight: 0.9990 chunk 434 optimal weight: 0.2980 chunk 460 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 411 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 156 HIS A 233 GLN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN ** A1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN B 197 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 558 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN B 803 GLN B1025 GLN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN O 469 ASN O 599 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2809 moved from start: 0.7361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39016 Z= 0.189 Angle : 0.744 14.345 52687 Z= 0.381 Chirality : 0.046 0.256 5961 Planarity : 0.005 0.094 6778 Dihedral : 6.771 77.230 5227 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.77 % Favored : 87.89 % Rotamer: Outliers : 1.95 % Allowed : 15.47 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.37 % 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: -3.56 (0.11), residues: 4765 helix: -1.59 (0.12), residues: 1517 sheet: -1.55 (0.21), residues: 554 loop : -3.15 (0.10), residues: 2694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP O 583 HIS 0.012 0.001 HIS A 736 PHE 0.027 0.002 PHE O 47 TYR 0.025 0.002 TYR P 249 ARG 0.009 0.001 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 407 time to evaluate : 4.274 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 31 residues processed: 469 average time/residue: 0.4903 time to fit residues: 394.8049 Evaluate side-chains 384 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 353 time to evaluate : 4.211 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3516 time to fit residues: 27.1925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 383 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 342 optimal weight: 6.9990 chunk 189 optimal weight: 0.6980 chunk 392 optimal weight: 0.7980 chunk 318 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 234 optimal weight: 0.3980 chunk 412 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 ASN ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS G 36 ASN H 33 GLN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 377 ASN O 202 GLN O 584 ASN O 631 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3409 moved from start: 0.8706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 39016 Z= 0.267 Angle : 0.790 15.765 52687 Z= 0.402 Chirality : 0.048 0.426 5961 Planarity : 0.006 0.081 6778 Dihedral : 6.532 76.825 5227 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.58 % Favored : 86.15 % Rotamer: Outliers : 2.46 % Allowed : 16.48 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.41 % 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: -3.25 (0.11), residues: 4765 helix: -1.15 (0.13), residues: 1495 sheet: -1.42 (0.22), residues: 519 loop : -3.04 (0.11), residues: 2751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP O 583 HIS 0.017 0.002 HIS O 152 PHE 0.067 0.002 PHE H 118 TYR 0.031 0.002 TYR B 842 ARG 0.014 0.001 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 435 time to evaluate : 4.235 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: 105 outliers final: 52 residues processed: 515 average time/residue: 0.5291 time to fit residues: 456.5151 Evaluate side-chains 413 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 361 time to evaluate : 4.516 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.3704 time to fit residues: 42.9466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 154 optimal weight: 2.9990 chunk 414 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 270 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 460 optimal weight: 7.9990 chunk 382 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 152 optimal weight: 0.5980 chunk 241 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 ASN ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS B 197 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN ** B 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN O 652 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3669 moved from start: 0.9562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 39016 Z= 0.202 Angle : 0.732 14.911 52687 Z= 0.370 Chirality : 0.046 0.263 5961 Planarity : 0.005 0.118 6778 Dihedral : 6.268 76.495 5227 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.46 % Favored : 88.23 % Rotamer: Outliers : 1.48 % Allowed : 17.82 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.03 (0.11), residues: 4765 helix: -0.96 (0.13), residues: 1518 sheet: -1.19 (0.22), residues: 512 loop : -2.95 (0.11), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 583 HIS 0.009 0.001 HIS A 736 PHE 0.044 0.002 PHE H 118 TYR 0.022 0.002 TYR O 199 ARG 0.012 0.001 ARG B 915 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 428 time to evaluate : 4.493 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 outliers start: 63 outliers final: 20 residues processed: 478 average time/residue: 0.4961 time to fit residues: 402.1680 Evaluate side-chains 378 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 358 time to evaluate : 4.331 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3646 time to fit residues: 19.6220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 444 optimal weight: 4.9990 chunk 51 optimal weight: 0.0770 chunk 262 optimal weight: 0.3980 chunk 336 optimal weight: 0.4980 chunk 260 optimal weight: 1.9990 chunk 387 optimal weight: 10.0000 chunk 257 optimal weight: 0.8980 chunk 458 optimal weight: 2.9990 chunk 287 optimal weight: 0.9980 chunk 279 optimal weight: 0.9990 chunk 211 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 HIS ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 891 ASN B 918 GLN ** B 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN H 33 GLN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3855 moved from start: 1.0160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 39016 Z= 0.185 Angle : 0.714 12.812 52687 Z= 0.361 Chirality : 0.045 0.282 5961 Planarity : 0.005 0.082 6778 Dihedral : 6.040 76.381 5227 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.90 % Favored : 87.81 % Rotamer: Outliers : 1.34 % Allowed : 18.42 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.35 % 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: -2.81 (0.11), residues: 4765 helix: -0.71 (0.13), residues: 1520 sheet: -1.01 (0.23), residues: 501 loop : -2.87 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 79 HIS 0.008 0.001 HIS C 216 PHE 0.044 0.002 PHE A 852 TYR 0.027 0.002 TYR E 46 ARG 0.009 0.000 ARG B 915 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 422 time to evaluate : 4.313 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: 57 outliers final: 23 residues processed: 463 average time/residue: 0.5005 time to fit residues: 391.0243 Evaluate side-chains 392 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 369 time to evaluate : 4.313 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3625 time to fit residues: 22.3037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 283 optimal weight: 0.4980 chunk 183 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 90 optimal weight: 0.0000 chunk 88 optimal weight: 4.9990 chunk 291 optimal weight: 10.0000 chunk 312 optimal weight: 0.0010 chunk 226 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 360 optimal weight: 2.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 HIS ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN ** B 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 891 ASN B 893 GLN ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1077 GLN D 111 ASN D 133 HIS G 17 GLN G 29 GLN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 599 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4237 moved from start: 1.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 39016 Z= 0.197 Angle : 0.726 12.726 52687 Z= 0.369 Chirality : 0.046 0.244 5961 Planarity : 0.005 0.081 6778 Dihedral : 6.024 76.185 5227 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.16 % Favored : 88.48 % Rotamer: Outliers : 0.96 % Allowed : 18.73 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -2.81 (0.11), residues: 4765 helix: -0.71 (0.13), residues: 1542 sheet: -0.88 (0.23), residues: 485 loop : -2.90 (0.11), residues: 2738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 583 HIS 0.022 0.001 HIS D 133 PHE 0.044 0.002 PHE C 126 TYR 0.026 0.002 TYR B1073 ARG 0.009 0.001 ARG P 241 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 463 time to evaluate : 4.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 14 residues processed: 491 average time/residue: 0.5012 time to fit residues: 412.1493 Evaluate side-chains 413 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 399 time to evaluate : 4.582 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3453 time to fit residues: 16.0359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 417 optimal weight: 4.9990 chunk 439 optimal weight: 0.9990 chunk 401 optimal weight: 3.9990 chunk 427 optimal weight: 0.0470 chunk 257 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 335 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 chunk 386 optimal weight: 8.9990 chunk 404 optimal weight: 0.7980 chunk 426 optimal weight: 0.8980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 891 ASN ** B 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 918 GLN ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4482 moved from start: 1.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 39016 Z= 0.200 Angle : 0.732 21.436 52687 Z= 0.368 Chirality : 0.046 0.254 5961 Planarity : 0.005 0.072 6778 Dihedral : 5.958 76.013 5227 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.96 % Favored : 87.76 % Rotamer: Outliers : 0.56 % Allowed : 19.55 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.33 % 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: -2.65 (0.12), residues: 4765 helix: -0.54 (0.13), residues: 1534 sheet: -0.88 (0.23), residues: 489 loop : -2.80 (0.11), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 258 HIS 0.015 0.001 HIS A 92 PHE 0.041 0.002 PHE H 118 TYR 0.019 0.002 TYR O 219 ARG 0.028 0.001 ARG O 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 428 time to evaluate : 5.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 437 average time/residue: 0.5090 time to fit residues: 376.6481 Evaluate side-chains 404 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 391 time to evaluate : 4.523 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3757 time to fit residues: 15.8483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 280 optimal weight: 5.9990 chunk 452 optimal weight: 6.9990 chunk 275 optimal weight: 0.4980 chunk 214 optimal weight: 0.7980 chunk 314 optimal weight: 0.7980 chunk 474 optimal weight: 2.9990 chunk 436 optimal weight: 3.9990 chunk 377 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 291 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS G 31 ASN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN O 298 ASN O 587 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4719 moved from start: 1.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 39016 Z= 0.198 Angle : 0.736 13.829 52687 Z= 0.370 Chirality : 0.046 0.256 5961 Planarity : 0.005 0.098 6778 Dihedral : 5.928 76.075 5227 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.04 % Favored : 88.67 % Rotamer: Outliers : 0.28 % Allowed : 20.14 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.33 % 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: -2.65 (0.12), residues: 4765 helix: -0.59 (0.13), residues: 1538 sheet: -0.95 (0.23), residues: 489 loop : -2.75 (0.11), residues: 2738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP O 583 HIS 0.017 0.001 HIS D 133 PHE 0.037 0.002 PHE H 118 TYR 0.021 0.002 TYR B 715 ARG 0.020 0.001 ARG A 696 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 462 time to evaluate : 4.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 464 average time/residue: 0.5053 time to fit residues: 393.2762 Evaluate side-chains 410 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 404 time to evaluate : 4.473 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3957 time to fit residues: 10.5389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 299 optimal weight: 6.9990 chunk 402 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 348 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 378 optimal weight: 0.0270 chunk 158 optimal weight: 0.6980 chunk 388 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A 488 HIS ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN A 913 GLN ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 HIS ** B 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN K 95 HIS ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 HIS O 599 ASN P 189 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.244898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.220676 restraints weight = 62119.672| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 1.82 r_work: 0.4316 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5604 moved from start: 1.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 39016 Z= 0.265 Angle : 0.809 23.690 52687 Z= 0.406 Chirality : 0.048 0.255 5961 Planarity : 0.006 0.101 6778 Dihedral : 6.113 77.220 5227 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.55 % Favored : 87.14 % Rotamer: Outliers : 0.73 % Allowed : 20.37 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.33 % 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: -2.67 (0.12), residues: 4765 helix: -0.69 (0.13), residues: 1553 sheet: -0.93 (0.23), residues: 497 loop : -2.72 (0.11), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP O 583 HIS 0.024 0.002 HIS J 53 PHE 0.026 0.002 PHE B 51 TYR 0.037 0.002 TYR E 46 ARG 0.010 0.001 ARG J 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9224.56 seconds wall clock time: 168 minutes 28.39 seconds (10108.39 seconds total)