Starting phenix.real_space_refine on Sat Mar 23 18:10:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu3_3958/03_2024/6eu3_3958_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu3_3958/03_2024/6eu3_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_3958/03_2024/6eu3_3958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu3_3958/03_2024/6eu3_3958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu3_3958/03_2024/6eu3_3958_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu3_3958/03_2024/6eu3_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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 19.02, per 1000 atoms: 0.50 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: 13.33 Conformation dependent library (CDL) restraints added in 6.6 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: 4.09 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: 14.36 Time building geometry restraints manager: 14.61 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 8.500 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 98.560 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.380 ------------------------------------------------------------------------------- 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 : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.0867 (ttmt) cc_final: 0.0367 (mttt) REVERT: A 229 ASN cc_start: 0.3094 (m-40) cc_final: 0.0374 (p0) REVERT: A 326 TYR cc_start: 0.3424 (t80) cc_final: 0.2608 (t80) REVERT: A 427 HIS cc_start: 0.1644 (t-90) cc_final: 0.1220 (t-90) REVERT: A 742 ILE cc_start: -0.0420 (mm) cc_final: -0.0696 (tt) REVERT: A 774 ARG cc_start: -0.0086 (ppp80) cc_final: -0.1128 (ppp80) REVERT: A 1389 PHE cc_start: 0.3464 (t80) cc_final: 0.1952 (p90) REVERT: B 123 MET cc_start: -0.2480 (mtp) cc_final: -0.3149 (pmm) REVERT: B 188 ASN cc_start: 0.0660 (t0) cc_final: -0.0064 (t0) REVERT: B 405 LYS cc_start: 0.6451 (ttpp) cc_final: 0.6048 (mttm) REVERT: B 479 LYS cc_start: 0.2195 (pmtt) cc_final: 0.1829 (pttt) REVERT: B 935 ASP cc_start: 0.3158 (p0) cc_final: 0.2297 (t0) REVERT: B 1137 ILE cc_start: 0.0869 (mt) cc_final: 0.0596 (mt) REVERT: E 28 TYR cc_start: 0.2578 (m-10) cc_final: 0.1771 (m-80) REVERT: G 144 GLU cc_start: 0.3252 (pp20) cc_final: 0.2237 (pt0) REVERT: I 1 MET cc_start: 0.2096 (mmm) cc_final: 0.0802 (ptt) REVERT: K 121 LEU cc_start: -0.0498 (tp) cc_final: -0.0885 (pp) REVERT: N 305 MET cc_start: 0.0817 (mpt) cc_final: -0.0878 (mtm) REVERT: O 105 LYS cc_start: 0.3392 (mmtp) cc_final: 0.2742 (mttp) REVERT: O 500 LEU cc_start: 0.3965 (tp) cc_final: 0.3259 (tp) REVERT: P 175 ILE cc_start: 0.6034 (mt) cc_final: 0.5308 (tt) REVERT: P 239 ASN cc_start: 0.4786 (p0) cc_final: 0.4507 (m-40) outliers start: 11 outliers final: 2 residues processed: 574 average time/residue: 0.5054 time to fit residues: 468.6359 Evaluate side-chains 344 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 342 time to evaluate : 3.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain J residue 2 ILE 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: 0.0670 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: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 109 ASN A 161 ASN A 229 ASN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 626 HIS B 774 ASN B 800 ASN B 840 GLN B 861 ASN B 893 GLN B 916 HIS ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 997 ASN B1025 GLN B1049 GLN C 137 ASN C 143 ASN C 161 HIS C 207 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 E 174 GLN G 36 ASN H 33 GLN H 128 ASN I 10 ASN K 95 HIS ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 346 GLN O 362 ASN O 369 HIS O 464 ASN O 544 ASN ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 572 HIS O 631 ASN ** P 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0818 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39016 Z= 0.189 Angle : 0.722 15.507 52687 Z= 0.372 Chirality : 0.045 0.202 5961 Planarity : 0.005 0.083 6778 Dihedral : 6.612 73.794 5230 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.67 % Favored : 87.93 % Rotamer: Outliers : 1.90 % Allowed : 9.42 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.46 % 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: -4.09 (0.10), residues: 4765 helix: -2.41 (0.11), residues: 1540 sheet: -1.74 (0.21), residues: 563 loop : -3.25 (0.10), residues: 2662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 79 HIS 0.014 0.001 HIS B 244 PHE 0.031 0.002 PHE I 33 TYR 0.030 0.001 TYR L 29 ARG 0.007 0.001 ARG O 368 *********************** 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 470 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 389 time to evaluate : 3.719 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: A 197 TRP cc_start: 0.4114 (t60) cc_final: 0.3841 (t60) REVERT: A 427 HIS cc_start: 0.2012 (t-90) cc_final: 0.1443 (t-90) REVERT: A 1260 MET cc_start: 0.1513 (mmp) cc_final: 0.0783 (tmm) REVERT: A 1304 MET cc_start: -0.0091 (mmm) cc_final: -0.0334 (mmm) REVERT: B 80 ASN cc_start: 0.4479 (t0) cc_final: 0.4049 (p0) REVERT: B 117 GLU cc_start: 0.2110 (tt0) cc_final: 0.1316 (mt-10) REVERT: B 171 MET cc_start: -0.1123 (mtt) cc_final: -0.1353 (mtt) REVERT: B 188 ASN cc_start: 0.1342 (t0) cc_final: 0.0891 (m110) REVERT: B 283 PHE cc_start: 0.2279 (t80) cc_final: 0.1680 (t80) REVERT: B 312 MET cc_start: 0.0599 (pmm) cc_final: 0.0135 (pmm) REVERT: B 470 MET cc_start: 0.2593 (mmt) cc_final: 0.2328 (mmp) REVERT: C 1 MET cc_start: -0.0005 (tmm) cc_final: -0.1109 (ptt) REVERT: D 29 TRP cc_start: 0.2681 (m100) cc_final: 0.2421 (m100) REVERT: D 131 MET cc_start: 0.3522 (ttm) cc_final: 0.2932 (mtp) REVERT: E 50 MET cc_start: 0.1700 (tpt) cc_final: 0.0467 (ptt) REVERT: F 115 THR cc_start: 0.0149 (OUTLIER) cc_final: -0.0094 (p) REVERT: I 1 MET cc_start: 0.1815 (mmm) cc_final: 0.0529 (ptt) REVERT: K 121 LEU cc_start: -0.0013 (tp) cc_final: -0.1183 (pp) REVERT: N 305 MET cc_start: 0.0899 (mpt) cc_final: -0.0691 (mtm) REVERT: O 197 MET cc_start: 0.2491 (ppp) cc_final: 0.2112 (ppp) REVERT: O 326 ILE cc_start: 0.0265 (OUTLIER) cc_final: 0.0026 (mt) REVERT: P 175 ILE cc_start: 0.6379 (mt) cc_final: 0.6011 (tt) REVERT: P 247 LEU cc_start: 0.4586 (tt) cc_final: 0.4297 (tt) REVERT: P 294 PHE cc_start: 0.2618 (t80) cc_final: 0.1307 (t80) outliers start: 81 outliers final: 34 residues processed: 450 average time/residue: 0.4811 time to fit residues: 358.8918 Evaluate side-chains 369 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 333 time to evaluate : 4.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain N residue 409 LEU Chi-restraints excluded: chain O residue 90 SER Chi-restraints excluded: chain O residue 304 VAL Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 549 GLN Chi-restraints excluded: chain O residue 560 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 240 optimal weight: 0.0470 chunk 134 optimal weight: 4.9990 chunk 359 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 433 optimal weight: 3.9990 chunk 467 optimal weight: 6.9990 chunk 385 optimal weight: 0.7980 chunk 429 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 347 optimal weight: 8.9990 overall best weight: 2.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 229 ASN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN ** A 427 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 ** 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 217 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 321 GLN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 558 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 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN B 850 ASN B 893 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** 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 ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS M 89 GLN M 92 ASN M 155 ASN M 190 ASN ** N 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 HIS O 207 HIS O 240 GLN ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 310 GLN ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 GLN O 652 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2581 moved from start: 0.6388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.256 39016 Z= 0.464 Angle : 1.154 24.369 52687 Z= 0.604 Chirality : 0.060 0.567 5961 Planarity : 0.009 0.203 6778 Dihedral : 7.870 76.892 5230 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.40 % Allowed : 14.40 % Favored : 85.20 % Rotamer: Outliers : 4.17 % Allowed : 11.84 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.96 % Twisted General : 0.61 % 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: -4.10 (0.10), residues: 4765 helix: -2.21 (0.11), residues: 1498 sheet: -1.84 (0.21), residues: 522 loop : -3.36 (0.10), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP O 583 HIS 0.027 0.003 HIS A 80 PHE 0.043 0.004 PHE C 86 TYR 0.052 0.004 TYR B1073 ARG 0.041 0.002 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 646 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 468 time to evaluate : 3.702 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: A 205 LEU cc_start: 0.2977 (OUTLIER) cc_final: 0.2114 (tp) REVERT: A 314 GLU cc_start: 0.2120 (tp30) cc_final: 0.1354 (mt-10) REVERT: A 396 ASP cc_start: 0.3286 (OUTLIER) cc_final: 0.2312 (p0) REVERT: A 599 LYS cc_start: 0.5749 (tptp) cc_final: 0.5487 (ttpp) REVERT: A 789 ASN cc_start: 0.4997 (OUTLIER) cc_final: 0.4704 (p0) REVERT: A 926 MET cc_start: 0.3745 (tpt) cc_final: 0.2847 (mmm) REVERT: A 960 MET cc_start: 0.1713 (mmm) cc_final: 0.0640 (ptt) REVERT: A 1260 MET cc_start: 0.1541 (mmp) cc_final: 0.0858 (tmm) REVERT: A 1304 MET cc_start: 0.0714 (mmm) cc_final: -0.0594 (mtp) REVERT: A 1348 MET cc_start: 0.2224 (tpp) cc_final: 0.1954 (ttt) REVERT: B 356 VAL cc_start: 0.3487 (OUTLIER) cc_final: 0.2924 (p) REVERT: B 449 MET cc_start: -0.1229 (OUTLIER) cc_final: -0.1615 (mmp) REVERT: B 809 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.6969 (tpp) REVERT: B 821 HIS cc_start: 0.2789 (t70) cc_final: 0.2357 (t70) REVERT: B 944 MET cc_start: 0.1805 (pmm) cc_final: -0.1562 (mtp) REVERT: B 1119 MET cc_start: 0.5360 (pmm) cc_final: 0.3385 (ttt) REVERT: C 59 ILE cc_start: -0.0155 (OUTLIER) cc_final: -0.0752 (tt) REVERT: E 50 MET cc_start: 0.1329 (tpt) cc_final: 0.0168 (ptt) REVERT: G 144 GLU cc_start: 0.4618 (pp20) cc_final: 0.3218 (pt0) REVERT: I 1 MET cc_start: 0.1562 (mmm) cc_final: 0.0326 (ptt) REVERT: J 63 TYR cc_start: 0.4588 (m-80) cc_final: 0.3373 (m-10) REVERT: K 81 MET cc_start: 0.2420 (tpp) cc_final: 0.1894 (tmm) REVERT: K 125 MET cc_start: 0.3967 (mmm) cc_final: 0.3042 (mmp) REVERT: N 305 MET cc_start: 0.1974 (mpt) cc_final: -0.0894 (mtm) REVERT: O 84 ASP cc_start: 0.3843 (OUTLIER) cc_final: 0.3437 (m-30) REVERT: O 197 MET cc_start: 0.3259 (ppp) cc_final: 0.2973 (ppp) REVERT: O 288 MET cc_start: -0.1015 (pmm) cc_final: -0.1329 (tpt) REVERT: P 175 ILE cc_start: 0.6701 (mt) cc_final: 0.6361 (tt) REVERT: P 294 PHE cc_start: 0.2847 (t80) cc_final: 0.2411 (t80) outliers start: 178 outliers final: 70 residues processed: 604 average time/residue: 0.4845 time to fit residues: 484.6910 Evaluate side-chains 441 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 363 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 735 TYR Chi-restraints excluded: chain A residue 789 ASN Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1362 MET Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 1003 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 90 SER Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 293 SER Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 549 GLN Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 573 SER Chi-restraints excluded: chain P residue 307 LYS Chi-restraints excluded: chain Q residue 39 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 427 optimal weight: 0.6980 chunk 325 optimal weight: 0.1980 chunk 224 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 290 optimal weight: 0.0570 chunk 434 optimal weight: 3.9990 chunk 460 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 chunk 411 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS A 134 ASN A 156 HIS A 233 GLN A 427 HIS ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 558 ASN B 593 ASN B 596 GLN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN B 803 GLN ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 GLN ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 GLN C 158 ASN E 101 GLN K 95 HIS ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 155 ASN M 190 ASN O 298 ASN ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2527 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 39016 Z= 0.189 Angle : 0.729 15.658 52687 Z= 0.372 Chirality : 0.046 0.268 5961 Planarity : 0.005 0.090 6778 Dihedral : 6.601 77.322 5227 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.16 % Favored : 88.50 % Rotamer: Outliers : 2.32 % Allowed : 14.77 % Favored : 82.91 % 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: -3.40 (0.11), residues: 4765 helix: -1.36 (0.13), residues: 1494 sheet: -1.35 (0.22), residues: 522 loop : -3.12 (0.10), residues: 2749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP O 583 HIS 0.009 0.001 HIS B 244 PHE 0.032 0.002 PHE B 718 TYR 0.026 0.002 TYR P 249 ARG 0.008 0.001 ARG A 905 *********************** 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 492 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 393 time to evaluate : 4.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.5944 (pmt170) cc_final: 0.5644 (tpm170) REVERT: A 794 MET cc_start: 0.0330 (tpp) cc_final: -0.0952 (tpp) REVERT: A 926 MET cc_start: 0.3509 (tpt) cc_final: 0.2395 (mmm) REVERT: A 959 ILE cc_start: 0.1676 (OUTLIER) cc_final: 0.0956 (tp) REVERT: A 1260 MET cc_start: 0.1206 (mmp) cc_final: 0.0647 (tmm) REVERT: A 1348 MET cc_start: 0.2028 (tpp) cc_final: 0.1765 (ttt) REVERT: B 289 GLU cc_start: 0.3958 (OUTLIER) cc_final: 0.3642 (mt-10) REVERT: B 358 MET cc_start: -0.0252 (mmp) cc_final: -0.1338 (ptp) REVERT: B 360 MET cc_start: 0.4466 (mmt) cc_final: 0.3989 (mmt) REVERT: B 652 ASN cc_start: 0.1541 (OUTLIER) cc_final: 0.0256 (p0) REVERT: B 1119 MET cc_start: 0.5611 (pmm) cc_final: 0.4221 (ptp) REVERT: C 1 MET cc_start: -0.0005 (tmm) cc_final: -0.0862 (ptm) REVERT: E 50 MET cc_start: 0.1651 (tpt) cc_final: 0.0432 (ptt) REVERT: E 149 LEU cc_start: 0.2486 (tp) cc_final: 0.1624 (pt) REVERT: F 103 MET cc_start: 0.2435 (tpt) cc_final: 0.0777 (ptt) REVERT: G 144 GLU cc_start: 0.4319 (pp20) cc_final: 0.3332 (pt0) REVERT: I 1 MET cc_start: 0.1677 (mmm) cc_final: 0.0458 (ptt) REVERT: I 12 LEU cc_start: 0.1836 (OUTLIER) cc_final: 0.1069 (pp) REVERT: J 63 TYR cc_start: 0.4502 (m-80) cc_final: 0.4035 (m-10) REVERT: J 67 GLU cc_start: 0.3254 (mm-30) cc_final: 0.2706 (tm-30) REVERT: K 81 MET cc_start: 0.3041 (tpp) cc_final: 0.2413 (tmm) REVERT: K 121 LEU cc_start: 0.0418 (OUTLIER) cc_final: -0.0179 (mp) REVERT: L 28 LYS cc_start: 0.4553 (pttp) cc_final: 0.4059 (pttp) REVERT: N 305 MET cc_start: 0.1439 (mpt) cc_final: -0.0615 (mtm) REVERT: O 65 ILE cc_start: 0.1571 (OUTLIER) cc_final: 0.1197 (mt) REVERT: O 589 LEU cc_start: 0.2177 (OUTLIER) cc_final: 0.1750 (mp) REVERT: P 175 ILE cc_start: 0.6782 (mt) cc_final: 0.6491 (tt) REVERT: P 294 PHE cc_start: 0.2592 (t80) cc_final: 0.2291 (t80) outliers start: 99 outliers final: 46 residues processed: 467 average time/residue: 0.4651 time to fit residues: 368.3446 Evaluate side-chains 399 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 346 time to evaluate : 4.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 735 TYR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 753 GLN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 928 GLN Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 65 ILE Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 368 ARG Chi-restraints excluded: chain O residue 549 GLN Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain P residue 307 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 383 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 342 optimal weight: 0.7980 chunk 189 optimal weight: 0.7980 chunk 392 optimal weight: 0.5980 chunk 318 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 412 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 518 ASN ** 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** A1142 ASN ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 593 ASN B 596 GLN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 ASN N 377 ASN O 469 ASN ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 631 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2972 moved from start: 0.7709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.146 39016 Z= 0.218 Angle : 0.741 16.419 52687 Z= 0.379 Chirality : 0.046 0.240 5961 Planarity : 0.005 0.085 6778 Dihedral : 6.381 76.662 5227 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.29 % Allowed : 13.03 % Favored : 86.67 % Rotamer: Outliers : 3.02 % Allowed : 15.56 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % 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: -3.10 (0.11), residues: 4765 helix: -0.99 (0.13), residues: 1478 sheet: -1.33 (0.21), residues: 549 loop : -2.98 (0.11), residues: 2738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP O 583 HIS 0.016 0.001 HIS O 152 PHE 0.018 0.002 PHE B 933 TYR 0.029 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 520 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 391 time to evaluate : 4.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ASN cc_start: 0.2066 (OUTLIER) cc_final: 0.1081 (p0) REVERT: A 433 LEU cc_start: 0.3128 (OUTLIER) cc_final: 0.2821 (tt) REVERT: A 473 LEU cc_start: 0.4824 (pp) cc_final: 0.4471 (mp) REVERT: A 926 MET cc_start: 0.3882 (tpt) cc_final: 0.3640 (mmm) REVERT: A 1117 MET cc_start: 0.4948 (ttm) cc_final: 0.4707 (ttt) REVERT: A 1260 MET cc_start: 0.1171 (mmp) cc_final: 0.0474 (tmm) REVERT: B 171 MET cc_start: 0.1565 (tpp) cc_final: 0.1323 (tpp) REVERT: B 312 MET cc_start: 0.2580 (pmm) cc_final: 0.0987 (mtm) REVERT: B 356 VAL cc_start: 0.3435 (OUTLIER) cc_final: 0.2791 (p) REVERT: B 360 MET cc_start: 0.4300 (mmt) cc_final: 0.3680 (mmt) REVERT: B 439 THR cc_start: 0.6072 (m) cc_final: 0.5491 (p) REVERT: B 652 ASN cc_start: 0.2311 (OUTLIER) cc_final: 0.1187 (p0) REVERT: B 773 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5986 (mt) REVERT: B 945 ASN cc_start: 0.3374 (p0) cc_final: 0.2777 (p0) REVERT: C 1 MET cc_start: -0.0040 (tmm) cc_final: -0.0822 (ptm) REVERT: C 201 GLU cc_start: 0.4932 (tm-30) cc_final: 0.4548 (tt0) REVERT: E 1 MET cc_start: 0.0724 (mmm) cc_final: -0.0083 (mtm) REVERT: E 39 LEU cc_start: -0.0060 (OUTLIER) cc_final: -0.0403 (mt) REVERT: E 50 MET cc_start: 0.1725 (tpt) cc_final: 0.0346 (ptm) REVERT: E 149 LEU cc_start: 0.2661 (tp) cc_final: 0.1674 (pt) REVERT: E 215 MET cc_start: 0.3098 (mmp) cc_final: 0.2863 (mmp) REVERT: G 26 ILE cc_start: 0.7382 (mt) cc_final: 0.7115 (mt) REVERT: G 144 GLU cc_start: 0.4467 (pp20) cc_final: 0.3011 (pt0) REVERT: I 1 MET cc_start: 0.1751 (mmm) cc_final: 0.0454 (ptt) REVERT: J 41 LEU cc_start: 0.1300 (OUTLIER) cc_final: 0.0301 (mt) REVERT: J 63 TYR cc_start: 0.5213 (m-80) cc_final: 0.4019 (m-10) REVERT: J 67 GLU cc_start: 0.3673 (mm-30) cc_final: 0.3165 (tm-30) REVERT: L 28 LYS cc_start: 0.4705 (pttp) cc_final: 0.4344 (pttp) REVERT: N 305 MET cc_start: 0.1795 (mpt) cc_final: -0.0713 (mtm) REVERT: O 291 ARG cc_start: 0.3683 (mtp180) cc_final: 0.3291 (tpt170) REVERT: O 577 MET cc_start: 0.6350 (tpp) cc_final: 0.6001 (tpp) REVERT: P 175 ILE cc_start: 0.6791 (mt) cc_final: 0.6520 (tt) outliers start: 129 outliers final: 65 residues processed: 497 average time/residue: 0.4532 time to fit residues: 382.0306 Evaluate side-chains 420 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 348 time to evaluate : 4.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 735 TYR Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 753 GLN Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 88 TRP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain M residue 238 ASP Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 368 ARG Chi-restraints excluded: chain O residue 549 GLN Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 573 SER Chi-restraints excluded: chain P residue 307 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 154 optimal weight: 0.9990 chunk 414 optimal weight: 2.9990 chunk 90 optimal weight: 0.0060 chunk 270 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 460 optimal weight: 6.9990 chunk 382 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 241 optimal weight: 0.8980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 ASN ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** 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 733 GLN B 754 ASN ** B 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 HIS ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3283 moved from start: 0.8552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 39016 Z= 0.206 Angle : 0.706 15.035 52687 Z= 0.359 Chirality : 0.046 0.479 5961 Planarity : 0.005 0.099 6778 Dihedral : 6.161 76.691 5227 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.63 % Favored : 88.08 % Rotamer: Outliers : 2.93 % Allowed : 16.34 % Favored : 80.73 % 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: -2.89 (0.11), residues: 4765 helix: -0.72 (0.13), residues: 1490 sheet: -1.18 (0.23), residues: 511 loop : -2.90 (0.11), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP O 583 HIS 0.008 0.001 HIS A 736 PHE 0.024 0.002 PHE O 47 TYR 0.023 0.001 TYR G 49 ARG 0.017 0.001 ARG A 476 *********************** 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 532 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 407 time to evaluate : 4.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.2478 (OUTLIER) cc_final: 0.1746 (tp) REVERT: A 310 ASN cc_start: 0.2191 (OUTLIER) cc_final: 0.1182 (p0) REVERT: A 617 ASN cc_start: 0.3168 (OUTLIER) cc_final: 0.2931 (p0) REVERT: A 794 MET cc_start: 0.0707 (tpp) cc_final: 0.0422 (tpp) REVERT: A 926 MET cc_start: 0.3775 (tpt) cc_final: 0.3389 (mmm) REVERT: A 959 ILE cc_start: 0.1505 (OUTLIER) cc_final: 0.0611 (tp) REVERT: A 1260 MET cc_start: 0.1051 (mmp) cc_final: 0.0347 (tmm) REVERT: A 1275 LEU cc_start: 0.4278 (mm) cc_final: 0.4030 (mm) REVERT: B 171 MET cc_start: 0.2658 (tpp) cc_final: 0.0897 (mtt) REVERT: B 312 MET cc_start: 0.2379 (pmm) cc_final: 0.1073 (mtm) REVERT: B 356 VAL cc_start: 0.3217 (OUTLIER) cc_final: 0.2508 (p) REVERT: B 358 MET cc_start: -0.0559 (mmp) cc_final: -0.1438 (ptp) REVERT: B 360 MET cc_start: 0.4645 (mmt) cc_final: 0.4054 (mmt) REVERT: B 439 THR cc_start: 0.6718 (m) cc_final: 0.5824 (p) REVERT: B 652 ASN cc_start: 0.2286 (OUTLIER) cc_final: 0.1143 (p0) REVERT: B 753 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7490 (mm110) REVERT: B 760 MET cc_start: 0.3452 (OUTLIER) cc_final: 0.2969 (tpt) REVERT: B 884 VAL cc_start: 0.6708 (OUTLIER) cc_final: 0.6491 (p) REVERT: B 1040 ARG cc_start: 0.4900 (OUTLIER) cc_final: 0.4698 (ttm170) REVERT: C 1 MET cc_start: 0.0204 (tmm) cc_final: -0.0640 (ptm) REVERT: E 50 MET cc_start: 0.1903 (tpt) cc_final: 0.0431 (ptm) REVERT: E 149 LEU cc_start: 0.2517 (tp) cc_final: 0.1435 (pt) REVERT: E 215 MET cc_start: 0.3254 (mmp) cc_final: 0.3014 (mmp) REVERT: F 103 MET cc_start: 0.3813 (tpt) cc_final: 0.3261 (tpt) REVERT: G 144 GLU cc_start: 0.4483 (pp20) cc_final: 0.4251 (pt0) REVERT: I 1 MET cc_start: 0.1667 (mmm) cc_final: 0.0507 (ptt) REVERT: I 12 LEU cc_start: 0.1813 (OUTLIER) cc_final: 0.1043 (pp) REVERT: L 28 LYS cc_start: 0.4828 (pttp) cc_final: 0.4474 (mtpt) REVERT: N 305 MET cc_start: 0.1644 (mpt) cc_final: -0.0779 (mtm) REVERT: O 65 ILE cc_start: 0.3629 (OUTLIER) cc_final: 0.3321 (mt) REVERT: O 320 GLU cc_start: 0.4580 (mm-30) cc_final: 0.4306 (tp30) REVERT: O 577 MET cc_start: 0.6704 (tpp) cc_final: 0.6484 (tpp) REVERT: P 175 ILE cc_start: 0.6959 (mt) cc_final: 0.6629 (tt) REVERT: P 294 PHE cc_start: 0.3379 (t80) cc_final: 0.2507 (t80) outliers start: 125 outliers final: 74 residues processed: 508 average time/residue: 0.4785 time to fit residues: 410.9072 Evaluate side-chains 442 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 356 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 735 TYR Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1142 ASN Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 753 GLN Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 1040 ARG Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 88 TRP Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 65 ILE Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain O residue 144 MET Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 368 ARG Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 573 SER Chi-restraints excluded: chain P residue 307 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 444 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 262 optimal weight: 0.8980 chunk 336 optimal weight: 9.9990 chunk 260 optimal weight: 0.4980 chunk 387 optimal weight: 20.0000 chunk 257 optimal weight: 0.7980 chunk 458 optimal weight: 0.0980 chunk 287 optimal weight: 5.9990 chunk 279 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** 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 733 GLN B 754 ASN ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS H 33 GLN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 202 GLN O 298 ASN O 652 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3501 moved from start: 0.9178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 39016 Z= 0.189 Angle : 0.691 12.062 52687 Z= 0.352 Chirality : 0.045 0.246 5961 Planarity : 0.005 0.077 6778 Dihedral : 5.988 76.191 5227 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.00 % Favored : 87.72 % Rotamer: Outliers : 2.74 % Allowed : 16.88 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % 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: -2.71 (0.12), residues: 4765 helix: -0.54 (0.13), residues: 1508 sheet: -1.13 (0.22), residues: 504 loop : -2.82 (0.11), residues: 2753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 79 HIS 0.010 0.001 HIS A 427 PHE 0.023 0.001 PHE O 191 TYR 0.024 0.001 TYR B 842 ARG 0.014 0.001 ARG C 281 *********************** 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 516 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 399 time to evaluate : 4.026 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: A 205 LEU cc_start: 0.2392 (OUTLIER) cc_final: 0.1690 (tp) REVERT: A 274 MET cc_start: -0.0519 (OUTLIER) cc_final: -0.0790 (ptm) REVERT: A 310 ASN cc_start: 0.2264 (OUTLIER) cc_final: 0.1221 (p0) REVERT: A 450 MET cc_start: 0.3570 (mmt) cc_final: 0.2013 (mmt) REVERT: A 617 ASN cc_start: 0.3461 (OUTLIER) cc_final: 0.2798 (p0) REVERT: A 959 ILE cc_start: 0.1326 (OUTLIER) cc_final: 0.0527 (tp) REVERT: A 960 MET cc_start: 0.1593 (mmm) cc_final: 0.0933 (ttp) REVERT: A 1260 MET cc_start: 0.0836 (mmp) cc_final: 0.0132 (tmm) REVERT: B 312 MET cc_start: 0.2406 (pmm) cc_final: 0.1139 (mtm) REVERT: B 356 VAL cc_start: 0.3272 (OUTLIER) cc_final: 0.2681 (p) REVERT: B 360 MET cc_start: 0.4761 (mmt) cc_final: 0.4108 (mmt) REVERT: B 439 THR cc_start: 0.7015 (m) cc_final: 0.6161 (p) REVERT: B 510 LEU cc_start: 0.5651 (tt) cc_final: 0.5436 (tp) REVERT: B 517 MET cc_start: 0.4350 (mmp) cc_final: 0.4146 (mmm) REVERT: B 652 ASN cc_start: 0.2363 (OUTLIER) cc_final: 0.1348 (p0) REVERT: B 753 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.6463 (mm110) REVERT: B 760 MET cc_start: 0.3297 (OUTLIER) cc_final: 0.2915 (tpt) REVERT: B 884 VAL cc_start: 0.7369 (OUTLIER) cc_final: 0.7085 (p) REVERT: B 998 TYR cc_start: 0.4942 (p90) cc_final: 0.3704 (p90) REVERT: B 1040 ARG cc_start: 0.5387 (OUTLIER) cc_final: 0.5043 (ttm170) REVERT: C 1 MET cc_start: 0.0195 (tmm) cc_final: -0.0652 (ptp) REVERT: E 39 LEU cc_start: 0.0047 (OUTLIER) cc_final: -0.0545 (mt) REVERT: E 50 MET cc_start: 0.1915 (tpt) cc_final: 0.0417 (ptm) REVERT: F 103 MET cc_start: 0.4350 (tpt) cc_final: 0.4094 (tpt) REVERT: G 144 GLU cc_start: 0.4751 (pp20) cc_final: 0.4462 (pt0) REVERT: G 167 GLU cc_start: 0.6156 (tt0) cc_final: 0.5408 (pp20) REVERT: I 1 MET cc_start: 0.1664 (mmm) cc_final: 0.0526 (ptt) REVERT: I 12 LEU cc_start: 0.1778 (OUTLIER) cc_final: 0.1005 (pp) REVERT: J 49 MET cc_start: 0.5087 (mmt) cc_final: 0.4701 (tpt) REVERT: N 305 MET cc_start: 0.2003 (mpt) cc_final: -0.0551 (mtm) REVERT: O 494 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.5535 (t80) REVERT: O 579 GLN cc_start: 0.7169 (tp-100) cc_final: 0.6809 (tp-100) REVERT: P 175 ILE cc_start: 0.6953 (mt) cc_final: 0.6602 (tt) REVERT: P 241 ARG cc_start: 0.4299 (mmm160) cc_final: 0.4049 (tpp-160) REVERT: P 294 PHE cc_start: 0.3118 (t80) cc_final: 0.0305 (t80) outliers start: 117 outliers final: 80 residues processed: 488 average time/residue: 0.4522 time to fit residues: 378.4307 Evaluate side-chains 451 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 357 time to evaluate : 4.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 735 TYR Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 753 GLN Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 1024 TYR Chi-restraints excluded: chain B residue 1040 ARG Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 88 TRP Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain M residue 238 ASP Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain O residue 144 MET Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 368 ARG Chi-restraints excluded: chain O residue 494 TYR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain P residue 307 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 283 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 274 optimal weight: 0.5980 chunk 138 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 291 optimal weight: 9.9990 chunk 312 optimal weight: 0.1980 chunk 226 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 360 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS A 523 GLN A 539 ASN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 HIS ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 GLN B 456 HIS ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN O 549 GLN O 579 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3926 moved from start: 1.0271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 39016 Z= 0.212 Angle : 0.716 12.604 52687 Z= 0.365 Chirality : 0.045 0.217 5961 Planarity : 0.005 0.102 6778 Dihedral : 5.929 72.152 5227 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.19 % Favored : 88.52 % Rotamer: Outliers : 2.88 % Allowed : 17.49 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % 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: -2.71 (0.12), residues: 4765 helix: -0.49 (0.13), residues: 1529 sheet: -1.23 (0.22), residues: 529 loop : -2.85 (0.11), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 495 HIS 0.020 0.001 HIS O 222 PHE 0.023 0.002 PHE K 63 TYR 0.034 0.002 TYR E 46 ARG 0.017 0.001 ARG J 6 *********************** 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 573 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 450 time to evaluate : 3.837 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: A 205 LEU cc_start: 0.2441 (OUTLIER) cc_final: 0.1684 (tp) REVERT: A 273 MET cc_start: -0.1091 (ptt) cc_final: -0.1970 (mtm) REVERT: A 310 ASN cc_start: 0.2011 (OUTLIER) cc_final: 0.1117 (p0) REVERT: A 420 ILE cc_start: 0.4739 (tp) cc_final: 0.4498 (tt) REVERT: A 450 MET cc_start: 0.3998 (mmt) cc_final: 0.2415 (ptp) REVERT: A 617 ASN cc_start: 0.4020 (OUTLIER) cc_final: 0.3331 (p0) REVERT: A 802 SER cc_start: 0.5817 (p) cc_final: 0.5287 (m) REVERT: A 959 ILE cc_start: 0.1786 (OUTLIER) cc_final: 0.0890 (tp) REVERT: A 1260 MET cc_start: 0.0945 (mmp) cc_final: 0.0112 (tmm) REVERT: B 312 MET cc_start: 0.2685 (pmm) cc_final: 0.1347 (mtm) REVERT: B 356 VAL cc_start: 0.3146 (OUTLIER) cc_final: 0.2482 (p) REVERT: B 360 MET cc_start: 0.4905 (mmt) cc_final: 0.4384 (mmt) REVERT: B 435 ARG cc_start: 0.6771 (mtp180) cc_final: 0.6337 (mtm-85) REVERT: B 439 THR cc_start: 0.7600 (m) cc_final: 0.7050 (p) REVERT: B 652 ASN cc_start: 0.2052 (OUTLIER) cc_final: 0.1093 (p0) REVERT: B 1119 MET cc_start: 0.7557 (pmm) cc_final: 0.7309 (ptp) REVERT: C 1 MET cc_start: 0.0616 (tmm) cc_final: -0.0380 (ptp) REVERT: C 71 MET cc_start: 0.5216 (tpp) cc_final: 0.4932 (tpp) REVERT: C 129 GLU cc_start: 0.3649 (pm20) cc_final: 0.3097 (mm-30) REVERT: E 50 MET cc_start: 0.1947 (tpt) cc_final: 0.0571 (ptt) REVERT: G 49 TYR cc_start: 0.6365 (OUTLIER) cc_final: 0.5885 (m-80) REVERT: I 1 MET cc_start: 0.1675 (mmm) cc_final: 0.0575 (ptt) REVERT: I 12 LEU cc_start: 0.1838 (OUTLIER) cc_final: 0.1046 (pp) REVERT: N 305 MET cc_start: 0.2148 (mpt) cc_final: -0.0385 (mtm) REVERT: O 65 ILE cc_start: 0.5507 (OUTLIER) cc_final: 0.5288 (mt) REVERT: O 144 MET cc_start: 0.2426 (OUTLIER) cc_final: 0.1446 (pmm) REVERT: O 197 MET cc_start: 0.2503 (OUTLIER) cc_final: 0.1896 (ppp) REVERT: O 296 LEU cc_start: 0.6772 (mt) cc_final: 0.6482 (mm) REVERT: O 494 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.4975 (t80) REVERT: O 629 MET cc_start: 0.6703 (mtp) cc_final: 0.6273 (ttm) REVERT: P 294 PHE cc_start: 0.3318 (t80) cc_final: 0.0412 (t80) outliers start: 123 outliers final: 73 residues processed: 540 average time/residue: 0.4671 time to fit residues: 423.0375 Evaluate side-chains 465 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 380 time to evaluate : 4.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 735 TYR Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 49 TYR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain M residue 238 ASP Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 65 ILE Chi-restraints excluded: chain O residue 144 MET Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 197 MET Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 368 ARG Chi-restraints excluded: chain O residue 494 TYR Chi-restraints excluded: chain O residue 496 ILE Chi-restraints excluded: chain O residue 549 GLN Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain P residue 307 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 417 optimal weight: 2.9990 chunk 439 optimal weight: 0.0770 chunk 401 optimal weight: 5.9990 chunk 427 optimal weight: 0.8980 chunk 257 optimal weight: 0.9980 chunk 186 optimal weight: 0.0980 chunk 335 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 386 optimal weight: 1.9990 chunk 404 optimal weight: 8.9990 chunk 426 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 367 ASN ** A 815 GLN ** 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 441 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4151 moved from start: 1.0914 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= 0.185 Angle : 0.721 16.319 52687 Z= 0.362 Chirality : 0.045 0.252 5961 Planarity : 0.005 0.088 6778 Dihedral : 5.892 76.216 5227 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.44 % Favored : 88.27 % Rotamer: Outliers : 2.16 % Allowed : 18.92 % Favored : 78.93 % 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: -2.62 (0.12), residues: 4765 helix: -0.36 (0.14), residues: 1520 sheet: -1.19 (0.22), residues: 489 loop : -2.81 (0.11), residues: 2756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 583 HIS 0.007 0.001 HIS A 427 PHE 0.033 0.001 PHE C 126 TYR 0.027 0.001 TYR O 219 ARG 0.017 0.001 ARG G 147 *********************** 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 516 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 424 time to evaluate : 4.679 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: A 34 VAL cc_start: 0.7714 (m) cc_final: 0.7505 (t) REVERT: A 205 LEU cc_start: 0.2501 (OUTLIER) cc_final: 0.1804 (tp) REVERT: A 310 ASN cc_start: 0.2113 (OUTLIER) cc_final: 0.1153 (p0) REVERT: A 450 MET cc_start: 0.3914 (mmt) cc_final: 0.2646 (ptp) REVERT: A 802 SER cc_start: 0.5902 (p) cc_final: 0.5498 (m) REVERT: A 959 ILE cc_start: 0.2111 (OUTLIER) cc_final: 0.1157 (tp) REVERT: A 1117 MET cc_start: 0.4841 (ttp) cc_final: 0.4598 (ttt) REVERT: A 1260 MET cc_start: 0.1208 (mmp) cc_final: -0.0070 (tmm) REVERT: A 1395 HIS cc_start: 0.4756 (m90) cc_final: 0.4550 (m90) REVERT: B 312 MET cc_start: 0.2687 (pmm) cc_final: 0.2001 (mpp) REVERT: B 335 LEU cc_start: 0.2629 (OUTLIER) cc_final: 0.2365 (mp) REVERT: B 356 VAL cc_start: 0.2965 (OUTLIER) cc_final: 0.2272 (p) REVERT: B 360 MET cc_start: 0.4993 (mmt) cc_final: 0.4468 (mmt) REVERT: B 439 THR cc_start: 0.8659 (m) cc_final: 0.8327 (p) REVERT: B 652 ASN cc_start: 0.2258 (OUTLIER) cc_final: 0.1331 (p0) REVERT: B 760 MET cc_start: 0.3929 (tpt) cc_final: 0.0506 (ppp) REVERT: C 1 MET cc_start: 0.0875 (tmm) cc_final: -0.0030 (ptt) REVERT: D 100 ASP cc_start: 0.5454 (p0) cc_final: 0.5232 (p0) REVERT: D 120 LYS cc_start: 0.3356 (tttt) cc_final: 0.3095 (mtpt) REVERT: E 39 LEU cc_start: -0.0114 (OUTLIER) cc_final: -0.0626 (mt) REVERT: E 50 MET cc_start: 0.1890 (tpt) cc_final: 0.0466 (ptm) REVERT: I 1 MET cc_start: 0.1776 (mmm) cc_final: 0.0608 (ptt) REVERT: I 12 LEU cc_start: 0.1831 (OUTLIER) cc_final: 0.1105 (pp) REVERT: K 142 MET cc_start: 0.2711 (mmm) cc_final: 0.2402 (mpp) REVERT: M 118 LEU cc_start: 0.6481 (mt) cc_final: 0.6076 (mp) REVERT: O 52 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6411 (mt) REVERT: O 296 LEU cc_start: 0.6810 (mt) cc_final: 0.6561 (mm) REVERT: O 494 TYR cc_start: 0.6971 (OUTLIER) cc_final: 0.5014 (t80) REVERT: O 519 GLU cc_start: 0.0108 (mp0) cc_final: -0.0142 (mp0) outliers start: 92 outliers final: 61 residues processed: 493 average time/residue: 0.4660 time to fit residues: 388.7236 Evaluate side-chains 462 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 391 time to evaluate : 4.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 735 TYR Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1142 ASN Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 1025 GLN Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain M residue 238 ASP Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 368 ARG Chi-restraints excluded: chain O residue 494 TYR Chi-restraints excluded: chain O residue 560 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 280 optimal weight: 0.9980 chunk 452 optimal weight: 0.8980 chunk 275 optimal weight: 10.0000 chunk 214 optimal weight: 0.6980 chunk 314 optimal weight: 0.9990 chunk 474 optimal weight: 0.7980 chunk 436 optimal weight: 0.1980 chunk 377 optimal weight: 0.7980 chunk 39 optimal weight: 0.0980 chunk 291 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4287 moved from start: 1.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 39016 Z= 0.177 Angle : 0.699 13.474 52687 Z= 0.352 Chirality : 0.045 0.222 5961 Planarity : 0.005 0.081 6778 Dihedral : 5.801 73.483 5227 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.08 % Favored : 88.65 % Rotamer: Outliers : 1.78 % Allowed : 19.34 % Favored : 78.88 % 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: -2.54 (0.12), residues: 4765 helix: -0.32 (0.14), residues: 1532 sheet: -1.13 (0.23), residues: 485 loop : -2.75 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 442 HIS 0.013 0.001 HIS D 133 PHE 0.023 0.001 PHE P 174 TYR 0.018 0.001 TYR P 249 ARG 0.008 0.000 ARG B1048 ********************** 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 498 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 422 time to evaluate : 3.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.2476 (OUTLIER) cc_final: 0.1751 (tp) REVERT: A 273 MET cc_start: -0.1154 (ptt) cc_final: -0.1932 (mtm) REVERT: A 310 ASN cc_start: 0.2056 (OUTLIER) cc_final: 0.1143 (p0) REVERT: A 450 MET cc_start: 0.3934 (mmt) cc_final: 0.3391 (ptp) REVERT: A 542 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.5489 (tt) REVERT: A 802 SER cc_start: 0.5778 (p) cc_final: 0.5472 (m) REVERT: A 959 ILE cc_start: 0.2032 (OUTLIER) cc_final: 0.1025 (tp) REVERT: A 960 MET cc_start: 0.1710 (mmm) cc_final: 0.0922 (ttp) REVERT: A 1260 MET cc_start: 0.1462 (mmp) cc_final: 0.0246 (tmm) REVERT: B 312 MET cc_start: 0.2597 (pmm) cc_final: 0.1885 (mpp) REVERT: B 335 LEU cc_start: 0.2320 (OUTLIER) cc_final: 0.2090 (mp) REVERT: B 358 MET cc_start: -0.0550 (OUTLIER) cc_final: -0.0905 (ptp) REVERT: B 360 MET cc_start: 0.4870 (mmt) cc_final: 0.4172 (mmt) REVERT: B 760 MET cc_start: 0.4023 (OUTLIER) cc_final: 0.0435 (ppp) REVERT: B 944 MET cc_start: 0.3269 (mmp) cc_final: 0.3041 (mmp) REVERT: C 1 MET cc_start: 0.0815 (tmm) cc_final: -0.0054 (ptt) REVERT: D 130 ASN cc_start: 0.2830 (t0) cc_final: 0.1936 (p0) REVERT: E 39 LEU cc_start: -0.0137 (OUTLIER) cc_final: -0.0642 (mt) REVERT: E 50 MET cc_start: 0.1888 (tpt) cc_final: 0.0489 (ptm) REVERT: E 149 LEU cc_start: 0.0951 (tt) cc_final: 0.0463 (mm) REVERT: G 49 TYR cc_start: 0.6322 (OUTLIER) cc_final: 0.5715 (m-80) REVERT: I 1 MET cc_start: 0.1971 (mmm) cc_final: 0.0736 (ptt) REVERT: I 12 LEU cc_start: 0.1814 (OUTLIER) cc_final: 0.1088 (pp) REVERT: K 142 MET cc_start: 0.3066 (mmm) cc_final: 0.2776 (mpp) REVERT: M 118 LEU cc_start: 0.6372 (mt) cc_final: 0.5984 (mp) REVERT: O 65 ILE cc_start: 0.6200 (OUTLIER) cc_final: 0.5746 (mm) REVERT: O 296 LEU cc_start: 0.6960 (mt) cc_final: 0.6737 (mm) REVERT: P 247 LEU cc_start: 0.5758 (tt) cc_final: 0.5544 (tt) REVERT: P 294 PHE cc_start: 0.3330 (t80) cc_final: 0.2531 (t80) outliers start: 76 outliers final: 59 residues processed: 477 average time/residue: 0.4525 time to fit residues: 369.7315 Evaluate side-chains 454 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 384 time to evaluate : 3.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 735 TYR Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 49 TYR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain M residue 238 ASP Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 65 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 368 ARG Chi-restraints excluded: chain O residue 563 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 299 optimal weight: 0.1980 chunk 402 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 348 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 378 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 92 HIS A 229 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 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 891 ASN B 918 GLN ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.249416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.227143 restraints weight = 63185.487| |-----------------------------------------------------------------------------| r_work (start): 0.4519 rms_B_bonded: 1.80 r_work: 0.4393 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4789 moved from start: 1.1895 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= 0.184 Angle : 0.701 20.232 52687 Z= 0.353 Chirality : 0.045 0.234 5961 Planarity : 0.005 0.112 6778 Dihedral : 5.738 75.086 5227 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.54 % Favored : 88.21 % Rotamer: Outliers : 1.92 % Allowed : 19.53 % Favored : 78.55 % 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: -2.44 (0.12), residues: 4765 helix: -0.21 (0.14), residues: 1537 sheet: -1.02 (0.23), residues: 486 loop : -2.71 (0.11), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 583 HIS 0.015 0.001 HIS D 133 PHE 0.026 0.001 PHE H 118 TYR 0.048 0.002 TYR O 119 ARG 0.014 0.001 ARG B 607 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8827.68 seconds wall clock time: 159 minutes 54.79 seconds (9594.79 seconds total)