Starting phenix.real_space_refine on Wed Feb 21 22:02:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0h_0567/02_2024/6o0h_0567_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0h_0567/02_2024/6o0h_0567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0h_0567/02_2024/6o0h_0567.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0h_0567/02_2024/6o0h_0567.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0h_0567/02_2024/6o0h_0567_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0h_0567/02_2024/6o0h_0567_updated.pdb" } resolution = 3.67 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= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians P 8 5.49 5 S 192 5.16 5 Cl 4 4.86 5 C 20480 2.51 5 N 5400 2.21 5 O 5920 1.98 5 F 8 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 835": "NH1" <-> "NH2" Residue "A ARG 915": "NH1" <-> "NH2" Residue "A ARG 934": "NH1" <-> "NH2" Residue "A ARG 976": "NH1" <-> "NH2" Residue "A ARG 986": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1038": "NH1" <-> "NH2" Residue "A ARG 1045": "NH1" <-> "NH2" Residue "A ARG 1065": "NH1" <-> "NH2" Residue "A ARG 1078": "NH1" <-> "NH2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 835": "NH1" <-> "NH2" Residue "B ARG 915": "NH1" <-> "NH2" Residue "B ARG 934": "NH1" <-> "NH2" Residue "B ARG 976": "NH1" <-> "NH2" Residue "B ARG 986": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1038": "NH1" <-> "NH2" Residue "B ARG 1045": "NH1" <-> "NH2" Residue "B ARG 1065": "NH1" <-> "NH2" Residue "B ARG 1078": "NH1" <-> "NH2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 835": "NH1" <-> "NH2" Residue "C ARG 915": "NH1" <-> "NH2" Residue "C ARG 934": "NH1" <-> "NH2" Residue "C ARG 976": "NH1" <-> "NH2" Residue "C ARG 986": "NH1" <-> "NH2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1038": "NH1" <-> "NH2" Residue "C ARG 1045": "NH1" <-> "NH2" Residue "C ARG 1065": "NH1" <-> "NH2" Residue "C ARG 1078": "NH1" <-> "NH2" Residue "D TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 835": "NH1" <-> "NH2" Residue "D ARG 915": "NH1" <-> "NH2" Residue "D ARG 934": "NH1" <-> "NH2" Residue "D ARG 976": "NH1" <-> "NH2" Residue "D ARG 986": "NH1" <-> "NH2" Residue "D ARG 995": "NH1" <-> "NH2" Residue "D ARG 1038": "NH1" <-> "NH2" Residue "D ARG 1045": "NH1" <-> "NH2" Residue "D ARG 1065": "NH1" <-> "NH2" Residue "D ARG 1078": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32012 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7946 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 bond proxies already assigned to first conformer: 8100 Chain: "B" Number of atoms: 7946 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 bond proxies already assigned to first conformer: 8100 Chain: "C" Number of atoms: 7946 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 bond proxies already assigned to first conformer: 8100 Chain: "D" Number of atoms: 7946 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 bond proxies already assigned to first conformer: 8100 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'ADP': 1, 'LBG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'ADP': 1, 'LBG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'ADP': 1, 'LBG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'ADP': 1, 'LBG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 31.02, per 1000 atoms: 0.97 Number of scatterers: 32012 At special positions: 0 Unit cell: (147.41, 160.136, 174.983, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 4 17.00 S 192 16.00 P 8 15.00 F 8 9.00 O 5920 8.00 N 5400 7.00 C 20480 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: 12.32 Conformation dependent library (CDL) restraints added in 10.6 seconds 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 32 sheets defined 38.9% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.06 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.751A pdb=" N SER A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 233 removed outlier: 7.011A pdb=" N VAL A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 removed outlier: 3.543A pdb=" N LEU A 256 " --> pdb=" O TYR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 294 removed outlier: 3.762A pdb=" N CYS A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 313 through 327 Processing helix chain 'A' and resid 350 through 362 removed outlier: 3.973A pdb=" N PHE A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 358 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.686A pdb=" N LYS A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 385 through 397 removed outlier: 3.590A pdb=" N LYS A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 506 through 518 Processing helix chain 'A' and resid 556 through 561 Processing helix chain 'A' and resid 578 through 585 Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.660A pdb=" N ARG A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 649 removed outlier: 4.129A pdb=" N ALA A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 675 removed outlier: 3.838A pdb=" N ASN A 668 " --> pdb=" O GLY A 665 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A 670 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 674 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 705 Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 747 through 749 No H-bonds generated for 'chain 'A' and resid 747 through 749' Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 790 through 805 removed outlier: 4.859A pdb=" N GLY A 794 " --> pdb=" O ASP A 791 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU A 802 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 828 No H-bonds generated for 'chain 'A' and resid 825 through 828' Processing helix chain 'A' and resid 859 through 864 Processing helix chain 'A' and resid 869 through 877 removed outlier: 4.064A pdb=" N GLY A 874 " --> pdb=" O GLY A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 896 removed outlier: 3.735A pdb=" N PHE A 889 " --> pdb=" O TYR A 885 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 891 " --> pdb=" O CYS A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 915 removed outlier: 4.013A pdb=" N CYS A 913 " --> pdb=" O ASN A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 930 removed outlier: 3.844A pdb=" N SER A 926 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 927 " --> pdb=" O SER A 923 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N THR A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 951 removed outlier: 3.582A pdb=" N LYS A 944 " --> pdb=" O ASP A 940 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 965 Processing helix chain 'A' and resid 985 through 997 Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.840A pdb=" N GLU A1009 " --> pdb=" O ASP A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1039 removed outlier: 4.166A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A1034 " --> pdb=" O GLY A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1048 No H-bonds generated for 'chain 'A' and resid 1045 through 1048' Processing helix chain 'A' and resid 1050 through 1054 Processing helix chain 'A' and resid 1056 through 1078 removed outlier: 4.232A pdb=" N PHE A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A1062 " --> pdb=" O ASN A1058 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A1063 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'B' and resid 40 through 46 Processing helix chain 'B' and resid 48 through 51 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 178 through 194 removed outlier: 3.751A pdb=" N SER B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 233 removed outlier: 7.011A pdb=" N VAL B 231 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.526A pdb=" N LEU B 256 " --> pdb=" O TYR B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 removed outlier: 3.732A pdb=" N CYS B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 313 through 327 Processing helix chain 'B' and resid 350 through 362 removed outlier: 3.978A pdb=" N PHE B 354 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 358 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.693A pdb=" N LYS B 369 " --> pdb=" O GLN B 365 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 385 through 397 removed outlier: 3.654A pdb=" N LYS B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 506 through 518 Processing helix chain 'B' and resid 556 through 561 Processing helix chain 'B' and resid 578 through 585 Processing helix chain 'B' and resid 603 through 616 removed outlier: 3.640A pdb=" N ARG B 607 " --> pdb=" O GLU B 603 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 649 removed outlier: 4.106A pdb=" N ALA B 648 " --> pdb=" O ASP B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 675 removed outlier: 3.864A pdb=" N ASN B 668 " --> pdb=" O GLY B 665 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 670 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 674 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 705 Processing helix chain 'B' and resid 725 through 732 Processing helix chain 'B' and resid 747 through 749 No H-bonds generated for 'chain 'B' and resid 747 through 749' Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 772 through 782 Processing helix chain 'B' and resid 790 through 805 removed outlier: 4.854A pdb=" N GLY B 794 " --> pdb=" O ASP B 791 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 797 " --> pdb=" O GLY B 794 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B 802 " --> pdb=" O SER B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 828 No H-bonds generated for 'chain 'B' and resid 825 through 828' Processing helix chain 'B' and resid 859 through 864 Processing helix chain 'B' and resid 869 through 877 removed outlier: 4.063A pdb=" N GLY B 874 " --> pdb=" O GLY B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 896 removed outlier: 3.735A pdb=" N PHE B 889 " --> pdb=" O TYR B 885 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 891 " --> pdb=" O CYS B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 915 removed outlier: 4.004A pdb=" N CYS B 913 " --> pdb=" O ASN B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 930 removed outlier: 3.840A pdb=" N SER B 926 " --> pdb=" O SER B 922 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 927 " --> pdb=" O SER B 923 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N THR B 930 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 951 removed outlier: 3.582A pdb=" N LYS B 944 " --> pdb=" O ASP B 940 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 951 " --> pdb=" O SER B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 965 Processing helix chain 'B' and resid 985 through 997 Processing helix chain 'B' and resid 1004 through 1015 removed outlier: 3.841A pdb=" N GLU B1009 " --> pdb=" O ASP B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1039 removed outlier: 4.164A pdb=" N GLY B1030 " --> pdb=" O ASP B1026 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL B1034 " --> pdb=" O GLY B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 No H-bonds generated for 'chain 'B' and resid 1045 through 1048' Processing helix chain 'B' and resid 1050 through 1054 Processing helix chain 'B' and resid 1056 through 1078 removed outlier: 4.229A pdb=" N PHE B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B1062 " --> pdb=" O ASN B1058 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B1063 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 51 Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 78 through 86 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 178 through 194 removed outlier: 3.751A pdb=" N SER C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 233 removed outlier: 7.012A pdb=" N VAL C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 removed outlier: 3.524A pdb=" N LEU C 256 " --> pdb=" O TYR C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 294 removed outlier: 3.729A pdb=" N CYS C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 313 through 327 Processing helix chain 'C' and resid 350 through 362 removed outlier: 3.978A pdb=" N PHE C 354 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 358 " --> pdb=" O PHE C 354 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.695A pdb=" N LYS C 369 " --> pdb=" O GLN C 365 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 385 through 397 removed outlier: 3.654A pdb=" N LYS C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 506 through 518 Processing helix chain 'C' and resid 556 through 561 Processing helix chain 'C' and resid 578 through 585 Processing helix chain 'C' and resid 603 through 616 removed outlier: 3.640A pdb=" N ARG C 607 " --> pdb=" O GLU C 603 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 649 removed outlier: 4.106A pdb=" N ALA C 648 " --> pdb=" O ASP C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 675 removed outlier: 3.862A pdb=" N ASN C 668 " --> pdb=" O GLY C 665 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU C 670 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 674 " --> pdb=" O ASN C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 705 Processing helix chain 'C' and resid 725 through 732 Processing helix chain 'C' and resid 747 through 749 No H-bonds generated for 'chain 'C' and resid 747 through 749' Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 772 through 780 Processing helix chain 'C' and resid 790 through 805 removed outlier: 4.839A pdb=" N GLY C 794 " --> pdb=" O ASP C 791 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 797 " --> pdb=" O GLY C 794 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU C 802 " --> pdb=" O SER C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 828 No H-bonds generated for 'chain 'C' and resid 825 through 828' Processing helix chain 'C' and resid 859 through 864 Processing helix chain 'C' and resid 869 through 877 removed outlier: 4.062A pdb=" N GLY C 874 " --> pdb=" O GLY C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 896 removed outlier: 3.734A pdb=" N PHE C 889 " --> pdb=" O TYR C 885 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 891 " --> pdb=" O CYS C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 915 removed outlier: 3.995A pdb=" N CYS C 913 " --> pdb=" O ASN C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 930 removed outlier: 3.846A pdb=" N SER C 926 " --> pdb=" O SER C 922 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY C 927 " --> pdb=" O SER C 923 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N THR C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 951 removed outlier: 3.554A pdb=" N LYS C 944 " --> pdb=" O ASP C 940 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP C 951 " --> pdb=" O SER C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 965 Processing helix chain 'C' and resid 985 through 997 Processing helix chain 'C' and resid 1004 through 1015 removed outlier: 3.841A pdb=" N GLU C1009 " --> pdb=" O ASP C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1039 removed outlier: 4.162A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL C1034 " --> pdb=" O GLY C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1045 through 1048 No H-bonds generated for 'chain 'C' and resid 1045 through 1048' Processing helix chain 'C' and resid 1050 through 1054 Processing helix chain 'C' and resid 1056 through 1078 removed outlier: 4.234A pdb=" N PHE C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL C1062 " --> pdb=" O ASN C1058 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C1063 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'D' and resid 40 through 46 Processing helix chain 'D' and resid 48 through 51 Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 78 through 86 Processing helix chain 'D' and resid 162 through 168 Processing helix chain 'D' and resid 178 through 194 removed outlier: 3.751A pdb=" N SER D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 233 removed outlier: 7.012A pdb=" N VAL D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 removed outlier: 3.516A pdb=" N LEU D 256 " --> pdb=" O TYR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 294 removed outlier: 3.750A pdb=" N CYS D 293 " --> pdb=" O SER D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 313 through 327 Processing helix chain 'D' and resid 350 through 362 removed outlier: 3.975A pdb=" N PHE D 354 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 358 " --> pdb=" O PHE D 354 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 removed outlier: 3.981A pdb=" N LYS D 369 " --> pdb=" O GLN D 365 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 370' Processing helix chain 'D' and resid 385 through 397 removed outlier: 3.620A pdb=" N LYS D 396 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 506 through 518 Processing helix chain 'D' and resid 556 through 561 Processing helix chain 'D' and resid 578 through 585 Processing helix chain 'D' and resid 603 through 616 removed outlier: 3.646A pdb=" N ARG D 607 " --> pdb=" O GLU D 603 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 649 removed outlier: 4.104A pdb=" N ALA D 648 " --> pdb=" O ASP D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 removed outlier: 3.855A pdb=" N ASN D 668 " --> pdb=" O GLY D 665 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU D 670 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 674 " --> pdb=" O ASN D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 705 Processing helix chain 'D' and resid 725 through 732 Processing helix chain 'D' and resid 747 through 749 No H-bonds generated for 'chain 'D' and resid 747 through 749' Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 772 through 780 Processing helix chain 'D' and resid 790 through 805 removed outlier: 4.872A pdb=" N GLY D 794 " --> pdb=" O ASP D 791 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 797 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU D 802 " --> pdb=" O SER D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 828 No H-bonds generated for 'chain 'D' and resid 825 through 828' Processing helix chain 'D' and resid 859 through 864 Processing helix chain 'D' and resid 869 through 877 removed outlier: 4.061A pdb=" N GLY D 874 " --> pdb=" O GLY D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 896 removed outlier: 3.725A pdb=" N PHE D 889 " --> pdb=" O TYR D 885 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU D 891 " --> pdb=" O CYS D 887 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 915 removed outlier: 3.995A pdb=" N CYS D 913 " --> pdb=" O ASN D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 930 removed outlier: 3.850A pdb=" N SER D 926 " --> pdb=" O SER D 922 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY D 927 " --> pdb=" O SER D 923 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N THR D 930 " --> pdb=" O SER D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 951 removed outlier: 3.580A pdb=" N LYS D 944 " --> pdb=" O ASP D 940 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS D 948 " --> pdb=" O LYS D 944 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP D 951 " --> pdb=" O SER D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 965 Processing helix chain 'D' and resid 985 through 997 Processing helix chain 'D' and resid 1004 through 1015 removed outlier: 3.841A pdb=" N GLU D1009 " --> pdb=" O ASP D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1025 through 1039 removed outlier: 4.161A pdb=" N GLY D1030 " --> pdb=" O ASP D1026 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL D1034 " --> pdb=" O GLY D1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 1045 through 1048 No H-bonds generated for 'chain 'D' and resid 1045 through 1048' Processing helix chain 'D' and resid 1050 through 1054 Processing helix chain 'D' and resid 1056 through 1078 removed outlier: 4.231A pdb=" N PHE D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D1062 " --> pdb=" O ASN D1058 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D1063 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.350A pdb=" N ALA A 219 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 124 " --> pdb=" O TYR A 131 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 92 through 95 removed outlier: 3.502A pdb=" N ALA A 93 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 100 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 205 through 207 removed outlier: 3.772A pdb=" N VAL A 206 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 275 through 278 removed outlier: 6.508A pdb=" N ILE A 337 " --> pdb=" O TRP A 276 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N MET A 278 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 339 " --> pdb=" O MET A 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 374 through 378 removed outlier: 7.781A pdb=" N VAL A 377 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N HIS A 403 " --> pdb=" O VAL A 377 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 619 through 621 removed outlier: 6.782A pdb=" N LEU A 569 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 500 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA A 528 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N MET A 529 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 739 through 745 removed outlier: 7.649A pdb=" N TYR A 659 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY A 684 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER A 661 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA A 686 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 3 through 6 removed outlier: 4.349A pdb=" N ALA B 219 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP B 222 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE B 197 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR B 124 " --> pdb=" O TYR B 131 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 31 through 34 Processing sheet with id= K, first strand: chain 'B' and resid 92 through 95 removed outlier: 3.502A pdb=" N ALA B 93 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY B 100 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 205 through 207 removed outlier: 3.773A pdb=" N VAL B 206 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.502A pdb=" N ILE B 337 " --> pdb=" O TRP B 276 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N MET B 278 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE B 339 " --> pdb=" O MET B 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 374 through 378 removed outlier: 7.817A pdb=" N VAL B 377 " --> pdb=" O PRO B 401 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N HIS B 403 " --> pdb=" O VAL B 377 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'B' and resid 619 through 621 removed outlier: 6.781A pdb=" N LEU B 569 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 500 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ALA B 528 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N MET B 529 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 739 through 745 removed outlier: 3.520A pdb=" N GLY B 717 " --> pdb=" O TRP B 743 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR B 659 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY B 684 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER B 661 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA B 686 " --> pdb=" O SER B 661 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 3 through 6 removed outlier: 4.350A pdb=" N ALA C 219 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR C 124 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 31 through 34 Processing sheet with id= S, first strand: chain 'C' and resid 92 through 95 removed outlier: 3.502A pdb=" N ALA C 93 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY C 100 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 205 through 207 removed outlier: 3.772A pdb=" N VAL C 206 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 275 through 278 removed outlier: 6.502A pdb=" N ILE C 337 " --> pdb=" O TRP C 276 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N MET C 278 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE C 339 " --> pdb=" O MET C 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'C' and resid 374 through 378 removed outlier: 7.816A pdb=" N VAL C 377 " --> pdb=" O PRO C 401 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N HIS C 403 " --> pdb=" O VAL C 377 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'C' and resid 619 through 621 removed outlier: 6.783A pdb=" N LEU C 569 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE C 500 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ALA C 528 " --> pdb=" O VAL C 501 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N MET C 529 " --> pdb=" O LEU C 549 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 739 through 745 removed outlier: 3.520A pdb=" N GLY C 717 " --> pdb=" O TRP C 743 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR C 659 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY C 684 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N SER C 661 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA C 686 " --> pdb=" O SER C 661 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 3 through 6 removed outlier: 4.350A pdb=" N ALA D 219 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR D 124 " --> pdb=" O TYR D 131 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 31 through 34 Processing sheet with id= AA, first strand: chain 'D' and resid 92 through 95 removed outlier: 3.502A pdb=" N ALA D 93 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY D 100 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 205 through 207 removed outlier: 3.772A pdb=" N VAL D 206 " --> pdb=" O TYR D 213 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 275 through 278 removed outlier: 6.509A pdb=" N ILE D 337 " --> pdb=" O TRP D 276 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N MET D 278 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE D 339 " --> pdb=" O MET D 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'D' and resid 374 through 378 removed outlier: 7.791A pdb=" N VAL D 377 " --> pdb=" O PRO D 401 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N HIS D 403 " --> pdb=" O VAL D 377 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'D' and resid 619 through 621 removed outlier: 6.782A pdb=" N LEU D 569 " --> pdb=" O ALA D 595 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE D 500 " --> pdb=" O ILE D 570 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ALA D 528 " --> pdb=" O VAL D 501 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N MET D 529 " --> pdb=" O LEU D 549 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 739 through 745 removed outlier: 7.646A pdb=" N TYR D 659 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY D 684 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER D 661 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA D 686 " --> pdb=" O SER D 661 " (cutoff:3.500A) 1001 hydrogen bonds defined for protein. 2724 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: 12.34 Time building geometry restraints manager: 13.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9637 1.33 - 1.45: 5378 1.45 - 1.57: 17373 1.57 - 1.69: 12 1.69 - 1.81: 324 Bond restraints: 32724 Sorted by residual: bond pdb=" C ARG C 244 " pdb=" N GLU C 245 " ideal model delta sigma weight residual 1.330 1.243 0.087 1.32e-02 5.74e+03 4.37e+01 bond pdb=" C ARG B 244 " pdb=" N GLU B 245 " ideal model delta sigma weight residual 1.330 1.247 0.083 1.32e-02 5.74e+03 3.97e+01 bond pdb=" CA TYR B 542 " pdb=" CB TYR B 542 " ideal model delta sigma weight residual 1.528 1.486 0.043 1.51e-02 4.39e+03 8.00e+00 bond pdb=" CB THR C 925 " pdb=" CG2 THR C 925 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.95e+00 bond pdb=" CA TYR D 542 " pdb=" CB TYR D 542 " ideal model delta sigma weight residual 1.528 1.486 0.042 1.51e-02 4.39e+03 7.91e+00 ... (remaining 32719 not shown) Histogram of bond angle deviations from ideal: 96.47 - 104.37: 635 104.37 - 112.26: 15923 112.26 - 120.15: 14320 120.15 - 128.04: 13223 128.04 - 135.94: 227 Bond angle restraints: 44328 Sorted by residual: angle pdb=" N TRP C 877 " pdb=" CA TRP C 877 " pdb=" C TRP C 877 " ideal model delta sigma weight residual 111.14 118.27 -7.13 1.08e+00 8.57e-01 4.35e+01 angle pdb=" N TRP D 877 " pdb=" CA TRP D 877 " pdb=" C TRP D 877 " ideal model delta sigma weight residual 111.14 118.24 -7.10 1.08e+00 8.57e-01 4.32e+01 angle pdb=" N TRP A 877 " pdb=" CA TRP A 877 " pdb=" C TRP A 877 " ideal model delta sigma weight residual 111.14 118.19 -7.05 1.08e+00 8.57e-01 4.26e+01 angle pdb=" N TRP B 877 " pdb=" CA TRP B 877 " pdb=" C TRP B 877 " ideal model delta sigma weight residual 111.14 118.17 -7.03 1.08e+00 8.57e-01 4.24e+01 angle pdb=" N ARG A 829 " pdb=" CA ARG A 829 " pdb=" C ARG A 829 " ideal model delta sigma weight residual 113.12 106.60 6.52 1.25e+00 6.40e-01 2.72e+01 ... (remaining 44323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 19325 34.94 - 69.89: 169 69.89 - 104.83: 16 104.83 - 139.77: 4 139.77 - 174.71: 2 Dihedral angle restraints: 19516 sinusoidal: 7852 harmonic: 11664 Sorted by residual: dihedral pdb=" C5' ADP D2002 " pdb=" O5' ADP D2002 " pdb=" PA ADP D2002 " pdb=" O2A ADP D2002 " ideal model delta sinusoidal sigma weight residual 300.00 125.29 174.71 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP C2002 " pdb=" O5' ADP C2002 " pdb=" PA ADP C2002 " pdb=" O2A ADP C2002 " ideal model delta sinusoidal sigma weight residual 300.00 125.33 174.67 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP C2002 " pdb=" O3A ADP C2002 " pdb=" PA ADP C2002 " pdb=" PB ADP C2002 " ideal model delta sinusoidal sigma weight residual -60.00 74.42 -134.42 1 2.00e+01 2.50e-03 4.08e+01 ... (remaining 19513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3676 0.065 - 0.130: 1034 0.130 - 0.195: 166 0.195 - 0.260: 34 0.260 - 0.325: 6 Chirality restraints: 4916 Sorted by residual: chirality pdb=" CB ILE A 911 " pdb=" CA ILE A 911 " pdb=" CG1 ILE A 911 " pdb=" CG2 ILE A 911 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB ILE D 911 " pdb=" CA ILE D 911 " pdb=" CG1 ILE D 911 " pdb=" CG2 ILE D 911 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB ILE C 911 " pdb=" CA ILE C 911 " pdb=" CG1 ILE C 911 " pdb=" CG2 ILE C 911 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 4913 not shown) Planarity restraints: 5656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 901 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO A 902 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 902 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 902 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 901 " -0.050 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO C 902 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 902 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 902 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 901 " 0.050 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO B 902 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 902 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 902 " 0.041 5.00e-02 4.00e+02 ... (remaining 5653 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8064 2.79 - 3.32: 28358 3.32 - 3.84: 52803 3.84 - 4.37: 60961 4.37 - 4.90: 104291 Nonbonded interactions: 254477 Sorted by model distance: nonbonded pdb=" O GLU C1011 " pdb=" OG1 THR C1015 " model vdw 2.262 2.440 nonbonded pdb=" O GLU B1011 " pdb=" OG1 THR B1015 " model vdw 2.262 2.440 nonbonded pdb=" O GLU A1011 " pdb=" OG1 THR A1015 " model vdw 2.263 2.440 nonbonded pdb=" O THR A 35 " pdb=" OG1 THR A 38 " model vdw 2.263 2.440 nonbonded pdb=" O THR B 35 " pdb=" OG1 THR B 38 " model vdw 2.263 2.440 ... (remaining 254472 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099 or resid 2001 through 2002)) selection = (chain 'B' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099 or resid 2001 through 2002)) selection = (chain 'C' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099 or resid 2001 through 2002)) selection = (chain 'D' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099 or resid 2001 through 2002)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.300 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 102.920 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.250 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.009 0.095 32724 Z= 0.582 Angle : 1.165 14.896 44328 Z= 0.660 Chirality : 0.063 0.325 4916 Planarity : 0.009 0.076 5656 Dihedral : 10.835 174.713 12108 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.35 % Allowed : 2.47 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.11), residues: 4076 helix: -3.26 (0.08), residues: 1736 sheet: -1.80 (0.21), residues: 564 loop : -2.29 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP B 502 HIS 0.013 0.003 HIS D 997 PHE 0.036 0.004 PHE D 863 TYR 0.033 0.004 TYR D 854 ARG 0.017 0.002 ARG B 915 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 954 time to evaluate : 3.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ILE cc_start: 0.8062 (mt) cc_final: 0.7516 (pt) REVERT: A 265 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7740 (mtpp) REVERT: A 327 MET cc_start: 0.6963 (mmm) cc_final: 0.6739 (mmm) REVERT: A 412 THR cc_start: 0.8934 (p) cc_final: 0.8689 (p) REVERT: A 556 MET cc_start: 0.6595 (mtp) cc_final: 0.6365 (mtp) REVERT: A 618 VAL cc_start: 0.8822 (t) cc_final: 0.8496 (p) REVERT: B 202 ILE cc_start: 0.8134 (mt) cc_final: 0.7588 (pt) REVERT: B 265 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7730 (mtpp) REVERT: B 327 MET cc_start: 0.6894 (mmm) cc_final: 0.6681 (mmm) REVERT: C 202 ILE cc_start: 0.8136 (mt) cc_final: 0.7596 (pt) REVERT: C 265 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7732 (mtpp) REVERT: C 327 MET cc_start: 0.6907 (mmm) cc_final: 0.6688 (mmm) REVERT: D 202 ILE cc_start: 0.8085 (mt) cc_final: 0.7539 (pt) REVERT: D 265 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7750 (mtpp) REVERT: D 327 MET cc_start: 0.6963 (mmm) cc_final: 0.6696 (mmm) REVERT: D 618 VAL cc_start: 0.8838 (t) cc_final: 0.8528 (p) outliers start: 12 outliers final: 8 residues processed: 966 average time/residue: 0.4679 time to fit residues: 696.4052 Evaluate side-chains 502 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 494 time to evaluate : 3.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 233 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 3.9990 chunk 309 optimal weight: 0.0270 chunk 171 optimal weight: 0.1980 chunk 105 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 319 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 370 optimal weight: 0.3980 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 54 ASN A 61 GLN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS A 510 GLN A 671 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 54 ASN B 61 GLN B 172 HIS B 315 GLN B 410 HIS B 510 GLN B 590 GLN B 671 ASN B1072 HIS ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN C 54 ASN C 61 GLN C 172 HIS C 315 GLN C 410 HIS C 510 GLN C 590 GLN C 671 ASN ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN D 54 ASN D 61 GLN D 172 HIS D 315 GLN D 410 HIS D 510 GLN D 671 ASN ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32724 Z= 0.237 Angle : 0.681 12.326 44328 Z= 0.343 Chirality : 0.047 0.206 4916 Planarity : 0.006 0.064 5656 Dihedral : 8.640 159.302 4540 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.65 % Allowed : 10.44 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.12), residues: 4076 helix: -2.07 (0.10), residues: 1716 sheet: -1.25 (0.22), residues: 580 loop : -1.78 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 502 HIS 0.008 0.001 HIS D 410 PHE 0.016 0.002 PHE A 110 TYR 0.021 0.002 TYR C 319 ARG 0.010 0.001 ARG D 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 585 time to evaluate : 3.781 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 65 ARG cc_start: 0.6650 (mtp-110) cc_final: 0.6270 (mtt90) REVERT: A 202 ILE cc_start: 0.8079 (mt) cc_final: 0.7651 (pt) REVERT: A 233 TRP cc_start: 0.8795 (OUTLIER) cc_final: 0.8296 (m-10) REVERT: A 781 GLU cc_start: 0.7782 (tp30) cc_final: 0.6949 (mt-10) REVERT: A 909 ASN cc_start: 0.8061 (p0) cc_final: 0.7789 (p0) REVERT: A 1075 ASP cc_start: 0.8468 (t70) cc_final: 0.8140 (t0) REVERT: B 65 ARG cc_start: 0.6740 (mtp-110) cc_final: 0.6283 (mtt90) REVERT: B 202 ILE cc_start: 0.8112 (mt) cc_final: 0.7663 (pt) REVERT: B 233 TRP cc_start: 0.8875 (OUTLIER) cc_final: 0.8413 (m-10) REVERT: B 909 ASN cc_start: 0.7954 (p0) cc_final: 0.7591 (p0) REVERT: B 928 LEU cc_start: 0.9218 (mm) cc_final: 0.9006 (mt) REVERT: B 1075 ASP cc_start: 0.8477 (t70) cc_final: 0.8152 (t0) REVERT: C 65 ARG cc_start: 0.6753 (mtp-110) cc_final: 0.6307 (mtt90) REVERT: C 202 ILE cc_start: 0.8113 (mt) cc_final: 0.7660 (pt) REVERT: C 233 TRP cc_start: 0.8872 (OUTLIER) cc_final: 0.8412 (m-10) REVERT: C 909 ASN cc_start: 0.7742 (p0) cc_final: 0.7409 (p0) REVERT: C 1075 ASP cc_start: 0.8482 (t70) cc_final: 0.8129 (t0) REVERT: D 65 ARG cc_start: 0.6702 (mtp-110) cc_final: 0.6304 (mtt90) REVERT: D 202 ILE cc_start: 0.8093 (mt) cc_final: 0.7657 (pt) REVERT: D 233 TRP cc_start: 0.8788 (OUTLIER) cc_final: 0.8289 (m-10) REVERT: D 909 ASN cc_start: 0.8150 (p0) cc_final: 0.7787 (p0) REVERT: D 928 LEU cc_start: 0.9246 (mm) cc_final: 0.9045 (mt) REVERT: D 1075 ASP cc_start: 0.8490 (t70) cc_final: 0.8115 (t0) outliers start: 90 outliers final: 53 residues processed: 645 average time/residue: 0.4374 time to fit residues: 448.8107 Evaluate side-chains 519 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 462 time to evaluate : 3.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 233 TRP Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 638 ASN Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 1049 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 308 optimal weight: 0.0670 chunk 252 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 6.9990 chunk 400 optimal weight: 0.4980 chunk 330 optimal weight: 0.8980 chunk 368 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 GLN A 908 HIS A1072 HIS ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 HIS ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 HIS C 908 HIS C1072 HIS D 365 GLN ** D 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 GLN D 908 HIS D1072 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32724 Z= 0.216 Angle : 0.622 11.020 44328 Z= 0.308 Chirality : 0.046 0.180 4916 Planarity : 0.005 0.057 5656 Dihedral : 7.651 149.424 4524 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.12 % Allowed : 13.71 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.13), residues: 4076 helix: -1.31 (0.11), residues: 1740 sheet: -0.83 (0.22), residues: 568 loop : -1.41 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 84 HIS 0.003 0.001 HIS C 908 PHE 0.018 0.002 PHE C 863 TYR 0.016 0.002 TYR C 364 ARG 0.008 0.001 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 497 time to evaluate : 3.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6461 (tt0) cc_final: 0.6158 (tt0) REVERT: A 65 ARG cc_start: 0.6825 (mtp-110) cc_final: 0.6257 (mpt180) REVERT: A 103 LYS cc_start: 0.6836 (ptmt) cc_final: 0.6174 (ttpp) REVERT: A 202 ILE cc_start: 0.8127 (mt) cc_final: 0.7685 (pt) REVERT: A 222 ASP cc_start: 0.8056 (t0) cc_final: 0.7446 (t0) REVERT: A 233 TRP cc_start: 0.8858 (OUTLIER) cc_final: 0.8464 (m-10) REVERT: A 364 TYR cc_start: 0.5444 (m-80) cc_final: 0.4887 (m-10) REVERT: B 13 GLU cc_start: 0.6501 (tt0) cc_final: 0.6196 (tt0) REVERT: B 65 ARG cc_start: 0.6807 (mtp-110) cc_final: 0.6269 (mpt180) REVERT: B 103 LYS cc_start: 0.6779 (ptmt) cc_final: 0.6133 (ttpp) REVERT: B 202 ILE cc_start: 0.8188 (mt) cc_final: 0.7690 (pt) REVERT: B 222 ASP cc_start: 0.8058 (t0) cc_final: 0.7397 (t0) REVERT: B 233 TRP cc_start: 0.8871 (OUTLIER) cc_final: 0.8423 (m-10) REVERT: B 603 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6881 (mp0) REVERT: C 13 GLU cc_start: 0.6514 (tt0) cc_final: 0.6212 (tt0) REVERT: C 65 ARG cc_start: 0.6821 (mtp-110) cc_final: 0.6321 (mpt180) REVERT: C 103 LYS cc_start: 0.6769 (ptmt) cc_final: 0.6118 (ttpp) REVERT: C 202 ILE cc_start: 0.8163 (mt) cc_final: 0.7672 (pt) REVERT: C 222 ASP cc_start: 0.8045 (t0) cc_final: 0.7386 (t0) REVERT: C 233 TRP cc_start: 0.8870 (OUTLIER) cc_final: 0.8421 (m-10) REVERT: C 603 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6872 (mp0) REVERT: D 13 GLU cc_start: 0.6415 (tt0) cc_final: 0.6103 (tt0) REVERT: D 65 ARG cc_start: 0.6834 (mtp-110) cc_final: 0.6313 (mpt180) REVERT: D 103 LYS cc_start: 0.6821 (ptmt) cc_final: 0.6156 (ttpp) REVERT: D 202 ILE cc_start: 0.8113 (mt) cc_final: 0.7680 (pt) REVERT: D 233 TRP cc_start: 0.8853 (OUTLIER) cc_final: 0.8450 (m-10) REVERT: D 292 ILE cc_start: 0.8511 (mm) cc_final: 0.8096 (mt) REVERT: D 928 LEU cc_start: 0.9264 (mm) cc_final: 0.9009 (mt) outliers start: 72 outliers final: 49 residues processed: 543 average time/residue: 0.4267 time to fit residues: 372.3510 Evaluate side-chains 485 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 432 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1089 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 233 TRP Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 638 ASN Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1089 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.9990 chunk 279 optimal weight: 0.7980 chunk 192 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 249 optimal weight: 0.9990 chunk 372 optimal weight: 1.9990 chunk 394 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 353 optimal weight: 8.9990 chunk 106 optimal weight: 0.0980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN D 671 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32724 Z= 0.177 Angle : 0.584 9.912 44328 Z= 0.286 Chirality : 0.045 0.296 4916 Planarity : 0.005 0.057 5656 Dihedral : 6.898 136.522 4524 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.32 % Allowed : 15.50 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 4076 helix: -0.86 (0.12), residues: 1724 sheet: -0.59 (0.23), residues: 572 loop : -1.25 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 84 HIS 0.005 0.001 HIS D 908 PHE 0.013 0.001 PHE D 533 TYR 0.013 0.001 TYR A 364 ARG 0.007 0.001 ARG A 788 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 455 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6423 (tt0) cc_final: 0.6168 (tt0) REVERT: A 65 ARG cc_start: 0.6811 (mtp-110) cc_final: 0.6373 (mtt90) REVERT: A 202 ILE cc_start: 0.8150 (mt) cc_final: 0.7712 (pt) REVERT: A 233 TRP cc_start: 0.8826 (OUTLIER) cc_final: 0.8427 (m-10) REVERT: A 364 TYR cc_start: 0.5706 (m-80) cc_final: 0.5140 (m-10) REVERT: A 1057 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8427 (mt) REVERT: B 13 GLU cc_start: 0.6455 (tt0) cc_final: 0.6203 (tt0) REVERT: B 65 ARG cc_start: 0.6812 (mtp-110) cc_final: 0.6373 (mtt90) REVERT: B 103 LYS cc_start: 0.6882 (ptmt) cc_final: 0.6210 (ttpp) REVERT: B 202 ILE cc_start: 0.8141 (mt) cc_final: 0.7708 (pt) REVERT: B 233 TRP cc_start: 0.8877 (OUTLIER) cc_final: 0.8415 (m-10) REVERT: B 327 MET cc_start: 0.6264 (mmm) cc_final: 0.5937 (mmm) REVERT: B 1057 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8408 (mt) REVERT: C 13 GLU cc_start: 0.6476 (tt0) cc_final: 0.6222 (tt0) REVERT: C 65 ARG cc_start: 0.6777 (mtp-110) cc_final: 0.6406 (mtt90) REVERT: C 103 LYS cc_start: 0.6869 (ptmt) cc_final: 0.6202 (ttpp) REVERT: C 202 ILE cc_start: 0.8092 (mt) cc_final: 0.7668 (pt) REVERT: C 233 TRP cc_start: 0.8874 (OUTLIER) cc_final: 0.8412 (m-10) REVERT: C 327 MET cc_start: 0.6248 (mmm) cc_final: 0.5910 (mmm) REVERT: C 1057 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8406 (mt) REVERT: D 13 GLU cc_start: 0.6432 (tt0) cc_final: 0.6188 (tt0) REVERT: D 65 ARG cc_start: 0.6853 (mtp-110) cc_final: 0.6424 (mtt90) REVERT: D 202 ILE cc_start: 0.8155 (mt) cc_final: 0.7731 (pt) REVERT: D 233 TRP cc_start: 0.8806 (OUTLIER) cc_final: 0.8392 (m-10) REVERT: D 928 LEU cc_start: 0.9150 (mm) cc_final: 0.8899 (mt) REVERT: D 1057 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8398 (mt) outliers start: 79 outliers final: 56 residues processed: 505 average time/residue: 0.4183 time to fit residues: 343.3586 Evaluate side-chains 482 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 418 time to evaluate : 3.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 857 MET Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1089 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1089 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 233 TRP Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 638 ASN Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 857 MET Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1089 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 0.7980 chunk 223 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 293 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 336 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 201 optimal weight: 1.9990 chunk 353 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS B 671 ASN ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32724 Z= 0.218 Angle : 0.589 9.846 44328 Z= 0.288 Chirality : 0.045 0.164 4916 Planarity : 0.004 0.053 5656 Dihedral : 6.584 124.440 4524 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.62 % Allowed : 15.56 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 4076 helix: -0.65 (0.12), residues: 1744 sheet: -0.18 (0.24), residues: 544 loop : -1.17 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 84 HIS 0.007 0.001 HIS B 908 PHE 0.012 0.001 PHE A 533 TYR 0.012 0.002 TYR C 319 ARG 0.009 0.001 ARG B 703 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 455 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6560 (tt0) cc_final: 0.6282 (tt0) REVERT: A 36 PRO cc_start: 0.7033 (Cg_exo) cc_final: 0.6832 (Cg_endo) REVERT: A 65 ARG cc_start: 0.6979 (mtp-110) cc_final: 0.6515 (mtt90) REVERT: A 103 LYS cc_start: 0.6932 (ptmt) cc_final: 0.6342 (ttpt) REVERT: A 202 ILE cc_start: 0.8257 (mt) cc_final: 0.7835 (pt) REVERT: A 233 TRP cc_start: 0.8871 (OUTLIER) cc_final: 0.8531 (m-10) REVERT: A 540 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8065 (tppt) REVERT: A 928 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8937 (mt) REVERT: A 1047 GLU cc_start: 0.7883 (tp30) cc_final: 0.7623 (tp30) REVERT: A 1057 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8473 (mt) REVERT: A 1060 ILE cc_start: 0.9017 (tp) cc_final: 0.8599 (tp) REVERT: B 13 GLU cc_start: 0.6613 (tt0) cc_final: 0.6349 (tt0) REVERT: B 65 ARG cc_start: 0.6853 (mtp-110) cc_final: 0.6465 (mtt90) REVERT: B 103 LYS cc_start: 0.7054 (ptmt) cc_final: 0.6366 (ttpt) REVERT: B 202 ILE cc_start: 0.8371 (mt) cc_final: 0.7896 (pt) REVERT: B 233 TRP cc_start: 0.8884 (OUTLIER) cc_final: 0.8563 (m-10) REVERT: B 327 MET cc_start: 0.6312 (mmm) cc_final: 0.6026 (mmm) REVERT: B 540 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8119 (tppt) REVERT: B 928 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8918 (mt) REVERT: B 1047 GLU cc_start: 0.7871 (tp30) cc_final: 0.7604 (tp30) REVERT: B 1057 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8469 (mt) REVERT: C 13 GLU cc_start: 0.6625 (tt0) cc_final: 0.6358 (tt0) REVERT: C 65 ARG cc_start: 0.6800 (mtp-110) cc_final: 0.6416 (mtt90) REVERT: C 103 LYS cc_start: 0.7063 (ptmt) cc_final: 0.6377 (ttpt) REVERT: C 202 ILE cc_start: 0.8312 (mt) cc_final: 0.7852 (pt) REVERT: C 233 TRP cc_start: 0.8879 (OUTLIER) cc_final: 0.8554 (m-10) REVERT: C 540 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8046 (tppt) REVERT: C 1047 GLU cc_start: 0.7849 (tp30) cc_final: 0.7602 (tp30) REVERT: C 1057 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8452 (mt) REVERT: C 1060 ILE cc_start: 0.9021 (tp) cc_final: 0.8621 (tp) REVERT: D 13 GLU cc_start: 0.6569 (tt0) cc_final: 0.6321 (tt0) REVERT: D 36 PRO cc_start: 0.7009 (Cg_exo) cc_final: 0.6806 (Cg_endo) REVERT: D 65 ARG cc_start: 0.6824 (mtp-110) cc_final: 0.6462 (mtt90) REVERT: D 103 LYS cc_start: 0.7035 (ptmt) cc_final: 0.6358 (ttpt) REVERT: D 202 ILE cc_start: 0.8270 (mt) cc_final: 0.7852 (pt) REVERT: D 233 TRP cc_start: 0.8888 (OUTLIER) cc_final: 0.8556 (m-10) REVERT: D 540 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8005 (tppt) REVERT: D 1047 GLU cc_start: 0.7853 (tp30) cc_final: 0.7594 (tp30) REVERT: D 1057 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8472 (mt) outliers start: 89 outliers final: 63 residues processed: 505 average time/residue: 0.4238 time to fit residues: 348.8022 Evaluate side-chains 494 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 417 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 857 MET Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1089 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 540 LYS Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 857 MET Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1089 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 233 TRP Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 540 LYS Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 638 ASN Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 857 MET Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1089 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 6.9990 chunk 355 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 231 optimal weight: 0.7980 chunk 97 optimal weight: 0.0970 chunk 394 optimal weight: 3.9990 chunk 327 optimal weight: 8.9990 chunk 182 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 207 optimal weight: 0.0010 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 HIS ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 HIS D 421 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 32724 Z= 0.157 Angle : 0.577 9.727 44328 Z= 0.279 Chirality : 0.045 0.315 4916 Planarity : 0.004 0.039 5656 Dihedral : 6.079 100.829 4524 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.44 % Allowed : 15.85 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 4076 helix: -0.40 (0.12), residues: 1760 sheet: -0.22 (0.23), residues: 592 loop : -1.07 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 84 HIS 0.006 0.001 HIS D 908 PHE 0.015 0.001 PHE A 533 TYR 0.015 0.001 TYR B 993 ARG 0.006 0.000 ARG A 788 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 456 time to evaluate : 3.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6533 (tt0) cc_final: 0.6297 (tt0) REVERT: A 36 PRO cc_start: 0.7112 (Cg_exo) cc_final: 0.6850 (Cg_endo) REVERT: A 65 ARG cc_start: 0.6994 (mtp-110) cc_final: 0.6553 (mtt90) REVERT: A 103 LYS cc_start: 0.7015 (ptmt) cc_final: 0.6371 (ttpt) REVERT: A 202 ILE cc_start: 0.8162 (mt) cc_final: 0.7760 (pt) REVERT: A 233 TRP cc_start: 0.8849 (OUTLIER) cc_final: 0.8496 (m-10) REVERT: A 292 ILE cc_start: 0.8504 (mm) cc_final: 0.8065 (mp) REVERT: A 1057 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8472 (mt) REVERT: A 1060 ILE cc_start: 0.8952 (tp) cc_final: 0.8549 (tp) REVERT: B 13 GLU cc_start: 0.6584 (tt0) cc_final: 0.6351 (tt0) REVERT: B 65 ARG cc_start: 0.6904 (mtp-110) cc_final: 0.6510 (mtt90) REVERT: B 202 ILE cc_start: 0.8289 (mt) cc_final: 0.7846 (pt) REVERT: B 233 TRP cc_start: 0.8888 (OUTLIER) cc_final: 0.8510 (m-10) REVERT: B 292 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.7940 (mt) REVERT: B 327 MET cc_start: 0.6412 (mmm) cc_final: 0.6144 (mmm) REVERT: B 1057 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8470 (mt) REVERT: C 13 GLU cc_start: 0.6602 (tt0) cc_final: 0.6375 (tt0) REVERT: C 65 ARG cc_start: 0.6861 (mtp-110) cc_final: 0.6462 (mtt90) REVERT: C 103 LYS cc_start: 0.7080 (ptmt) cc_final: 0.6415 (ttpp) REVERT: C 202 ILE cc_start: 0.8242 (mt) cc_final: 0.7816 (pt) REVERT: C 233 TRP cc_start: 0.8887 (OUTLIER) cc_final: 0.8515 (m-10) REVERT: C 292 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.7948 (mt) REVERT: C 1057 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8445 (mt) REVERT: C 1060 ILE cc_start: 0.8959 (tp) cc_final: 0.8585 (tp) REVERT: D 13 GLU cc_start: 0.6546 (tt0) cc_final: 0.6315 (tt0) REVERT: D 65 ARG cc_start: 0.6833 (mtp-110) cc_final: 0.6544 (mtt90) REVERT: D 202 ILE cc_start: 0.8186 (mt) cc_final: 0.7800 (pt) REVERT: D 233 TRP cc_start: 0.8883 (OUTLIER) cc_final: 0.8458 (m-10) REVERT: D 928 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8881 (mt) REVERT: D 1057 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8437 (mt) REVERT: D 1060 ILE cc_start: 0.8951 (tp) cc_final: 0.8575 (tp) outliers start: 83 outliers final: 52 residues processed: 513 average time/residue: 0.4549 time to fit residues: 375.2288 Evaluate side-chains 484 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 421 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 857 MET Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1089 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 857 MET Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1089 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 233 TRP Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 638 ASN Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 857 MET Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1089 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 288 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 332 optimal weight: 9.9990 chunk 220 optimal weight: 0.3980 chunk 393 optimal weight: 2.9990 chunk 246 optimal weight: 0.0470 chunk 239 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32724 Z= 0.170 Angle : 0.573 10.162 44328 Z= 0.276 Chirality : 0.044 0.156 4916 Planarity : 0.004 0.050 5656 Dihedral : 5.842 88.422 4524 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.18 % Allowed : 16.44 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.13), residues: 4076 helix: -0.20 (0.12), residues: 1752 sheet: -0.13 (0.23), residues: 592 loop : -1.05 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 84 HIS 0.006 0.001 HIS A 908 PHE 0.014 0.001 PHE A 533 TYR 0.015 0.001 TYR D 319 ARG 0.005 0.000 ARG B 703 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 441 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 PRO cc_start: 0.7059 (Cg_exo) cc_final: 0.6800 (Cg_endo) REVERT: A 65 ARG cc_start: 0.6905 (mtp-110) cc_final: 0.6512 (mtt90) REVERT: A 103 LYS cc_start: 0.7063 (ptmt) cc_final: 0.6452 (ttpt) REVERT: A 202 ILE cc_start: 0.8219 (mt) cc_final: 0.7835 (pt) REVERT: A 233 TRP cc_start: 0.8869 (OUTLIER) cc_final: 0.8514 (m-10) REVERT: A 292 ILE cc_start: 0.8578 (mm) cc_final: 0.8162 (mp) REVERT: A 925 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8727 (m) REVERT: A 928 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8807 (mt) REVERT: A 1057 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8412 (mt) REVERT: A 1060 ILE cc_start: 0.8950 (tp) cc_final: 0.8543 (tp) REVERT: B 65 ARG cc_start: 0.6881 (mtp-110) cc_final: 0.6460 (mtt90) REVERT: B 103 LYS cc_start: 0.7100 (ptmt) cc_final: 0.6460 (ttpt) REVERT: B 202 ILE cc_start: 0.8319 (mt) cc_final: 0.7863 (pt) REVERT: B 233 TRP cc_start: 0.8895 (OUTLIER) cc_final: 0.8527 (m-10) REVERT: B 495 ARG cc_start: 0.7194 (ptm160) cc_final: 0.6851 (ttm170) REVERT: B 928 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8795 (mt) REVERT: B 1057 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8388 (mt) REVERT: B 1060 ILE cc_start: 0.8947 (tp) cc_final: 0.8550 (tp) REVERT: C 65 ARG cc_start: 0.6790 (mtp-110) cc_final: 0.6424 (mtt90) REVERT: C 103 LYS cc_start: 0.7150 (ptmt) cc_final: 0.6506 (ttpt) REVERT: C 202 ILE cc_start: 0.8281 (mt) cc_final: 0.7837 (pt) REVERT: C 233 TRP cc_start: 0.8892 (OUTLIER) cc_final: 0.8523 (m-10) REVERT: C 495 ARG cc_start: 0.7198 (ptm160) cc_final: 0.6853 (ttm170) REVERT: C 1057 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8388 (mt) REVERT: C 1060 ILE cc_start: 0.8957 (tp) cc_final: 0.8548 (tp) REVERT: D 65 ARG cc_start: 0.6907 (mtp-110) cc_final: 0.6550 (mtt90) REVERT: D 202 ILE cc_start: 0.8199 (mt) cc_final: 0.7831 (pt) REVERT: D 233 TRP cc_start: 0.8898 (OUTLIER) cc_final: 0.8492 (m-10) REVERT: D 495 ARG cc_start: 0.7190 (ptm160) cc_final: 0.6809 (ttm170) REVERT: D 928 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8863 (mt) REVERT: D 1057 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8376 (mt) REVERT: D 1060 ILE cc_start: 0.8960 (tp) cc_final: 0.8550 (tp) outliers start: 74 outliers final: 59 residues processed: 492 average time/residue: 0.4133 time to fit residues: 329.0869 Evaluate side-chains 490 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 419 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 857 MET Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1089 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 857 MET Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1089 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 233 TRP Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 638 ASN Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 857 MET Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1089 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 118 optimal weight: 0.0010 chunk 77 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 267 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 309 optimal weight: 9.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS B 421 HIS C 403 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32724 Z= 0.195 Angle : 0.584 10.903 44328 Z= 0.281 Chirality : 0.044 0.162 4916 Planarity : 0.004 0.056 5656 Dihedral : 5.758 77.798 4524 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.38 % Allowed : 16.53 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4076 helix: -0.07 (0.12), residues: 1744 sheet: -0.15 (0.23), residues: 592 loop : -1.00 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 84 HIS 0.006 0.001 HIS C 908 PHE 0.013 0.001 PHE A 533 TYR 0.020 0.001 TYR D 120 ARG 0.005 0.001 ARG D 703 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 429 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 PRO cc_start: 0.7016 (Cg_exo) cc_final: 0.6750 (Cg_endo) REVERT: A 65 ARG cc_start: 0.6879 (mtp-110) cc_final: 0.6430 (mtt90) REVERT: A 103 LYS cc_start: 0.7213 (ptmt) cc_final: 0.6604 (ttpt) REVERT: A 202 ILE cc_start: 0.8308 (mt) cc_final: 0.7915 (pt) REVERT: A 233 TRP cc_start: 0.8910 (OUTLIER) cc_final: 0.8585 (m-10) REVERT: A 292 ILE cc_start: 0.8574 (mm) cc_final: 0.8160 (mp) REVERT: A 925 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8702 (m) REVERT: A 928 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8761 (mt) REVERT: A 1047 GLU cc_start: 0.7770 (tp30) cc_final: 0.7483 (tp30) REVERT: A 1057 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 1060 ILE cc_start: 0.8969 (tp) cc_final: 0.8608 (tp) REVERT: B 65 ARG cc_start: 0.6785 (mtp-110) cc_final: 0.6367 (mtt90) REVERT: B 103 LYS cc_start: 0.7027 (ptmt) cc_final: 0.6436 (ttpt) REVERT: B 202 ILE cc_start: 0.8384 (mt) cc_final: 0.7925 (pt) REVERT: B 233 TRP cc_start: 0.8932 (OUTLIER) cc_final: 0.8634 (m-10) REVERT: B 495 ARG cc_start: 0.7184 (ptm160) cc_final: 0.6908 (ttm170) REVERT: B 928 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8729 (mt) REVERT: B 1047 GLU cc_start: 0.7752 (tp30) cc_final: 0.7468 (tp30) REVERT: B 1057 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8407 (mt) REVERT: B 1060 ILE cc_start: 0.8960 (tp) cc_final: 0.8560 (tp) REVERT: C 65 ARG cc_start: 0.6840 (mtp-110) cc_final: 0.6454 (mtt90) REVERT: C 103 LYS cc_start: 0.7135 (ptmt) cc_final: 0.6522 (ttpt) REVERT: C 202 ILE cc_start: 0.8334 (mt) cc_final: 0.7897 (pt) REVERT: C 233 TRP cc_start: 0.8936 (OUTLIER) cc_final: 0.8636 (m-10) REVERT: C 495 ARG cc_start: 0.7188 (ptm160) cc_final: 0.6914 (ttm170) REVERT: C 1047 GLU cc_start: 0.7736 (tp30) cc_final: 0.7466 (tp30) REVERT: C 1057 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8413 (mt) REVERT: C 1060 ILE cc_start: 0.8969 (tp) cc_final: 0.8555 (tp) REVERT: D 65 ARG cc_start: 0.6862 (mtp-110) cc_final: 0.6464 (mtt90) REVERT: D 202 ILE cc_start: 0.8284 (mt) cc_final: 0.7876 (pt) REVERT: D 233 TRP cc_start: 0.8932 (OUTLIER) cc_final: 0.8596 (m-10) REVERT: D 495 ARG cc_start: 0.7183 (ptm160) cc_final: 0.6897 (ttm170) REVERT: D 928 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8873 (mt) REVERT: D 1047 GLU cc_start: 0.7743 (tp30) cc_final: 0.7460 (tp30) REVERT: D 1057 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8400 (mt) REVERT: D 1060 ILE cc_start: 0.8972 (tp) cc_final: 0.8560 (tp) outliers start: 81 outliers final: 60 residues processed: 485 average time/residue: 0.4242 time to fit residues: 334.1710 Evaluate side-chains 489 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 417 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 857 MET Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1089 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 857 MET Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1089 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 233 TRP Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 638 ASN Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 857 MET Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1089 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 7.9990 chunk 376 optimal weight: 9.9990 chunk 343 optimal weight: 5.9990 chunk 366 optimal weight: 0.6980 chunk 220 optimal weight: 0.6980 chunk 159 optimal weight: 6.9990 chunk 287 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 331 optimal weight: 0.9980 chunk 346 optimal weight: 3.9990 chunk 365 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS D 421 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32724 Z= 0.184 Angle : 0.581 12.538 44328 Z= 0.278 Chirality : 0.044 0.153 4916 Planarity : 0.004 0.056 5656 Dihedral : 5.633 67.770 4524 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.15 % Allowed : 16.82 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 4076 helix: 0.04 (0.12), residues: 1748 sheet: -0.14 (0.23), residues: 592 loop : -0.95 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 84 HIS 0.006 0.001 HIS C 908 PHE 0.014 0.001 PHE A 533 TYR 0.015 0.001 TYR A 319 ARG 0.006 0.000 ARG A 788 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 426 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 PRO cc_start: 0.7066 (Cg_exo) cc_final: 0.6832 (Cg_endo) REVERT: A 65 ARG cc_start: 0.6884 (mtp-110) cc_final: 0.6401 (mtt90) REVERT: A 103 LYS cc_start: 0.7075 (ptmt) cc_final: 0.6494 (ttpt) REVERT: A 202 ILE cc_start: 0.8325 (mt) cc_final: 0.7924 (pt) REVERT: A 233 TRP cc_start: 0.8928 (OUTLIER) cc_final: 0.8620 (m-10) REVERT: A 292 ILE cc_start: 0.8564 (mm) cc_final: 0.8194 (mp) REVERT: A 925 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8678 (m) REVERT: A 928 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8799 (mt) REVERT: A 957 MET cc_start: 0.5839 (mmm) cc_final: 0.5601 (mmm) REVERT: A 1057 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8432 (mt) REVERT: A 1060 ILE cc_start: 0.8948 (tp) cc_final: 0.8599 (tp) REVERT: B 59 PRO cc_start: 0.7646 (Cg_endo) cc_final: 0.7417 (Cg_exo) REVERT: B 65 ARG cc_start: 0.6750 (mtp-110) cc_final: 0.6328 (mtt90) REVERT: B 103 LYS cc_start: 0.7126 (ptmt) cc_final: 0.6536 (ttpt) REVERT: B 202 ILE cc_start: 0.8395 (mt) cc_final: 0.7944 (pt) REVERT: B 233 TRP cc_start: 0.8937 (OUTLIER) cc_final: 0.8652 (m-10) REVERT: B 495 ARG cc_start: 0.7131 (ptm160) cc_final: 0.6902 (ttm170) REVERT: B 928 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8773 (mt) REVERT: B 957 MET cc_start: 0.5702 (mmm) cc_final: 0.5485 (mmm) REVERT: B 1057 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8398 (mt) REVERT: B 1060 ILE cc_start: 0.8943 (tp) cc_final: 0.8549 (tp) REVERT: C 59 PRO cc_start: 0.7629 (Cg_endo) cc_final: 0.7398 (Cg_exo) REVERT: C 65 ARG cc_start: 0.6730 (mtp-110) cc_final: 0.6422 (mtt90) REVERT: C 103 LYS cc_start: 0.7062 (ptmt) cc_final: 0.6465 (ttpt) REVERT: C 202 ILE cc_start: 0.8351 (mt) cc_final: 0.7915 (pt) REVERT: C 233 TRP cc_start: 0.8928 (OUTLIER) cc_final: 0.8633 (m-10) REVERT: C 495 ARG cc_start: 0.7133 (ptm160) cc_final: 0.6910 (ttm170) REVERT: C 1057 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8393 (mt) REVERT: C 1060 ILE cc_start: 0.8949 (tp) cc_final: 0.8562 (tp) REVERT: D 65 ARG cc_start: 0.6901 (mtp-110) cc_final: 0.6511 (mtt90) REVERT: D 202 ILE cc_start: 0.8276 (mt) cc_final: 0.7857 (pt) REVERT: D 233 TRP cc_start: 0.8937 (OUTLIER) cc_final: 0.8584 (m-10) REVERT: D 292 ILE cc_start: 0.8514 (mm) cc_final: 0.8077 (mp) REVERT: D 495 ARG cc_start: 0.7099 (ptm160) cc_final: 0.6894 (ttm170) REVERT: D 928 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8891 (mt) REVERT: D 1057 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8387 (mt) REVERT: D 1060 ILE cc_start: 0.8956 (tp) cc_final: 0.8544 (tp) outliers start: 73 outliers final: 56 residues processed: 475 average time/residue: 0.4423 time to fit residues: 341.5129 Evaluate side-chains 477 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 409 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 857 MET Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1089 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 857 MET Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1089 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 233 TRP Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 638 ASN Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 857 MET Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1089 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 0.3980 chunk 387 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 269 optimal weight: 1.9990 chunk 406 optimal weight: 4.9990 chunk 374 optimal weight: 0.0040 chunk 323 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 250 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN B 54 ASN B1024 ASN C 54 ASN C1024 ASN D1024 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32724 Z= 0.164 Angle : 0.587 13.368 44328 Z= 0.280 Chirality : 0.045 0.315 4916 Planarity : 0.004 0.043 5656 Dihedral : 5.450 60.260 4524 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.00 % Allowed : 17.03 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.13), residues: 4076 helix: 0.18 (0.12), residues: 1748 sheet: -0.05 (0.23), residues: 592 loop : -0.83 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 84 HIS 0.006 0.001 HIS A 908 PHE 0.015 0.001 PHE C 533 TYR 0.014 0.001 TYR C 319 ARG 0.007 0.000 ARG A 788 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 439 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 PRO cc_start: 0.7045 (Cg_exo) cc_final: 0.6810 (Cg_endo) REVERT: A 65 ARG cc_start: 0.7001 (mtp-110) cc_final: 0.6519 (mtt90) REVERT: A 103 LYS cc_start: 0.7064 (ptmt) cc_final: 0.6468 (ttpt) REVERT: A 202 ILE cc_start: 0.8276 (mt) cc_final: 0.7897 (pt) REVERT: A 233 TRP cc_start: 0.8910 (OUTLIER) cc_final: 0.8565 (m-10) REVERT: A 292 ILE cc_start: 0.8554 (mm) cc_final: 0.8189 (mp) REVERT: A 925 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8647 (m) REVERT: A 928 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8687 (mt) REVERT: A 1057 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8452 (mt) REVERT: A 1060 ILE cc_start: 0.8932 (tp) cc_final: 0.8565 (tp) REVERT: B 59 PRO cc_start: 0.7605 (Cg_endo) cc_final: 0.7379 (Cg_exo) REVERT: B 65 ARG cc_start: 0.6959 (mtp-110) cc_final: 0.6498 (mtt90) REVERT: B 103 LYS cc_start: 0.7060 (ptmt) cc_final: 0.6462 (ttpt) REVERT: B 202 ILE cc_start: 0.8355 (mt) cc_final: 0.7890 (pt) REVERT: B 925 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8737 (m) REVERT: B 928 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8678 (mt) REVERT: B 957 MET cc_start: 0.5750 (mmm) cc_final: 0.5547 (mmm) REVERT: B 1057 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8421 (mt) REVERT: B 1060 ILE cc_start: 0.8916 (tp) cc_final: 0.8519 (tp) REVERT: C 59 PRO cc_start: 0.7591 (Cg_endo) cc_final: 0.7362 (Cg_exo) REVERT: C 103 LYS cc_start: 0.7084 (ptmt) cc_final: 0.6508 (ttpt) REVERT: C 202 ILE cc_start: 0.8270 (mt) cc_final: 0.7855 (pt) REVERT: C 1057 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8409 (mt) REVERT: C 1060 ILE cc_start: 0.8918 (tp) cc_final: 0.8535 (tp) REVERT: D 65 ARG cc_start: 0.6922 (mtp-110) cc_final: 0.6563 (mtt90) REVERT: D 202 ILE cc_start: 0.8204 (mt) cc_final: 0.7786 (pt) REVERT: D 233 TRP cc_start: 0.8936 (OUTLIER) cc_final: 0.8580 (m-10) REVERT: D 292 ILE cc_start: 0.8508 (mm) cc_final: 0.8100 (mp) REVERT: D 928 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8832 (mt) REVERT: D 1047 GLU cc_start: 0.7732 (tp30) cc_final: 0.7451 (tp30) REVERT: D 1057 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8402 (mt) REVERT: D 1060 ILE cc_start: 0.8928 (tp) cc_final: 0.8524 (tp) outliers start: 68 outliers final: 55 residues processed: 485 average time/residue: 0.4526 time to fit residues: 352.5504 Evaluate side-chains 479 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 413 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 857 MET Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1089 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 857 MET Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1089 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 233 TRP Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 638 ASN Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 857 MET Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1089 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 4.9990 chunk 344 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 298 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 0.0000 chunk 324 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 332 optimal weight: 8.9990 chunk 41 optimal weight: 0.5980 chunk 59 optimal weight: 0.2980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 HIS C 421 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.165585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.138281 restraints weight = 108136.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.142391 restraints weight = 129979.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.144598 restraints weight = 46608.096| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32724 Z= 0.167 Angle : 0.583 13.624 44328 Z= 0.278 Chirality : 0.044 0.320 4916 Planarity : 0.004 0.055 5656 Dihedral : 5.234 54.600 4520 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.03 % Allowed : 17.15 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 4076 helix: 0.30 (0.12), residues: 1748 sheet: 0.03 (0.23), residues: 592 loop : -0.83 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 84 HIS 0.006 0.001 HIS D 908 PHE 0.016 0.001 PHE D 18 TYR 0.014 0.001 TYR B 319 ARG 0.008 0.000 ARG C 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7502.47 seconds wall clock time: 136 minutes 48.62 seconds (8208.62 seconds total)