Starting phenix.real_space_refine on Thu Feb 22 00:16:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0p_26262/02_2024/7u0p_26262.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0p_26262/02_2024/7u0p_26262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0p_26262/02_2024/7u0p_26262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0p_26262/02_2024/7u0p_26262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0p_26262/02_2024/7u0p_26262.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0p_26262/02_2024/7u0p_26262.pdb" } resolution = 3.76 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= 0.002 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 146 5.16 5 C 20576 2.51 5 N 5345 2.21 5 O 6304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B ASP 1084": "OD1" <-> "OD2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 28": "OD1" <-> "OD2" Residue "F ASP 82": "OD1" <-> "OD2" Residue "F GLU 144": "OE1" <-> "OE2" 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: 32371 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8366 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 56, 'TRANS': 1012} Chain breaks: 5 Chain: "B" Number of atoms: 8515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 Chain: "C" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8350 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 56, 'TRANS': 1010} Chain breaks: 5 Chain: "E" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1684 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "D" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1684 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "I" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1662 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "F" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1662 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "B1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 16.56, per 1000 atoms: 0.51 Number of scatterers: 32371 At special positions: 0 Unit cell: (172.7, 159.5, 240.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 146 16.00 O 6304 8.00 N 5345 7.00 C 20576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 135 " - pdb=" SG CYS I 195 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAGB1 1 " - " NAGB1 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 603 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 343 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B 343 " " NAGB1 1 " - " ASN B1134 " Time building additional restraints: 12.12 Conformation dependent library (CDL) restraints added in 6.1 seconds 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7662 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 68 sheets defined 20.6% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.04 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.572A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.558A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.562A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.952A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.614A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 removed outlier: 3.552A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.569A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.747A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.805A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.807A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 removed outlier: 3.645A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 940 removed outlier: 4.051A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.782A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 992 through 1033 removed outlier: 3.836A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.405A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 336 through 341 removed outlier: 4.412A pdb=" N GLY B 339 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.104A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.762A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.769A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.619A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 removed outlier: 4.157A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.203A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 771 removed outlier: 3.636A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 783 removed outlier: 4.203A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.870A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.691A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.674A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 890' Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.826A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 918 Processing helix chain 'B' and resid 919 through 938 removed outlier: 3.622A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 4.440A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 967 No H-bonds generated for 'chain 'B' and resid 965 through 967' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.981A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1149 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.540A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 338 through 343' Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.789A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.538A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.202A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.708A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.164A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.805A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.570A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 855 removed outlier: 3.847A pdb=" N LYS C 854 " --> pdb=" O CYS C 851 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 855 " --> pdb=" O ALA C 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 851 through 855' Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.530A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.503A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.608A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.587A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.149A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.629A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.653A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE C1018 " --> pdb=" O ARG C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.381A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'D' and resid 28 through 32 removed outlier: 4.230A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.976A pdb=" N GLN D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.169A pdb=" N THR D 197 " --> pdb=" O SER D 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 129 Processing helix chain 'I' and resid 184 through 190 removed outlier: 3.728A pdb=" N HIS I 190 " --> pdb=" O ASP I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 215 No H-bonds generated for 'chain 'I' and resid 213 through 215' Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.069A pdb=" N ILE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 184 through 190 removed outlier: 3.757A pdb=" N HIS F 190 " --> pdb=" O ASP F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.859A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.468A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.984A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 121 removed outlier: 3.713A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 153 removed outlier: 6.394A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.749A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.487A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.811A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.162A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.750A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.453A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 672 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.022A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.714A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 28 removed outlier: 6.386A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 229 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.902A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.408A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS B 146 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.196A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.318A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.537A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.572A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.860A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.868A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.678A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 714 Processing sheet with id=AD4, first strand: chain 'B' and resid 717 through 719 Processing sheet with id=AD5, first strand: chain 'B' and resid 722 through 728 removed outlier: 4.091A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.541A pdb=" N PHE B1121 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.229A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.865A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 104 through 107 Processing sheet with id=AE3, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.804A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.354A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.405A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.073A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.626A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.721A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF6, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AF7, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.011A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 127 through 130 removed outlier: 3.808A pdb=" N ASP E 150 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR E 182 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 127 through 130 removed outlier: 3.808A pdb=" N ASP E 150 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR E 182 " --> pdb=" O ASP E 150 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER E 183 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL E 175 " --> pdb=" O SER E 183 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 157 through 160 removed outlier: 4.067A pdb=" N TYR E 200 " --> pdb=" O VAL E 217 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.879A pdb=" N SER D 71 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.525A pdb=" N GLU D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 127 through 130 Processing sheet with id=AG5, first strand: chain 'D' and resid 127 through 130 removed outlier: 3.595A pdb=" N VAL D 175 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 157 through 160 removed outlier: 4.150A pdb=" N TYR D 200 " --> pdb=" O VAL D 217 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.814A pdb=" N LEU I 11 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 115 through 119 removed outlier: 6.367A pdb=" N TYR I 174 " --> pdb=" O ASN I 139 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 155 through 156 removed outlier: 4.736A pdb=" N TRP I 149 " --> pdb=" O GLN I 156 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AH3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.862A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE F 48 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 115 through 119 removed outlier: 6.151A pdb=" N TYR F 174 " --> pdb=" O ASN F 139 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 154 through 155 1140 hydrogen bonds defined for protein. 3048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.24 Time building geometry restraints manager: 13.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 1 1.11 - 1.29: 5283 1.29 - 1.47: 13458 1.47 - 1.65: 14195 1.65 - 1.83: 186 Bond restraints: 33123 Sorted by residual: bond pdb=" CB PRO C 209 " pdb=" CG PRO C 209 " ideal model delta sigma weight residual 1.492 0.934 0.558 5.00e-02 4.00e+02 1.25e+02 bond pdb=" CG PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 1.503 1.190 0.313 3.40e-02 8.65e+02 8.45e+01 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" N PRO C 209 " pdb=" CA PRO C 209 " ideal model delta sigma weight residual 1.469 1.504 -0.035 1.28e-02 6.10e+03 7.51e+00 ... (remaining 33118 not shown) Histogram of bond angle deviations from ideal: 74.41 - 90.20: 2 90.20 - 105.99: 779 105.99 - 121.78: 36439 121.78 - 137.57: 7861 137.57 - 153.36: 1 Bond angle restraints: 45082 Sorted by residual: angle pdb=" N PRO C 209 " pdb=" CD PRO C 209 " pdb=" CG PRO C 209 " ideal model delta sigma weight residual 103.20 76.92 26.28 1.50e+00 4.44e-01 3.07e+02 angle pdb=" CA PRO C 209 " pdb=" CB PRO C 209 " pdb=" CG PRO C 209 " ideal model delta sigma weight residual 104.50 74.41 30.09 1.90e+00 2.77e-01 2.51e+02 angle pdb=" CB PRO C 209 " pdb=" CG PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 106.10 153.36 -47.26 3.20e+00 9.77e-02 2.18e+02 angle pdb=" CA PRO C 209 " pdb=" N PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 112.00 101.86 10.14 1.40e+00 5.10e-01 5.24e+01 angle pdb=" CA MET D 101 " pdb=" C MET D 101 " pdb=" N THR D 102 " ideal model delta sigma weight residual 117.92 123.98 -6.06 1.35e+00 5.49e-01 2.02e+01 ... (remaining 45077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.84: 18552 24.84 - 49.68: 1312 49.68 - 74.52: 185 74.52 - 99.36: 67 99.36 - 124.20: 7 Dihedral angle restraints: 20123 sinusoidal: 8194 harmonic: 11929 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -26.40 -59.60 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -28.88 -57.12 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -33.61 -52.39 1 1.00e+01 1.00e-02 3.74e+01 ... (remaining 20120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4079 0.049 - 0.098: 822 0.098 - 0.147: 273 0.147 - 0.196: 0 0.196 - 0.245: 6 Chirality restraints: 5180 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB THR B 259 " pdb=" CA THR B 259 " pdb=" OG1 THR B 259 " pdb=" CG2 THR B 259 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 5177 not shown) Planarity restraints: 5814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " -0.061 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO C 209 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 791 " -0.037 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 792 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 792 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 792 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO A 987 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.030 5.00e-02 4.00e+02 ... (remaining 5811 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 689 2.69 - 3.24: 28903 3.24 - 3.79: 45061 3.79 - 4.35: 55921 4.35 - 4.90: 97536 Nonbonded interactions: 228110 Sorted by model distance: nonbonded pdb=" OG SER I 63 " pdb=" OG1 THR I 74 " model vdw 2.132 2.440 nonbonded pdb=" O4 NAG C1301 " pdb=" O7 NAG C1301 " model vdw 2.209 2.440 nonbonded pdb=" OE1 GLN I 167 " pdb=" OH TYR I 174 " model vdw 2.213 2.440 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.213 2.440 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLN A 218 " model vdw 2.224 2.440 ... (remaining 228105 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 14 through 675 or resid 690 through 827 or resid 852 throu \ gh 1146 or resid 1303 through 1308)) selection = (chain 'B' and (resid 14 through 617 or resid 641 through 827 or resid 852 throu \ gh 940 or resid 944 through 1146 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 675 or resid 690 through 827 or resid 852 throu \ gh 1146 or resid 1303 through 1308)) } ncs_group { reference = chain 'B1' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'I' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 15.550 Check model and map are aligned: 0.510 Set scattering table: 0.330 Process input model: 83.900 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.260 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 : 0.005 0.558 33123 Z= 0.259 Angle : 0.625 47.256 45082 Z= 0.312 Chirality : 0.044 0.245 5180 Planarity : 0.004 0.087 5787 Dihedral : 17.207 124.198 12392 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.42 % Allowed : 23.41 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.13 (0.13), residues: 4060 helix: 1.39 (0.22), residues: 667 sheet: 0.81 (0.16), residues: 1061 loop : -1.00 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 160 HIS 0.004 0.001 HIS A1083 PHE 0.012 0.001 PHE A1121 TYR 0.018 0.001 TYR C 904 ARG 0.002 0.000 ARG I 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 344 time to evaluate : 3.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.1327 (tmm) cc_final: -0.1763 (ptm) REVERT: A 392 PHE cc_start: 0.8527 (m-80) cc_final: 0.8127 (m-10) REVERT: A 451 TYR cc_start: 0.7413 (m-80) cc_final: 0.7187 (m-10) REVERT: A 1002 GLN cc_start: 0.8398 (tt0) cc_final: 0.8176 (tp40) REVERT: B 88 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8082 (p0) REVERT: B 97 LYS cc_start: 0.8388 (pttm) cc_final: 0.7947 (mmtm) REVERT: B 177 MET cc_start: 0.1758 (tpt) cc_final: 0.1146 (mmt) REVERT: C 138 ASP cc_start: 0.6928 (m-30) cc_final: 0.6631 (m-30) REVERT: C 139 PRO cc_start: 0.7550 (Cg_endo) cc_final: 0.7312 (Cg_exo) REVERT: C 258 TRP cc_start: 0.2981 (m100) cc_final: 0.2754 (m-90) REVERT: C 427 ASP cc_start: 0.8176 (m-30) cc_final: 0.7907 (t0) REVERT: C 988 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8187 (mp0) REVERT: D 109 TRP cc_start: 0.6827 (m100) cc_final: 0.6481 (m100) outliers start: 15 outliers final: 5 residues processed: 357 average time/residue: 0.4242 time to fit residues: 247.5562 Evaluate side-chains 202 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 196 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 894 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 342 optimal weight: 8.9990 chunk 307 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 368 optimal weight: 30.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 115 GLN A 121 ASN A 122 ASN A 134 GLN A 207 HIS ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 935 GLN A1135 ASN B 99 ASN B 115 GLN B 360 ASN B 422 ASN B 563 GLN B 655 HIS B 658 ASN B 954 GLN B1088 HIS C 207 HIS C 239 GLN C 439 ASN C 493 GLN C 498 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 913 GLN C 920 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS D 111 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN F 79 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 33123 Z= 0.385 Angle : 0.662 11.123 45082 Z= 0.341 Chirality : 0.048 0.316 5180 Planarity : 0.005 0.069 5787 Dihedral : 8.954 106.594 5078 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.52 % Allowed : 22.15 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.52 (0.13), residues: 4060 helix: 1.05 (0.21), residues: 662 sheet: 0.65 (0.16), residues: 1059 loop : -1.29 (0.12), residues: 2339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 97 HIS 0.009 0.001 HIS B1064 PHE 0.022 0.002 PHE A 906 TYR 0.021 0.002 TYR I 91 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 203 time to evaluate : 3.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.1010 (tmm) cc_final: -0.1276 (ptm) REVERT: A 392 PHE cc_start: 0.8526 (m-80) cc_final: 0.8074 (m-10) REVERT: A 660 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.8313 (m-10) REVERT: A 1018 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8092 (tt) REVERT: A 1029 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8562 (tpp) REVERT: B 97 LYS cc_start: 0.8421 (pttm) cc_final: 0.8015 (mmtm) REVERT: B 129 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7831 (ptpt) REVERT: B 177 MET cc_start: 0.2014 (tpt) cc_final: 0.1119 (mmt) REVERT: B 220 PHE cc_start: 0.6529 (t80) cc_final: 0.6221 (t80) REVERT: B 906 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8012 (t80) REVERT: B 990 GLU cc_start: 0.8153 (tt0) cc_final: 0.7550 (tm-30) REVERT: B 1010 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7945 (mm-40) REVERT: C 906 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.7540 (t80) REVERT: C 988 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8237 (mp0) REVERT: E 156 VAL cc_start: -0.1084 (OUTLIER) cc_final: -0.1324 (m) REVERT: I 147 VAL cc_start: 0.1107 (OUTLIER) cc_final: 0.0828 (p) outliers start: 198 outliers final: 111 residues processed: 386 average time/residue: 0.3912 time to fit residues: 255.1303 Evaluate side-chains 291 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 171 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain I residue 24 GLN Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain F residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 204 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 306 optimal weight: 0.8980 chunk 251 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 369 optimal weight: 10.0000 chunk 399 optimal weight: 20.0000 chunk 328 optimal weight: 4.9990 chunk 366 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 296 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 115 GLN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN C 30 ASN C 564 GLN C 658 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 33123 Z= 0.165 Angle : 0.542 10.546 45082 Z= 0.275 Chirality : 0.044 0.256 5180 Planarity : 0.004 0.057 5787 Dihedral : 7.988 104.022 5077 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.68 % Allowed : 23.74 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.36 (0.13), residues: 4060 helix: 1.32 (0.22), residues: 651 sheet: 0.72 (0.16), residues: 1091 loop : -1.24 (0.12), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.004 0.001 HIS A1083 PHE 0.033 0.001 PHE A 133 TYR 0.024 0.001 TYR C 369 ARG 0.006 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 187 time to evaluate : 3.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7134 (pmm) cc_final: 0.6365 (pmm) REVERT: A 177 MET cc_start: -0.0972 (OUTLIER) cc_final: -0.1228 (ptm) REVERT: A 392 PHE cc_start: 0.8497 (m-80) cc_final: 0.8061 (m-10) REVERT: A 1029 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8384 (tpp) REVERT: B 97 LYS cc_start: 0.8424 (pttm) cc_final: 0.8000 (mmtm) REVERT: B 129 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7868 (ptpt) REVERT: B 177 MET cc_start: 0.1985 (tpt) cc_final: 0.1271 (mmt) REVERT: B 220 PHE cc_start: 0.6461 (t80) cc_final: 0.5995 (t80) REVERT: B 906 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8236 (t80) REVERT: C 906 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.7669 (t80) REVERT: C 988 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8225 (mp0) REVERT: E 51 ILE cc_start: 0.8461 (pt) cc_final: 0.8155 (mt) outliers start: 132 outliers final: 81 residues processed: 299 average time/residue: 0.4099 time to fit residues: 208.1395 Evaluate side-chains 255 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 169 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain F residue 88 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 364 optimal weight: 8.9990 chunk 277 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 176 optimal weight: 0.0980 chunk 248 optimal weight: 2.9990 chunk 370 optimal weight: 7.9990 chunk 392 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 351 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 450 ASN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 33123 Z= 0.305 Angle : 0.594 10.742 45082 Z= 0.304 Chirality : 0.046 0.252 5180 Planarity : 0.004 0.054 5787 Dihedral : 7.572 96.897 5073 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 5.55 % Allowed : 22.21 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.54 (0.13), residues: 4060 helix: 1.13 (0.22), residues: 652 sheet: 0.57 (0.16), residues: 1107 loop : -1.33 (0.12), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 886 HIS 0.006 0.001 HIS B1064 PHE 0.031 0.002 PHE A 133 TYR 0.020 0.001 TYR A 421 ARG 0.003 0.000 ARG I 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 182 time to evaluate : 3.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7358 (pmm) cc_final: 0.6425 (pmm) REVERT: A 177 MET cc_start: -0.0955 (OUTLIER) cc_final: -0.1213 (ptm) REVERT: A 240 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8315 (t) REVERT: A 392 PHE cc_start: 0.8543 (m-80) cc_final: 0.8246 (m-80) REVERT: A 660 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.8211 (m-10) REVERT: A 733 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7429 (ptpt) REVERT: A 985 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7435 (p0) REVERT: A 1018 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8031 (tt) REVERT: A 1029 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8312 (tpp) REVERT: B 97 LYS cc_start: 0.8353 (pttm) cc_final: 0.7954 (mmtm) REVERT: B 129 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7856 (ptpt) REVERT: B 177 MET cc_start: 0.1731 (tpt) cc_final: 0.0866 (mmt) REVERT: B 220 PHE cc_start: 0.6552 (t80) cc_final: 0.6228 (t80) REVERT: B 906 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8142 (t80) REVERT: B 990 GLU cc_start: 0.8234 (tt0) cc_final: 0.7599 (tm-30) REVERT: B 991 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8708 (p) REVERT: C 58 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: C 65 PHE cc_start: 0.6884 (m-80) cc_final: 0.6558 (m-80) REVERT: C 231 ILE cc_start: 0.6216 (OUTLIER) cc_final: 0.5829 (mp) REVERT: C 534 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8807 (m) REVERT: C 906 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7534 (t80) REVERT: C 988 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8174 (mp0) REVERT: E 51 ILE cc_start: 0.8557 (pt) cc_final: 0.8301 (mt) REVERT: E 156 VAL cc_start: -0.0726 (OUTLIER) cc_final: -0.0952 (m) REVERT: D 48 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6463 (ptm) REVERT: I 147 VAL cc_start: 0.1533 (OUTLIER) cc_final: 0.1168 (p) outliers start: 199 outliers final: 135 residues processed: 361 average time/residue: 0.3988 time to fit residues: 245.0453 Evaluate side-chains 316 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 164 time to evaluate : 3.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 109 TRP Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 326 optimal weight: 0.0030 chunk 222 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 292 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 334 optimal weight: 50.0000 chunk 271 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 200 optimal weight: 0.9980 chunk 352 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33123 Z= 0.186 Angle : 0.546 11.118 45082 Z= 0.277 Chirality : 0.044 0.262 5180 Planarity : 0.004 0.053 5787 Dihedral : 7.131 89.026 5073 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.58 % Allowed : 23.38 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.45 (0.13), residues: 4060 helix: 1.32 (0.22), residues: 647 sheet: 0.64 (0.16), residues: 1082 loop : -1.29 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 104 HIS 0.004 0.001 HIS A1083 PHE 0.020 0.001 PHE C 140 TYR 0.023 0.001 TYR B 369 ARG 0.007 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 173 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7263 (pmm) cc_final: 0.6828 (pmm) REVERT: A 236 THR cc_start: 0.7020 (OUTLIER) cc_final: 0.6780 (p) REVERT: A 237 ARG cc_start: 0.6558 (mtm-85) cc_final: 0.6353 (mpt180) REVERT: A 392 PHE cc_start: 0.8511 (m-80) cc_final: 0.8276 (m-80) REVERT: A 733 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7404 (ptpt) REVERT: A 1029 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8180 (tpp) REVERT: B 97 LYS cc_start: 0.8264 (pttm) cc_final: 0.7912 (mmtm) REVERT: B 133 PHE cc_start: 0.6520 (m-80) cc_final: 0.5748 (m-80) REVERT: B 220 PHE cc_start: 0.6496 (t80) cc_final: 0.6105 (t80) REVERT: B 238 PHE cc_start: 0.5881 (p90) cc_final: 0.5596 (p90) REVERT: B 505 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.6954 (t80) REVERT: B 906 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8264 (t80) REVERT: B 990 GLU cc_start: 0.8171 (tt0) cc_final: 0.7536 (tm-30) REVERT: C 65 PHE cc_start: 0.6824 (m-80) cc_final: 0.6499 (m-80) REVERT: C 136 CYS cc_start: 0.6785 (m) cc_final: 0.5722 (t) REVERT: C 906 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.7571 (t80) REVERT: C 988 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8215 (mp0) REVERT: E 156 VAL cc_start: -0.0561 (OUTLIER) cc_final: -0.0798 (m) REVERT: D 48 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6534 (ptm) REVERT: D 82 GLN cc_start: 0.7816 (mt0) cc_final: 0.7424 (mp-120) outliers start: 164 outliers final: 122 residues processed: 324 average time/residue: 0.3961 time to fit residues: 218.1688 Evaluate side-chains 292 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 162 time to evaluate : 3.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain E residue 109 TRP Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 117 PHE Chi-restraints excluded: chain F residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 132 optimal weight: 7.9990 chunk 353 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 230 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 392 optimal weight: 7.9990 chunk 326 optimal weight: 3.9990 chunk 181 optimal weight: 0.0170 chunk 32 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 ASN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33123 Z= 0.258 Angle : 0.575 12.316 45082 Z= 0.293 Chirality : 0.045 0.247 5180 Planarity : 0.004 0.124 5787 Dihedral : 7.045 82.427 5073 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.13 % Allowed : 23.24 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.53 (0.13), residues: 4060 helix: 1.22 (0.22), residues: 651 sheet: 0.53 (0.16), residues: 1102 loop : -1.33 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.005 0.001 HIS B1064 PHE 0.028 0.001 PHE A 133 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 164 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7518 (pmm) cc_final: 0.6981 (pmm) REVERT: A 392 PHE cc_start: 0.8567 (m-80) cc_final: 0.8290 (m-80) REVERT: A 508 TYR cc_start: 0.7614 (m-80) cc_final: 0.7297 (m-80) REVERT: A 697 MET cc_start: 0.8511 (mmm) cc_final: 0.8095 (tpt) REVERT: A 733 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7415 (ptpt) REVERT: A 985 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7487 (p0) REVERT: A 1018 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8014 (tt) REVERT: A 1029 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8253 (tpp) REVERT: B 97 LYS cc_start: 0.8230 (pttm) cc_final: 0.7923 (mmtm) REVERT: B 220 PHE cc_start: 0.6458 (t80) cc_final: 0.6094 (t80) REVERT: B 238 PHE cc_start: 0.5960 (p90) cc_final: 0.5669 (p90) REVERT: B 906 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8246 (t80) REVERT: B 990 GLU cc_start: 0.8195 (tt0) cc_final: 0.7596 (tm-30) REVERT: C 58 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7648 (m-80) REVERT: C 65 PHE cc_start: 0.6833 (m-80) cc_final: 0.6539 (m-80) REVERT: C 191 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7932 (tt0) REVERT: C 231 ILE cc_start: 0.6050 (OUTLIER) cc_final: 0.5710 (mp) REVERT: C 534 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8795 (m) REVERT: C 906 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.7599 (t80) REVERT: C 988 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8193 (mp0) REVERT: E 156 VAL cc_start: -0.0433 (OUTLIER) cc_final: -0.0687 (m) REVERT: D 48 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6572 (ptm) REVERT: D 82 GLN cc_start: 0.7786 (mt0) cc_final: 0.7446 (mp10) outliers start: 184 outliers final: 144 residues processed: 334 average time/residue: 0.4080 time to fit residues: 234.9899 Evaluate side-chains 309 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 154 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 109 TRP Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 117 PHE Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 378 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 chunk 222 optimal weight: 0.6980 chunk 330 optimal weight: 0.6980 chunk 219 optimal weight: 8.9990 chunk 391 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 180 optimal weight: 0.4980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A1106 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 658 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33123 Z= 0.192 Angle : 0.546 13.394 45082 Z= 0.276 Chirality : 0.044 0.248 5180 Planarity : 0.004 0.054 5787 Dihedral : 6.829 77.162 5073 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.85 % Allowed : 23.60 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.48 (0.13), residues: 4060 helix: 1.32 (0.22), residues: 646 sheet: 0.59 (0.16), residues: 1088 loop : -1.30 (0.12), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.004 0.001 HIS A1083 PHE 0.034 0.001 PHE C 133 TYR 0.033 0.001 TYR A 160 ARG 0.006 0.000 ARG F 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 168 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7490 (pmm) cc_final: 0.6912 (pmm) REVERT: A 236 THR cc_start: 0.7037 (OUTLIER) cc_final: 0.6513 (p) REVERT: A 392 PHE cc_start: 0.8566 (m-80) cc_final: 0.8170 (m-80) REVERT: A 508 TYR cc_start: 0.7658 (m-80) cc_final: 0.7330 (m-80) REVERT: A 697 MET cc_start: 0.8466 (mmm) cc_final: 0.8035 (tpt) REVERT: A 733 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7377 (ptpt) REVERT: A 985 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7543 (p0) REVERT: A 1029 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8161 (tpp) REVERT: B 97 LYS cc_start: 0.8223 (pttm) cc_final: 0.7920 (mmtm) REVERT: B 220 PHE cc_start: 0.6488 (t80) cc_final: 0.6093 (t80) REVERT: B 238 PHE cc_start: 0.5961 (p90) cc_final: 0.5690 (p90) REVERT: B 505 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7047 (t80) REVERT: B 906 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8311 (t80) REVERT: B 990 GLU cc_start: 0.8111 (tt0) cc_final: 0.7532 (tm-30) REVERT: C 58 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: C 65 PHE cc_start: 0.6786 (m-80) cc_final: 0.6482 (m-80) REVERT: C 191 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7901 (tt0) REVERT: C 231 ILE cc_start: 0.6001 (OUTLIER) cc_final: 0.5663 (mp) REVERT: C 534 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8775 (m) REVERT: C 906 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.7574 (t80) REVERT: C 923 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8687 (mm) REVERT: C 988 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8205 (mp0) REVERT: E 156 VAL cc_start: -0.0382 (OUTLIER) cc_final: -0.0640 (m) REVERT: D 48 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6613 (ptm) REVERT: D 82 GLN cc_start: 0.7814 (mt0) cc_final: 0.7468 (mp10) outliers start: 174 outliers final: 146 residues processed: 330 average time/residue: 0.3839 time to fit residues: 218.7323 Evaluate side-chains 315 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 156 time to evaluate : 3.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 109 TRP Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 117 PHE Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 242 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 307 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33123 Z= 0.276 Angle : 0.585 13.733 45082 Z= 0.297 Chirality : 0.045 0.242 5180 Planarity : 0.004 0.055 5787 Dihedral : 6.858 72.552 5073 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.33 % Allowed : 23.38 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.62 (0.13), residues: 4060 helix: 1.15 (0.22), residues: 651 sheet: 0.44 (0.16), residues: 1120 loop : -1.37 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.005 0.001 HIS B1064 PHE 0.049 0.002 PHE C 133 TYR 0.027 0.001 TYR A 160 ARG 0.016 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 165 time to evaluate : 4.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7471 (pmm) cc_final: 0.6856 (pmm) REVERT: A 392 PHE cc_start: 0.8499 (m-80) cc_final: 0.8242 (m-80) REVERT: A 508 TYR cc_start: 0.7697 (m-80) cc_final: 0.7346 (m-80) REVERT: A 697 MET cc_start: 0.8483 (mmm) cc_final: 0.8036 (tpt) REVERT: A 733 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7414 (ptpt) REVERT: A 985 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7594 (p0) REVERT: A 1029 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8286 (tpp) REVERT: B 97 LYS cc_start: 0.8090 (pttm) cc_final: 0.7823 (mmtm) REVERT: B 220 PHE cc_start: 0.6418 (t80) cc_final: 0.6050 (t80) REVERT: B 238 PHE cc_start: 0.5860 (p90) cc_final: 0.5620 (p90) REVERT: B 505 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7042 (t80) REVERT: B 906 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8269 (t80) REVERT: B 990 GLU cc_start: 0.8201 (tt0) cc_final: 0.7631 (tm-30) REVERT: C 58 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7648 (m-80) REVERT: C 65 PHE cc_start: 0.6823 (m-80) cc_final: 0.6509 (m-80) REVERT: C 231 ILE cc_start: 0.5990 (OUTLIER) cc_final: 0.5655 (mp) REVERT: C 408 ARG cc_start: 0.8666 (ppt170) cc_final: 0.8460 (ppt170) REVERT: C 534 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8792 (m) REVERT: C 655 HIS cc_start: 0.7771 (OUTLIER) cc_final: 0.7515 (p90) REVERT: C 906 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.7598 (t80) REVERT: C 923 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8713 (mm) REVERT: C 988 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8195 (mp0) REVERT: E 156 VAL cc_start: -0.0257 (OUTLIER) cc_final: -0.0515 (m) REVERT: D 48 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6643 (ptm) REVERT: D 82 GLN cc_start: 0.7949 (mt0) cc_final: 0.7548 (mp10) outliers start: 191 outliers final: 162 residues processed: 342 average time/residue: 0.3775 time to fit residues: 223.2628 Evaluate side-chains 333 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 158 time to evaluate : 4.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 109 TRP Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 117 PHE Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 167 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 355 optimal weight: 0.0010 chunk 374 optimal weight: 5.9990 chunk 342 optimal weight: 9.9990 chunk 364 optimal weight: 0.9990 chunk 219 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 329 optimal weight: 20.0000 chunk 344 optimal weight: 2.9990 chunk 363 optimal weight: 6.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33123 Z= 0.282 Angle : 0.593 14.333 45082 Z= 0.301 Chirality : 0.045 0.253 5180 Planarity : 0.004 0.055 5787 Dihedral : 6.829 67.655 5073 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.27 % Allowed : 23.69 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.68 (0.13), residues: 4060 helix: 1.07 (0.22), residues: 651 sheet: 0.42 (0.16), residues: 1116 loop : -1.41 (0.12), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.005 0.001 HIS A1083 PHE 0.051 0.002 PHE C 133 TYR 0.030 0.001 TYR B 369 ARG 0.005 0.000 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 165 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7477 (pmm) cc_final: 0.6833 (pmm) REVERT: A 392 PHE cc_start: 0.8593 (m-80) cc_final: 0.8218 (m-80) REVERT: A 508 TYR cc_start: 0.7711 (m-80) cc_final: 0.7344 (m-80) REVERT: A 697 MET cc_start: 0.8483 (mmm) cc_final: 0.8184 (tpp) REVERT: A 733 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7421 (ptpt) REVERT: A 985 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7626 (p0) REVERT: A 1029 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8288 (tpp) REVERT: B 97 LYS cc_start: 0.8141 (pttm) cc_final: 0.7664 (mmtt) REVERT: B 220 PHE cc_start: 0.6347 (t80) cc_final: 0.5947 (t80) REVERT: B 238 PHE cc_start: 0.5862 (p90) cc_final: 0.5620 (p90) REVERT: B 505 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7047 (t80) REVERT: B 906 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8258 (t80) REVERT: B 990 GLU cc_start: 0.8249 (tt0) cc_final: 0.7651 (tm-30) REVERT: C 58 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7649 (m-80) REVERT: C 65 PHE cc_start: 0.6817 (m-80) cc_final: 0.6496 (m-80) REVERT: C 191 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7932 (tt0) REVERT: C 231 ILE cc_start: 0.5930 (OUTLIER) cc_final: 0.5593 (mp) REVERT: C 534 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8769 (m) REVERT: C 655 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7497 (p90) REVERT: C 906 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7592 (t80) REVERT: C 923 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8699 (mm) REVERT: C 988 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8173 (mp0) REVERT: E 156 VAL cc_start: -0.0147 (OUTLIER) cc_final: -0.0444 (m) REVERT: D 48 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6696 (ptm) REVERT: D 82 GLN cc_start: 0.8019 (mt0) cc_final: 0.7581 (mp10) REVERT: I 147 VAL cc_start: 0.1783 (OUTLIER) cc_final: 0.1433 (p) outliers start: 189 outliers final: 165 residues processed: 340 average time/residue: 0.3788 time to fit residues: 222.7957 Evaluate side-chains 337 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 158 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 117 PHE Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 167 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 239 optimal weight: 4.9990 chunk 385 optimal weight: 20.0000 chunk 235 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 404 optimal weight: 40.0000 chunk 372 optimal weight: 4.9990 chunk 322 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 197 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 33123 Z= 0.306 Angle : 0.609 13.913 45082 Z= 0.310 Chirality : 0.046 0.245 5180 Planarity : 0.004 0.056 5787 Dihedral : 6.836 63.348 5073 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.11 % Allowed : 23.74 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.75 (0.13), residues: 4060 helix: 0.99 (0.22), residues: 651 sheet: 0.34 (0.16), residues: 1121 loop : -1.44 (0.12), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.005 0.001 HIS B1064 PHE 0.052 0.002 PHE A 133 TYR 0.045 0.001 TYR A 160 ARG 0.005 0.000 ARG F 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 162 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.6386 (t80) REVERT: A 153 MET cc_start: 0.7515 (pmm) cc_final: 0.6850 (pmm) REVERT: A 392 PHE cc_start: 0.8537 (m-80) cc_final: 0.8254 (m-80) REVERT: A 508 TYR cc_start: 0.7688 (m-80) cc_final: 0.7331 (m-80) REVERT: A 697 MET cc_start: 0.8478 (mmm) cc_final: 0.8175 (tpp) REVERT: A 733 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7427 (ptpt) REVERT: A 985 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7797 (p0) REVERT: A 1029 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8269 (tpp) REVERT: B 97 LYS cc_start: 0.8172 (pttm) cc_final: 0.7664 (mmtt) REVERT: B 220 PHE cc_start: 0.6350 (t80) cc_final: 0.5982 (t80) REVERT: B 505 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7049 (t80) REVERT: B 906 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8204 (t80) REVERT: B 990 GLU cc_start: 0.8225 (tt0) cc_final: 0.7643 (tm-30) REVERT: C 58 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7586 (m-80) REVERT: C 65 PHE cc_start: 0.6802 (m-80) cc_final: 0.6469 (m-80) REVERT: C 191 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7931 (tt0) REVERT: C 231 ILE cc_start: 0.5884 (OUTLIER) cc_final: 0.5549 (mp) REVERT: C 534 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8773 (m) REVERT: C 655 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.7470 (p90) REVERT: C 906 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7586 (t80) REVERT: C 988 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8158 (mp0) REVERT: E 156 VAL cc_start: -0.0056 (OUTLIER) cc_final: -0.0374 (m) REVERT: D 28 ASN cc_start: 0.7079 (t0) cc_final: 0.6735 (t0) REVERT: D 48 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6731 (ptm) REVERT: D 82 GLN cc_start: 0.8043 (mt0) cc_final: 0.7541 (mp10) REVERT: I 147 VAL cc_start: 0.1744 (OUTLIER) cc_final: 0.1399 (p) outliers start: 183 outliers final: 163 residues processed: 331 average time/residue: 0.3694 time to fit residues: 210.8613 Evaluate side-chains 337 residues out of total 3584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 160 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 117 PHE Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 167 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 255 optimal weight: 1.9990 chunk 343 optimal weight: 0.0270 chunk 98 optimal weight: 0.9990 chunk 296 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 89 optimal weight: 0.2980 chunk 322 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 331 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.144672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.109666 restraints weight = 73972.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.105953 restraints weight = 93190.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.103114 restraints weight = 72365.182| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33123 Z= 0.169 Angle : 0.560 14.740 45082 Z= 0.279 Chirality : 0.044 0.247 5180 Planarity : 0.004 0.055 5787 Dihedral : 6.501 59.032 5073 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.19 % Allowed : 24.78 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % 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: -0.55 (0.13), residues: 4060 helix: 1.28 (0.22), residues: 641 sheet: 0.46 (0.16), residues: 1115 loop : -1.33 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 104 HIS 0.004 0.001 HIS A1083 PHE 0.029 0.001 PHE C 133 TYR 0.031 0.001 TYR B 369 ARG 0.004 0.000 ARG F 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5980.75 seconds wall clock time: 111 minutes 18.70 seconds (6678.70 seconds total)