Starting phenix.real_space_refine on Sat Feb 24 02:13:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8c_31014/02_2024/7e8c_31014_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8c_31014/02_2024/7e8c_31014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8c_31014/02_2024/7e8c_31014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8c_31014/02_2024/7e8c_31014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8c_31014/02_2024/7e8c_31014_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8c_31014/02_2024/7e8c_31014_neut.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 183 5.16 5 C 25504 2.51 5 N 6739 2.21 5 O 7799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 132": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "J ARG 82": "NH1" <-> "NH2" Residue "J GLU 110": "OE1" <-> "OE2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "M GLU 6": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "Z GLU 110": "OE1" <-> "OE2" Residue "a GLU 6": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 40225 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8216 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 55, 'TRANS': 996} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 8226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 8226 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 998} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 8210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8210 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 994} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 874 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "I" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "J" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "K" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "M" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 874 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "O" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 874 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "P" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "Q" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "S" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "T" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "V" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "Z" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "a" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Time building chain proxies: 20.67, per 1000 atoms: 0.51 Number of scatterers: 40225 At special positions: 0 Unit cell: (191.464, 205.14, 225.128, 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 183 16.00 O 7799 8.00 N 6739 7.00 C 25504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=60, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 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=2.04 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=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 93 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 93 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 95 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 95 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 87 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 87 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 93 " distance=2.04 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.85 Conformation dependent library (CDL) restraints added in 7.8 seconds 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9558 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 92 sheets defined 17.5% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.338A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 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 754 removed outlier: 3.681A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.618A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.566A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.671A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.590A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.050A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.581A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.969A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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 977 through 981 removed outlier: 3.698A pdb=" N ILE A 980 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.708A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.909A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.880A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 390' Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.482A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 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 783 removed outlier: 3.836A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.532A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.517A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.534A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.589A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.833A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.740A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1034 removed outlier: 3.731A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.825A 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: 3.540A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.723A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.539A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.617A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.570A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.704A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.778A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.520A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.847A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.579A pdb=" N SER D 31 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'H' and resid 26 through 32 removed outlier: 4.025A pdb=" N PHE H 29 " --> pdb=" O GLU H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.291A pdb=" N THR H 91 " --> pdb=" O VAL H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 110 removed outlier: 3.565A pdb=" N TRP H 107 " --> pdb=" O SER H 104 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER H 108 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.691A pdb=" N ASP K 90 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR K 91 " --> pdb=" O ALA K 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 87 through 91' Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'M' and resid 62 through 65 Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.691A pdb=" N ASP M 90 " --> pdb=" O ARG M 87 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR M 91 " --> pdb=" O ALA M 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 87 through 91' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.579A pdb=" N SER N 31 " --> pdb=" O ILE N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 90 Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.579A pdb=" N SER O 31 " --> pdb=" O ILE O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 90 Processing helix chain 'S' and resid 26 through 32 removed outlier: 4.025A pdb=" N PHE S 29 " --> pdb=" O GLU S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.292A pdb=" N THR S 91 " --> pdb=" O VAL S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 110 removed outlier: 3.564A pdb=" N TRP S 107 " --> pdb=" O SER S 104 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N SER S 108 " --> pdb=" O SER S 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 32 removed outlier: 4.025A pdb=" N PHE T 29 " --> pdb=" O GLU T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 91 removed outlier: 4.291A pdb=" N THR T 91 " --> pdb=" O VAL T 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 110 removed outlier: 3.565A pdb=" N TRP T 107 " --> pdb=" O SER T 104 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER T 108 " --> pdb=" O SER T 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 30 Processing helix chain 'U' and resid 78 through 82 Processing helix chain 'V' and resid 26 through 30 Processing helix chain 'V' and resid 78 through 82 Processing helix chain 'a' and resid 62 through 65 Processing helix chain 'a' and resid 87 through 91 removed outlier: 3.691A pdb=" N ASP a 90 " --> pdb=" O ARG a 87 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR a 91 " --> pdb=" O ALA a 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.363A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.480A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.701A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 157 removed outlier: 4.625A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 157 removed outlier: 4.625A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.379A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.534A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 568 removed outlier: 4.009A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.629A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.756A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.967A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.194A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.703A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.289A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 55 removed outlier: 6.535A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 154 through 160 removed outlier: 7.777A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 154 through 160 removed outlier: 7.777A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.530A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.906A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.576A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.246A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 removed outlier: 5.368A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.128A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.128A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.340A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.219A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.472A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 51 through 55 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 164 through 172 removed outlier: 7.633A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 141 through 144 Processing sheet with id=AE4, first strand: chain 'C' and resid 245 through 246 Processing sheet with id=AE5, first strand: chain 'C' and resid 278 through 279 removed outlier: 6.326A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.995A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 323 through 328 removed outlier: 4.016A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.557A 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: 6.656A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.656A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.624A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.509A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.374A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR D 33 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.504A pdb=" N THR E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.680A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.576A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.802A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.541A pdb=" N GLU I 110 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR I 107 " --> pdb=" O TYR I 91 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU I 42 " --> pdb=" O LEU I 51 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU I 51 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AG6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.542A pdb=" N GLU J 110 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR J 107 " --> pdb=" O TYR J 91 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU J 42 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU J 51 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.505A pdb=" N SER K 21 " --> pdb=" O SER K 7 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU K 18 " --> pdb=" O MET K 83 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.553A pdb=" N THR K 119 " --> pdb=" O TYR K 94 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET K 34 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.553A pdb=" N THR K 119 " --> pdb=" O TYR K 94 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR K 114 " --> pdb=" O LYS K 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.282A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.503A pdb=" N VAL L 96 " --> pdb=" O ALA L 89 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP L 91 " --> pdb=" O THR L 94 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AH4, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.505A pdb=" N SER M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU M 18 " --> pdb=" O MET M 83 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.554A pdb=" N THR M 119 " --> pdb=" O TYR M 94 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET M 34 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.554A pdb=" N THR M 119 " --> pdb=" O TYR M 94 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR M 114 " --> pdb=" O LYS M 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.510A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'N' and resid 57 through 59 removed outlier: 6.375A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N MET N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR N 33 " --> pdb=" O ASP N 98 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.510A pdb=" N GLN O 3 " --> pdb=" O SER O 25 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.375A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR O 33 " --> pdb=" O ASP O 98 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'P' and resid 4 through 7 removed outlier: 3.504A pdb=" N THR P 22 " --> pdb=" O SER P 7 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.678A pdb=" N ALA P 84 " --> pdb=" O LEU P 104 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE P 48 " --> pdb=" O TRP P 35 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 4 through 7 removed outlier: 3.504A pdb=" N THR Q 22 " --> pdb=" O SER Q 7 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 10 through 13 removed outlier: 3.679A pdb=" N ALA Q 84 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE Q 48 " --> pdb=" O TRP Q 35 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN Q 37 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU Q 46 " --> pdb=" O GLN Q 37 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.576A pdb=" N LEU S 81 " --> pdb=" O LEU S 20 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.802A pdb=" N MET S 34 " --> pdb=" O SER S 50 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'T' and resid 4 through 7 removed outlier: 3.576A pdb=" N LEU T 81 " --> pdb=" O LEU T 20 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'T' and resid 11 through 12 removed outlier: 6.802A pdb=" N MET T 34 " --> pdb=" O SER T 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER T 50 " --> pdb=" O MET T 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP T 36 " --> pdb=" O VAL T 48 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'U' and resid 9 through 12 removed outlier: 6.281A pdb=" N GLN U 36 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LEU U 45 " --> pdb=" O GLN U 36 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'U' and resid 9 through 12 removed outlier: 3.503A pdb=" N VAL U 96 " --> pdb=" O ALA U 89 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP U 91 " --> pdb=" O THR U 94 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'U' and resid 18 through 23 Processing sheet with id=AJ4, first strand: chain 'V' and resid 9 through 12 removed outlier: 6.281A pdb=" N GLN V 36 " --> pdb=" O LEU V 45 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LEU V 45 " --> pdb=" O GLN V 36 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'V' and resid 9 through 12 removed outlier: 3.503A pdb=" N VAL V 96 " --> pdb=" O ALA V 89 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP V 91 " --> pdb=" O THR V 94 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'V' and resid 18 through 23 Processing sheet with id=AJ7, first strand: chain 'Z' and resid 4 through 7 Processing sheet with id=AJ8, first strand: chain 'Z' and resid 10 through 12 removed outlier: 3.542A pdb=" N GLU Z 110 " --> pdb=" O LEU Z 11 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR Z 107 " --> pdb=" O TYR Z 91 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU Z 42 " --> pdb=" O LEU Z 51 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU Z 51 " --> pdb=" O LEU Z 42 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'a' and resid 3 through 7 removed outlier: 3.506A pdb=" N SER a 21 " --> pdb=" O SER a 7 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU a 18 " --> pdb=" O MET a 83 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'a' and resid 11 through 12 removed outlier: 3.554A pdb=" N THR a 119 " --> pdb=" O TYR a 94 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET a 34 " --> pdb=" O ALA a 50 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP a 36 " --> pdb=" O VAL a 48 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'a' and resid 11 through 12 removed outlier: 3.554A pdb=" N THR a 119 " --> pdb=" O TYR a 94 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR a 114 " --> pdb=" O LYS a 98 " (cutoff:3.500A) 1551 hydrogen bonds defined for protein. 3987 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: 23.22 Time building geometry restraints manager: 16.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11987 1.33 - 1.47: 11082 1.47 - 1.60: 17810 1.60 - 1.74: 0 1.74 - 1.87: 243 Bond restraints: 41122 Sorted by residual: bond pdb=" CA CYS C 538 " pdb=" C CYS C 538 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.34e-02 5.57e+03 4.04e+01 bond pdb=" N LEU C 335 " pdb=" CA LEU C 335 " ideal model delta sigma weight residual 1.457 1.508 -0.050 1.29e-02 6.01e+03 1.51e+01 bond pdb=" N VAL C 534 " pdb=" CA VAL C 534 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.15e-02 7.56e+03 1.42e+01 bond pdb=" N GLY C 566 " pdb=" CA GLY C 566 " ideal model delta sigma weight residual 1.445 1.477 -0.032 9.20e-03 1.18e+04 1.24e+01 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.24e+01 ... (remaining 41117 not shown) Histogram of bond angle deviations from ideal: 94.96 - 102.86: 198 102.86 - 110.76: 12879 110.76 - 118.66: 19583 118.66 - 126.57: 22730 126.57 - 134.47: 506 Bond angle restraints: 55896 Sorted by residual: angle pdb=" N PRO A 892 " pdb=" CA PRO A 892 " pdb=" CB PRO A 892 " ideal model delta sigma weight residual 103.34 110.86 -7.52 9.30e-01 1.16e+00 6.54e+01 angle pdb=" N PRO C 892 " pdb=" CA PRO C 892 " pdb=" CB PRO C 892 " ideal model delta sigma weight residual 103.19 110.84 -7.65 9.50e-01 1.11e+00 6.48e+01 angle pdb=" N PRO B 892 " pdb=" CA PRO B 892 " pdb=" CB PRO B 892 " ideal model delta sigma weight residual 103.34 110.72 -7.38 9.30e-01 1.16e+00 6.29e+01 angle pdb=" C PHE C 329 " pdb=" CA PHE C 329 " pdb=" CB PHE C 329 " ideal model delta sigma weight residual 108.86 120.27 -11.41 1.44e+00 4.82e-01 6.28e+01 angle pdb=" CB ARG S 87 " pdb=" CG ARG S 87 " pdb=" CD ARG S 87 " ideal model delta sigma weight residual 111.30 127.51 -16.21 2.30e+00 1.89e-01 4.97e+01 ... (remaining 55891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.98: 22774 26.98 - 53.95: 1426 53.95 - 80.93: 161 80.93 - 107.90: 19 107.90 - 134.88: 1 Dihedral angle restraints: 24381 sinusoidal: 9386 harmonic: 14995 Sorted by residual: dihedral pdb=" CA GLY C 526 " pdb=" C GLY C 526 " pdb=" N PRO C 527 " pdb=" CA PRO C 527 " ideal model delta harmonic sigma weight residual -180.00 -45.12 -134.88 0 5.00e+00 4.00e-02 7.28e+02 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 -9.36 -76.64 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -10.52 -75.48 1 1.00e+01 1.00e-02 7.19e+01 ... (remaining 24378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 5429 0.082 - 0.163: 722 0.163 - 0.245: 95 0.245 - 0.326: 12 0.326 - 0.408: 4 Chirality restraints: 6262 Sorted by residual: chirality pdb=" CA LEU C 335 " pdb=" N LEU C 335 " pdb=" C LEU C 335 " pdb=" CB LEU C 335 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CB VAL A 289 " pdb=" CA VAL A 289 " pdb=" CG1 VAL A 289 " pdb=" CG2 VAL A 289 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA CYS C 336 " pdb=" N CYS C 336 " pdb=" C CYS C 336 " pdb=" CB CYS C 336 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 6259 not shown) Planarity restraints: 7225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 524 " -0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C VAL B 524 " 0.060 2.00e-02 2.50e+03 pdb=" O VAL B 524 " -0.023 2.00e-02 2.50e+03 pdb=" N CYS B 525 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 490 " -0.016 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE B 490 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE B 490 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B 490 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE B 490 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 490 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 490 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE L 57 " -0.052 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO L 58 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO L 58 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO L 58 " -0.041 5.00e-02 4.00e+02 ... (remaining 7222 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 18 2.19 - 2.87: 14663 2.87 - 3.54: 52626 3.54 - 4.22: 96148 4.22 - 4.90: 165158 Nonbonded interactions: 328613 Sorted by model distance: nonbonded pdb=" O PRO B 330 " pdb=" CG PRO B 527 " model vdw 1.508 3.440 nonbonded pdb=" O PRO B 330 " pdb=" CD PRO B 527 " model vdw 1.515 3.440 nonbonded pdb=" CA PRO B 330 " pdb=" CG PRO B 527 " model vdw 1.742 3.870 nonbonded pdb=" C PRO B 330 " pdb=" CG PRO B 527 " model vdw 1.779 3.670 nonbonded pdb=" CB PRO B 330 " pdb=" CG PRO B 527 " model vdw 1.886 3.840 ... (remaining 328608 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 620 or resid 641 through 827 or resid 853 throu \ gh 1146)) selection = (chain 'B' and (resid 14 through 620 or resid 641 through 675 or resid 690 throu \ gh 1146)) selection = (chain 'C' and (resid 14 through 827 or resid 853 through 1146)) } ncs_group { reference = chain 'D' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'H' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'Z' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'L' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 14.930 Check model and map are aligned: 0.660 Set scattering table: 0.380 Process input model: 111.140 Find NCS groups from input model: 3.380 Set up NCS constraints: 0.460 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 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 : 0.006 0.108 41122 Z= 0.384 Angle : 0.980 16.210 55896 Z= 0.609 Chirality : 0.058 0.408 6262 Planarity : 0.005 0.075 7225 Dihedral : 16.362 134.879 14643 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.68 % Favored : 92.04 % Rotamer: Outliers : 9.23 % Allowed : 3.56 % Favored : 87.22 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.11), residues: 5140 helix: -0.62 (0.19), residues: 691 sheet: -0.81 (0.13), residues: 1537 loop : -1.74 (0.11), residues: 2912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 35 HIS 0.002 0.001 HIS T 103 PHE 0.056 0.002 PHE B 490 TYR 0.026 0.002 TYR U 85 ARG 0.027 0.001 ARG M 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 410 poor density : 580 time to evaluate : 4.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.5908 (ttp80) cc_final: 0.5680 (ttp80) REVERT: A 393 THR cc_start: 0.6508 (OUTLIER) cc_final: 0.5883 (m) REVERT: A 434 ILE cc_start: 0.5919 (OUTLIER) cc_final: 0.5681 (mt) REVERT: A 503 VAL cc_start: 0.6387 (OUTLIER) cc_final: 0.6155 (p) REVERT: B 331 ASN cc_start: 0.0873 (OUTLIER) cc_final: 0.0496 (m-40) REVERT: B 334 ASN cc_start: 0.1156 (OUTLIER) cc_final: 0.0710 (m-40) REVERT: C 207 HIS cc_start: 0.6860 (m-70) cc_final: 0.6651 (m-70) REVERT: C 396 TYR cc_start: 0.5032 (m-10) cc_final: 0.4821 (m-10) REVERT: C 425 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6217 (mt) REVERT: C 461 LEU cc_start: 0.5261 (OUTLIER) cc_final: 0.4917 (tp) REVERT: C 472 ILE cc_start: 0.5170 (OUTLIER) cc_final: 0.4901 (tp) REVERT: C 489 TYR cc_start: 0.3737 (OUTLIER) cc_final: 0.3396 (m-80) REVERT: C 533 LEU cc_start: 0.2859 (OUTLIER) cc_final: 0.2448 (mp) REVERT: C 787 GLN cc_start: 0.7780 (mt0) cc_final: 0.7557 (mt0) REVERT: D 46 GLU cc_start: 0.3108 (OUTLIER) cc_final: 0.2902 (tt0) REVERT: D 71 ARG cc_start: 0.1897 (mtm110) cc_final: 0.1694 (mtm110) REVERT: D 104 MET cc_start: 0.2076 (OUTLIER) cc_final: 0.1757 (mmm) REVERT: H 77 LYS cc_start: 0.6773 (pttt) cc_final: 0.6504 (ptpp) REVERT: I 74 THR cc_start: 0.3640 (p) cc_final: 0.2817 (p) REVERT: J 9 LEU cc_start: 0.2148 (tp) cc_final: 0.1356 (pp) REVERT: J 87 ASP cc_start: 0.6480 (m-30) cc_final: 0.5706 (t70) REVERT: K 79 LEU cc_start: 0.6538 (tp) cc_final: 0.6174 (tp) REVERT: L 29 ASP cc_start: 0.4686 (m-30) cc_final: 0.4429 (m-30) REVERT: L 51 SER cc_start: 0.4965 (OUTLIER) cc_final: 0.4707 (t) REVERT: L 61 PHE cc_start: 0.4305 (m-80) cc_final: 0.3748 (m-10) REVERT: M 34 MET cc_start: 0.6991 (mmm) cc_final: 0.6722 (mmm) REVERT: M 65 LYS cc_start: 0.4585 (OUTLIER) cc_final: 0.3952 (mmtt) REVERT: M 98 LYS cc_start: 0.6111 (ptmm) cc_final: 0.5698 (pttp) REVERT: M 106 ASP cc_start: 0.5044 (m-30) cc_final: 0.4534 (m-30) REVERT: N 94 TYR cc_start: 0.1667 (OUTLIER) cc_final: 0.1458 (m-80) REVERT: O 67 PHE cc_start: 0.0813 (m-80) cc_final: 0.0374 (m-10) REVERT: P 70 ASP cc_start: 0.2396 (OUTLIER) cc_final: 0.1946 (t70) REVERT: Q 47 LEU cc_start: 0.4882 (OUTLIER) cc_final: 0.4645 (tp) REVERT: Q 49 TYR cc_start: 0.5351 (OUTLIER) cc_final: 0.5129 (p90) REVERT: S 74 ASN cc_start: 0.4837 (m-40) cc_final: 0.4586 (m-40) REVERT: U 46 VAL cc_start: 0.7023 (m) cc_final: 0.6514 (t) REVERT: U 57 ILE cc_start: 0.3850 (OUTLIER) cc_final: 0.3548 (mm) REVERT: U 94 THR cc_start: 0.5483 (OUTLIER) cc_final: 0.5200 (p) REVERT: V 11 SER cc_start: 0.3171 (OUTLIER) cc_final: 0.2958 (p) REVERT: V 81 ASP cc_start: 0.2394 (m-30) cc_final: 0.1769 (m-30) REVERT: Z 59 ARG cc_start: 0.3591 (OUTLIER) cc_final: 0.3255 (mtm-85) REVERT: a 65 LYS cc_start: 0.5927 (OUTLIER) cc_final: 0.4387 (tttt) REVERT: a 90 ASP cc_start: 0.3921 (OUTLIER) cc_final: 0.3526 (p0) outliers start: 410 outliers final: 49 residues processed: 856 average time/residue: 0.5044 time to fit residues: 707.5242 Evaluate side-chains 436 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 363 time to evaluate : 4.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 65 LYS Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 83 SER Chi-restraints excluded: chain N residue 94 TYR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 95 CYS Chi-restraints excluded: chain P residue 49 TYR Chi-restraints excluded: chain P residue 70 ASP Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 49 TYR Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain V residue 11 SER Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain Z residue 23 CYS Chi-restraints excluded: chain Z residue 59 ARG Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 88 VAL Chi-restraints excluded: chain a residue 65 LYS Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain a residue 119 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 433 optimal weight: 0.3980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 132 optimal weight: 0.0870 chunk 262 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 402 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 chunk 465 optimal weight: 10.0000 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 437 ASN A 440 ASN A 580 GLN A 658 ASN A 901 GLN A1101 HIS B 751 ASN B 764 ASN B1106 GLN C 14 GLN C 17 ASN C 121 ASN C 658 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 68 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN S 35 ASN U 36 GLN ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 78 GLN V 36 GLN ** a 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 35 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 41122 Z= 0.221 Angle : 0.656 12.348 55896 Z= 0.348 Chirality : 0.046 0.189 6262 Planarity : 0.005 0.059 7225 Dihedral : 6.965 83.494 5749 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.81 % Rotamer: Outliers : 2.68 % Allowed : 10.49 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.02 % Twisted Proline : 0.41 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.11), residues: 5140 helix: 0.32 (0.20), residues: 679 sheet: -0.40 (0.13), residues: 1485 loop : -1.54 (0.11), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 47 HIS 0.006 0.001 HIS A1101 PHE 0.025 0.002 PHE a 29 TYR 0.025 0.002 TYR C 170 ARG 0.007 0.001 ARG V 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 411 time to evaluate : 4.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6452 (mt-10) REVERT: A 370 ASN cc_start: 0.4380 (t0) cc_final: 0.4118 (t0) REVERT: A 434 ILE cc_start: 0.5922 (OUTLIER) cc_final: 0.5668 (mt) REVERT: A 904 TYR cc_start: 0.5965 (t80) cc_final: 0.5652 (t80) REVERT: B 153 MET cc_start: 0.5109 (tmm) cc_final: 0.4872 (tmm) REVERT: B 331 ASN cc_start: 0.1910 (OUTLIER) cc_final: 0.1440 (m-40) REVERT: B 334 ASN cc_start: 0.0775 (OUTLIER) cc_final: 0.0423 (m110) REVERT: B 530 SER cc_start: -0.1252 (OUTLIER) cc_final: -0.1637 (t) REVERT: B 867 ASP cc_start: 0.7100 (m-30) cc_final: 0.6853 (m-30) REVERT: C 233 ILE cc_start: 0.7735 (pt) cc_final: 0.7449 (pt) REVERT: C 396 TYR cc_start: 0.5259 (m-10) cc_final: 0.5027 (m-10) REVERT: C 489 TYR cc_start: 0.3433 (OUTLIER) cc_final: 0.3110 (m-80) REVERT: E 36 TYR cc_start: 0.2572 (m-80) cc_final: 0.2366 (m-80) REVERT: E 107 LYS cc_start: 0.2589 (OUTLIER) cc_final: 0.2278 (mptp) REVERT: H 65 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7112 (mttp) REVERT: J 87 ASP cc_start: 0.6152 (m-30) cc_final: 0.5594 (t70) REVERT: J 91 TYR cc_start: 0.4689 (m-80) cc_final: 0.4478 (m-80) REVERT: L 29 ASP cc_start: 0.4699 (m-30) cc_final: 0.4301 (m-30) REVERT: L 61 PHE cc_start: 0.3871 (m-80) cc_final: 0.3654 (m-10) REVERT: L 65 ASN cc_start: 0.5063 (t0) cc_final: 0.4714 (t0) REVERT: M 102 ARG cc_start: 0.3603 (OUTLIER) cc_final: 0.1910 (ptp-170) REVERT: M 106 ASP cc_start: 0.4794 (m-30) cc_final: 0.4428 (m-30) REVERT: O 67 PHE cc_start: 0.1235 (m-80) cc_final: 0.0948 (m-10) REVERT: S 113 ASP cc_start: 0.4760 (OUTLIER) cc_final: 0.4557 (p0) REVERT: T 39 GLN cc_start: 0.6769 (OUTLIER) cc_final: 0.6206 (pt0) REVERT: Z 59 ARG cc_start: 0.4165 (OUTLIER) cc_final: 0.3174 (mtm-85) outliers start: 119 outliers final: 66 residues processed: 506 average time/residue: 0.5251 time to fit residues: 442.6693 Evaluate side-chains 404 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 326 time to evaluate : 4.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain M residue 102 ARG Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 83 SER Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain U residue 21 THR Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 23 SER Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain Z residue 59 ARG Chi-restraints excluded: chain a residue 30 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 258 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 387 optimal weight: 0.0670 chunk 317 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 466 optimal weight: 9.9990 chunk 504 optimal weight: 10.0000 chunk 415 optimal weight: 0.4980 chunk 462 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 374 optimal weight: 7.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 121 ASN A 440 ASN A 450 ASN B 804 GLN B1106 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 978 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN K 3 GLN L 41 GLN L 68 ASN ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 35 ASN U 65 ASN V 37 GLN Z 43 GLN a 3 GLN a 39 GLN ** a 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 41122 Z= 0.179 Angle : 0.582 11.086 55896 Z= 0.308 Chirality : 0.044 0.242 6262 Planarity : 0.004 0.054 7225 Dihedral : 5.681 54.904 5672 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.34 % Favored : 93.58 % Rotamer: Outliers : 2.81 % Allowed : 12.00 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.02 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.11), residues: 5140 helix: 0.62 (0.21), residues: 686 sheet: -0.23 (0.13), residues: 1496 loop : -1.39 (0.11), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 109 HIS 0.003 0.000 HIS A1101 PHE 0.019 0.001 PHE B 490 TYR 0.024 0.001 TYR C 170 ARG 0.006 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 367 time to evaluate : 4.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6452 (mt-10) REVERT: A 370 ASN cc_start: 0.4487 (t0) cc_final: 0.4217 (t0) REVERT: A 826 VAL cc_start: 0.6577 (OUTLIER) cc_final: 0.6350 (t) REVERT: A 904 TYR cc_start: 0.6029 (t80) cc_final: 0.5702 (t80) REVERT: B 153 MET cc_start: 0.5002 (tmm) cc_final: 0.4637 (tmm) REVERT: B 331 ASN cc_start: 0.1550 (OUTLIER) cc_final: 0.1211 (m-40) REVERT: B 334 ASN cc_start: 0.0283 (OUTLIER) cc_final: -0.0203 (m110) REVERT: B 878 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8436 (mt) REVERT: C 233 ILE cc_start: 0.7703 (pt) cc_final: 0.7433 (pt) REVERT: E 107 LYS cc_start: 0.2752 (OUTLIER) cc_final: 0.2319 (mptp) REVERT: J 87 ASP cc_start: 0.6121 (m-30) cc_final: 0.5555 (t70) REVERT: J 91 TYR cc_start: 0.4592 (m-80) cc_final: 0.4322 (m-80) REVERT: M 106 ASP cc_start: 0.4778 (m-30) cc_final: 0.4482 (m-30) REVERT: O 67 PHE cc_start: 0.1180 (m-80) cc_final: 0.0936 (m-10) REVERT: S 83 MET cc_start: 0.5285 (OUTLIER) cc_final: 0.4298 (mmm) REVERT: T 34 MET cc_start: 0.6234 (mmm) cc_final: 0.6000 (mmm) REVERT: T 39 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.6195 (pt0) REVERT: Z 59 ARG cc_start: 0.4340 (OUTLIER) cc_final: 0.3497 (mtm-85) outliers start: 125 outliers final: 68 residues processed: 463 average time/residue: 0.5186 time to fit residues: 402.6346 Evaluate side-chains 398 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 321 time to evaluate : 4.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 23 SER Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 96 VAL Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain Z residue 59 ARG Chi-restraints excluded: chain Z residue 94 MET Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 102 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 461 optimal weight: 10.0000 chunk 350 optimal weight: 5.9990 chunk 242 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 222 optimal weight: 8.9990 chunk 313 optimal weight: 0.5980 chunk 468 optimal weight: 10.0000 chunk 495 optimal weight: 9.9990 chunk 244 optimal weight: 0.0980 chunk 443 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 440 ASN A 658 ASN B 125 ASN B 331 ASN B 658 ASN B1106 GLN C 14 GLN C 474 GLN C 804 GLN E 3 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN I 47 GLN ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 GLN L 68 ASN ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN Q 6 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 GLN U 37 GLN a 84 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 41122 Z= 0.202 Angle : 0.578 12.675 55896 Z= 0.304 Chirality : 0.044 0.252 6262 Planarity : 0.004 0.064 7225 Dihedral : 5.408 58.412 5660 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.85 % Rotamer: Outliers : 2.97 % Allowed : 13.44 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.02 % Twisted Proline : 0.41 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.12), residues: 5140 helix: 0.71 (0.21), residues: 689 sheet: -0.17 (0.13), residues: 1508 loop : -1.30 (0.11), residues: 2943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 36 HIS 0.003 0.001 HIS T 103 PHE 0.025 0.001 PHE A 817 TYR 0.023 0.001 TYR C 170 ARG 0.007 0.000 ARG M 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 379 time to evaluate : 4.259 Fit side-chains revert: symmetry clash REVERT: A 165 ASN cc_start: 0.5268 (t0) cc_final: 0.4796 (m110) REVERT: A 188 ASN cc_start: 0.5840 (t0) cc_final: 0.5204 (t0) REVERT: A 370 ASN cc_start: 0.4690 (t0) cc_final: 0.4423 (t0) REVERT: A 826 VAL cc_start: 0.6507 (OUTLIER) cc_final: 0.6248 (t) REVERT: A 904 TYR cc_start: 0.6173 (t80) cc_final: 0.5773 (t80) REVERT: B 334 ASN cc_start: 0.0633 (OUTLIER) cc_final: 0.0152 (m110) REVERT: B 878 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8447 (mt) REVERT: C 213 VAL cc_start: 0.5801 (OUTLIER) cc_final: 0.5554 (p) REVERT: C 233 ILE cc_start: 0.7679 (pt) cc_final: 0.7407 (pt) REVERT: C 1138 TYR cc_start: 0.7591 (t80) cc_final: 0.7323 (t80) REVERT: E 107 LYS cc_start: 0.2735 (OUTLIER) cc_final: 0.2226 (mptp) REVERT: I 74 THR cc_start: 0.3940 (t) cc_final: 0.3695 (t) REVERT: J 87 ASP cc_start: 0.6168 (m-30) cc_final: 0.5676 (t70) REVERT: J 91 TYR cc_start: 0.4639 (m-80) cc_final: 0.4395 (m-80) REVERT: L 53 ARG cc_start: 0.7565 (ttm110) cc_final: 0.7077 (mtm-85) REVERT: M 34 MET cc_start: 0.6887 (mmm) cc_final: 0.6642 (mmm) REVERT: M 106 ASP cc_start: 0.4929 (m-30) cc_final: 0.4576 (m-30) REVERT: O 67 PHE cc_start: 0.1193 (m-80) cc_final: 0.0882 (m-10) REVERT: S 83 MET cc_start: 0.5525 (OUTLIER) cc_final: 0.4113 (mmm) REVERT: U 34 TRP cc_start: 0.5469 (m100) cc_final: 0.5074 (m100) REVERT: V 78 GLN cc_start: 0.3663 (pp30) cc_final: 0.3435 (pt0) REVERT: Z 59 ARG cc_start: 0.4418 (OUTLIER) cc_final: 0.3594 (mtm-85) REVERT: a 29 PHE cc_start: 0.7363 (t80) cc_final: 0.7116 (t80) outliers start: 132 outliers final: 81 residues processed: 489 average time/residue: 0.5061 time to fit residues: 414.3437 Evaluate side-chains 422 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 334 time to evaluate : 4.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 123 VAL Chi-restraints excluded: chain U residue 21 THR Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 80 MET Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 23 SER Chi-restraints excluded: chain V residue 96 VAL Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain Z residue 59 ARG Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 102 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 412 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 369 optimal weight: 10.0000 chunk 204 optimal weight: 0.7980 chunk 423 optimal weight: 4.9990 chunk 342 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 253 optimal weight: 4.9990 chunk 445 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN A 481 ASN A 901 GLN B 957 GLN B1106 GLN C 14 GLN C 81 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 GLN ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 41122 Z= 0.489 Angle : 0.767 15.115 55896 Z= 0.398 Chirality : 0.051 0.251 6262 Planarity : 0.006 0.074 7225 Dihedral : 6.166 56.881 5654 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.80 % Favored : 92.12 % Rotamer: Outliers : 3.69 % Allowed : 14.58 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.11), residues: 5140 helix: 0.21 (0.20), residues: 681 sheet: -0.21 (0.13), residues: 1442 loop : -1.56 (0.11), residues: 3017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP K 109 HIS 0.017 0.002 HIS H 103 PHE 0.023 0.003 PHE C 275 TYR 0.026 0.002 TYR C1067 ARG 0.006 0.001 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 349 time to evaluate : 5.500 Fit side-chains revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.6947 (m-30) REVERT: A 165 ASN cc_start: 0.5214 (t0) cc_final: 0.4794 (m110) REVERT: A 176 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7439 (mp) REVERT: A 188 ASN cc_start: 0.5819 (t0) cc_final: 0.5190 (t0) REVERT: A 370 ASN cc_start: 0.4722 (t0) cc_final: 0.4463 (t0) REVERT: A 826 VAL cc_start: 0.6399 (OUTLIER) cc_final: 0.6143 (t) REVERT: B 334 ASN cc_start: 0.1104 (OUTLIER) cc_final: 0.0499 (m110) REVERT: B 878 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8482 (mt) REVERT: B 973 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7307 (tp) REVERT: C 213 VAL cc_start: 0.5685 (OUTLIER) cc_final: 0.5340 (t) REVERT: C 233 ILE cc_start: 0.7917 (pt) cc_final: 0.7571 (pt) REVERT: C 535 LYS cc_start: 0.4819 (OUTLIER) cc_final: 0.3407 (tptm) REVERT: C 1138 TYR cc_start: 0.7813 (t80) cc_final: 0.7454 (t80) REVERT: E 62 PHE cc_start: 0.3224 (m-80) cc_final: 0.3019 (m-80) REVERT: E 107 LYS cc_start: 0.2802 (OUTLIER) cc_final: 0.2333 (mptp) REVERT: H 80 TYR cc_start: 0.6429 (m-10) cc_final: 0.6160 (m-10) REVERT: J 40 TRP cc_start: 0.5893 (m100) cc_final: 0.5611 (m100) REVERT: K 83 MET cc_start: 0.4674 (OUTLIER) cc_final: 0.3264 (mtm) REVERT: L 53 ARG cc_start: 0.7629 (ttm110) cc_final: 0.7260 (mtm-85) REVERT: M 100 ARG cc_start: 0.5807 (OUTLIER) cc_final: 0.4805 (mtp85) REVERT: M 106 ASP cc_start: 0.5570 (m-30) cc_final: 0.4817 (m-30) REVERT: O 67 PHE cc_start: 0.1105 (m-10) cc_final: 0.0812 (m-10) REVERT: P 45 ASN cc_start: 0.3658 (m-40) cc_final: 0.2899 (t0) REVERT: T 95 TYR cc_start: 0.5844 (m-10) cc_final: 0.5279 (m-10) REVERT: U 34 TRP cc_start: 0.5217 (m100) cc_final: 0.4926 (m100) outliers start: 164 outliers final: 110 residues processed: 487 average time/residue: 0.5042 time to fit residues: 411.2337 Evaluate side-chains 431 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 310 time to evaluate : 4.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 123 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain U residue 21 THR Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain V residue 23 SER Chi-restraints excluded: chain V residue 96 VAL Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 84 GLU Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 166 optimal weight: 1.9990 chunk 446 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 291 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 496 optimal weight: 0.0270 chunk 412 optimal weight: 5.9990 chunk 229 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 260 optimal weight: 4.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN A 658 ASN A 901 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B1106 GLN C 14 GLN C 901 GLN E 6 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 41122 Z= 0.201 Angle : 0.589 11.216 55896 Z= 0.309 Chirality : 0.044 0.203 6262 Planarity : 0.004 0.080 7225 Dihedral : 5.463 56.570 5650 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 3.02 % Allowed : 16.14 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.11), residues: 5140 helix: 0.67 (0.21), residues: 670 sheet: -0.08 (0.13), residues: 1410 loop : -1.38 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 109 HIS 0.002 0.000 HIS C 49 PHE 0.018 0.001 PHE B 490 TYR 0.020 0.001 TYR C1067 ARG 0.004 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 340 time to evaluate : 4.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 ASN cc_start: 0.5095 (t0) cc_final: 0.4785 (m110) REVERT: A 188 ASN cc_start: 0.5608 (t0) cc_final: 0.5294 (t0) REVERT: A 370 ASN cc_start: 0.4762 (t0) cc_final: 0.4525 (t0) REVERT: A 573 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8703 (m) REVERT: A 826 VAL cc_start: 0.6388 (OUTLIER) cc_final: 0.6160 (t) REVERT: B 334 ASN cc_start: 0.0857 (OUTLIER) cc_final: 0.0398 (m110) REVERT: B 878 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8434 (mt) REVERT: B 916 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8128 (tt) REVERT: C 213 VAL cc_start: 0.5748 (OUTLIER) cc_final: 0.5357 (t) REVERT: C 233 ILE cc_start: 0.7645 (pt) cc_final: 0.7389 (pt) REVERT: C 535 LYS cc_start: 0.4894 (OUTLIER) cc_final: 0.3681 (tptm) REVERT: C 916 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8214 (tt) REVERT: C 1138 TYR cc_start: 0.7758 (t80) cc_final: 0.7345 (t80) REVERT: E 107 LYS cc_start: 0.2581 (OUTLIER) cc_final: 0.2339 (tptp) REVERT: J 40 TRP cc_start: 0.5806 (m100) cc_final: 0.5520 (m100) REVERT: K 83 MET cc_start: 0.4618 (OUTLIER) cc_final: 0.3265 (mtm) REVERT: L 53 ARG cc_start: 0.7553 (ttm110) cc_final: 0.7112 (mtm-85) REVERT: M 106 ASP cc_start: 0.5482 (m-30) cc_final: 0.4870 (m-30) REVERT: O 67 PHE cc_start: 0.1114 (m-10) cc_final: 0.0864 (m-10) REVERT: P 45 ASN cc_start: 0.3670 (m-40) cc_final: 0.2486 (p0) REVERT: S 34 MET cc_start: 0.6075 (mmm) cc_final: 0.5811 (mmm) REVERT: T 95 TYR cc_start: 0.5397 (m-10) cc_final: 0.5123 (m-10) REVERT: U 34 TRP cc_start: 0.5200 (m100) cc_final: 0.4893 (m100) outliers start: 134 outliers final: 95 residues processed: 452 average time/residue: 0.5496 time to fit residues: 418.1120 Evaluate side-chains 423 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 318 time to evaluate : 4.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 123 VAL Chi-restraints excluded: chain U residue 21 THR Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain V residue 96 VAL Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 84 GLU Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 102 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 478 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 282 optimal weight: 0.0030 chunk 362 optimal weight: 0.0010 chunk 280 optimal weight: 0.8980 chunk 417 optimal weight: 10.0000 chunk 277 optimal weight: 0.3980 chunk 494 optimal weight: 9.9990 chunk 309 optimal weight: 0.7980 chunk 301 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 121 ASN A 556 ASN A 658 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 14 GLN C 856 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 41122 Z= 0.155 Angle : 0.548 9.274 55896 Z= 0.288 Chirality : 0.043 0.223 6262 Planarity : 0.004 0.081 7225 Dihedral : 5.009 53.187 5648 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.23 % Favored : 93.70 % Rotamer: Outliers : 2.90 % Allowed : 16.77 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.85 (0.12), residues: 5140 helix: 0.88 (0.21), residues: 670 sheet: 0.01 (0.13), residues: 1446 loop : -1.22 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 109 HIS 0.002 0.000 HIS C 49 PHE 0.021 0.001 PHE K 29 TYR 0.022 0.001 TYR H 80 ARG 0.013 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 356 time to evaluate : 4.351 Fit side-chains REVERT: A 165 ASN cc_start: 0.4742 (t0) cc_final: 0.4528 (m110) REVERT: A 370 ASN cc_start: 0.4784 (t0) cc_final: 0.4530 (t0) REVERT: A 573 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8661 (m) REVERT: A 826 VAL cc_start: 0.6204 (OUTLIER) cc_final: 0.5996 (t) REVERT: A 981 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7123 (mm) REVERT: B 334 ASN cc_start: 0.0739 (OUTLIER) cc_final: 0.0429 (m110) REVERT: B 878 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8416 (mt) REVERT: C 213 VAL cc_start: 0.5858 (OUTLIER) cc_final: 0.5488 (t) REVERT: C 233 ILE cc_start: 0.7595 (pt) cc_final: 0.7335 (pt) REVERT: C 294 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7992 (p0) REVERT: C 859 THR cc_start: 0.8356 (m) cc_final: 0.8077 (p) REVERT: C 916 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8214 (tt) REVERT: C 1138 TYR cc_start: 0.7715 (t80) cc_final: 0.7259 (t80) REVERT: E 107 LYS cc_start: 0.2551 (OUTLIER) cc_final: 0.2288 (tptp) REVERT: J 40 TRP cc_start: 0.5728 (m100) cc_final: 0.5445 (m100) REVERT: K 83 MET cc_start: 0.4527 (OUTLIER) cc_final: 0.3427 (mtm) REVERT: L 53 ARG cc_start: 0.7498 (ttm110) cc_final: 0.6924 (mtm-85) REVERT: M 106 ASP cc_start: 0.5294 (m-30) cc_final: 0.4780 (m-30) REVERT: O 67 PHE cc_start: 0.1244 (m-10) cc_final: 0.0934 (m-10) REVERT: P 45 ASN cc_start: 0.3358 (m-40) cc_final: 0.2570 (p0) REVERT: S 34 MET cc_start: 0.6081 (mmm) cc_final: 0.5831 (mmm) REVERT: T 39 GLN cc_start: 0.6091 (pt0) cc_final: 0.5343 (pt0) REVERT: U 34 TRP cc_start: 0.5148 (m100) cc_final: 0.4864 (m100) REVERT: Z 98 GLN cc_start: 0.5613 (mt0) cc_final: 0.5378 (mt0) REVERT: a 82 GLN cc_start: 0.5956 (OUTLIER) cc_final: 0.5246 (tp40) outliers start: 129 outliers final: 90 residues processed: 457 average time/residue: 0.4996 time to fit residues: 379.9485 Evaluate side-chains 431 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 330 time to evaluate : 4.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 123 VAL Chi-restraints excluded: chain U residue 21 THR Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain V residue 96 VAL Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 82 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 305 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 314 optimal weight: 5.9990 chunk 336 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 388 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 532 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN C 14 GLN C 564 GLN C 856 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 41122 Z= 0.346 Angle : 0.657 11.316 55896 Z= 0.342 Chirality : 0.047 0.208 6262 Planarity : 0.005 0.083 7225 Dihedral : 5.470 58.281 5644 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.37 % Favored : 92.55 % Rotamer: Outliers : 3.22 % Allowed : 16.84 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.98 (0.12), residues: 5140 helix: 0.56 (0.21), residues: 681 sheet: 0.00 (0.13), residues: 1460 loop : -1.31 (0.11), residues: 2999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 109 HIS 0.004 0.001 HIS B1064 PHE 0.024 0.002 PHE A 329 TYR 0.025 0.002 TYR E 49 ARG 0.010 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 337 time to evaluate : 4.470 Fit side-chains revert: symmetry clash REVERT: A 165 ASN cc_start: 0.4724 (t0) cc_final: 0.4453 (m110) REVERT: A 370 ASN cc_start: 0.4698 (t0) cc_final: 0.4446 (t0) REVERT: A 408 ARG cc_start: 0.6648 (tmm160) cc_final: 0.6402 (ttp-110) REVERT: A 573 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8748 (m) REVERT: B 334 ASN cc_start: 0.1997 (OUTLIER) cc_final: 0.1546 (m110) REVERT: B 878 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8463 (mt) REVERT: B 973 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7339 (tp) REVERT: C 135 PHE cc_start: 0.6506 (m-80) cc_final: 0.6215 (m-80) REVERT: C 213 VAL cc_start: 0.5870 (OUTLIER) cc_final: 0.5490 (t) REVERT: C 233 ILE cc_start: 0.7840 (pt) cc_final: 0.7542 (pt) REVERT: C 535 LYS cc_start: 0.4783 (OUTLIER) cc_final: 0.3514 (tptm) REVERT: C 916 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8417 (tt) REVERT: C 1138 TYR cc_start: 0.7760 (t80) cc_final: 0.7394 (t80) REVERT: D 67 PHE cc_start: 0.0218 (m-80) cc_final: -0.0275 (m-80) REVERT: E 107 LYS cc_start: 0.2644 (OUTLIER) cc_final: 0.2380 (tptp) REVERT: J 27 GLN cc_start: 0.6951 (tm-30) cc_final: 0.6641 (tm-30) REVERT: J 40 TRP cc_start: 0.5722 (m100) cc_final: 0.5392 (m100) REVERT: K 82 GLN cc_start: 0.4966 (tm-30) cc_final: 0.4269 (mp10) REVERT: K 83 MET cc_start: 0.4447 (OUTLIER) cc_final: 0.3103 (mtm) REVERT: L 53 ARG cc_start: 0.7553 (ttm110) cc_final: 0.7015 (mtm-85) REVERT: M 34 MET cc_start: 0.7080 (mmm) cc_final: 0.6859 (mmm) REVERT: M 100 ARG cc_start: 0.5706 (OUTLIER) cc_final: 0.3984 (mtp85) REVERT: M 106 ASP cc_start: 0.5565 (m-30) cc_final: 0.4933 (m-30) REVERT: O 67 PHE cc_start: 0.1284 (m-10) cc_final: 0.0984 (m-10) REVERT: P 45 ASN cc_start: 0.3018 (m-40) cc_final: 0.2406 (p0) REVERT: T 39 GLN cc_start: 0.6316 (pt0) cc_final: 0.6072 (pt0) REVERT: U 34 TRP cc_start: 0.5168 (m100) cc_final: 0.4894 (m100) REVERT: a 29 PHE cc_start: 0.7480 (t80) cc_final: 0.7102 (t80) REVERT: a 34 MET cc_start: 0.7565 (mmt) cc_final: 0.7364 (mmm) REVERT: a 82 GLN cc_start: 0.5807 (OUTLIER) cc_final: 0.5119 (tp40) outliers start: 143 outliers final: 109 residues processed: 454 average time/residue: 0.4954 time to fit residues: 377.4321 Evaluate side-chains 441 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 321 time to evaluate : 4.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 123 VAL Chi-restraints excluded: chain U residue 21 THR Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain V residue 96 VAL Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 82 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 449 optimal weight: 9.9990 chunk 473 optimal weight: 0.0470 chunk 432 optimal weight: 7.9990 chunk 460 optimal weight: 10.0000 chunk 277 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 361 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 416 optimal weight: 7.9990 chunk 435 optimal weight: 9.9990 chunk 459 optimal weight: 0.5980 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 14 GLN C 856 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN K 39 GLN ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 41122 Z= 0.217 Angle : 0.587 9.540 55896 Z= 0.306 Chirality : 0.044 0.188 6262 Planarity : 0.004 0.083 7225 Dihedral : 5.231 57.958 5644 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 3.04 % Allowed : 17.17 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.12), residues: 5140 helix: 0.74 (0.21), residues: 671 sheet: 0.05 (0.14), residues: 1426 loop : -1.25 (0.11), residues: 3043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 109 HIS 0.002 0.001 HIS A1048 PHE 0.021 0.002 PHE A 329 TYR 0.024 0.001 TYR E 49 ARG 0.004 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 346 time to evaluate : 4.486 Fit side-chains revert: symmetry clash REVERT: A 370 ASN cc_start: 0.4674 (t0) cc_final: 0.4422 (t0) REVERT: A 408 ARG cc_start: 0.6662 (tmm160) cc_final: 0.6414 (ttp-110) REVERT: A 573 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8693 (m) REVERT: B 856 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6457 (p0) REVERT: B 878 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8440 (mt) REVERT: B 973 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7347 (tp) REVERT: C 213 VAL cc_start: 0.5783 (OUTLIER) cc_final: 0.5411 (t) REVERT: C 233 ILE cc_start: 0.7671 (pt) cc_final: 0.7395 (pt) REVERT: C 535 LYS cc_start: 0.4942 (OUTLIER) cc_final: 0.3824 (tptm) REVERT: C 916 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8247 (tt) REVERT: C 1138 TYR cc_start: 0.7687 (t80) cc_final: 0.7292 (t80) REVERT: D 4 LEU cc_start: 0.3442 (tp) cc_final: 0.3223 (tp) REVERT: E 107 LYS cc_start: 0.2598 (OUTLIER) cc_final: 0.2313 (tptp) REVERT: J 27 GLN cc_start: 0.7053 (tm-30) cc_final: 0.6677 (tm-30) REVERT: J 40 TRP cc_start: 0.5642 (m100) cc_final: 0.5378 (m100) REVERT: K 19 ARG cc_start: 0.4614 (ttm170) cc_final: 0.4374 (ttm170) REVERT: K 82 GLN cc_start: 0.4927 (tm-30) cc_final: 0.4310 (mp10) REVERT: K 83 MET cc_start: 0.4479 (OUTLIER) cc_final: 0.3182 (mtm) REVERT: L 53 ARG cc_start: 0.7544 (ttm110) cc_final: 0.6987 (mtm-85) REVERT: M 34 MET cc_start: 0.6988 (mmm) cc_final: 0.6769 (mmm) REVERT: M 100 ARG cc_start: 0.5598 (OUTLIER) cc_final: 0.3926 (mtp85) REVERT: M 106 ASP cc_start: 0.5495 (m-30) cc_final: 0.4878 (m-30) REVERT: O 67 PHE cc_start: 0.1364 (m-10) cc_final: 0.1043 (m-10) REVERT: P 45 ASN cc_start: 0.3007 (m-40) cc_final: 0.2423 (p0) REVERT: T 39 GLN cc_start: 0.6365 (pt0) cc_final: 0.6147 (pt0) REVERT: U 34 TRP cc_start: 0.5129 (m100) cc_final: 0.4847 (m100) REVERT: Z 98 GLN cc_start: 0.5698 (mt0) cc_final: 0.5467 (mt0) REVERT: Z 108 ARG cc_start: 0.4142 (ptm160) cc_final: 0.3704 (ttt180) REVERT: a 29 PHE cc_start: 0.7467 (t80) cc_final: 0.7046 (t80) REVERT: a 82 GLN cc_start: 0.5767 (OUTLIER) cc_final: 0.5025 (tp40) outliers start: 135 outliers final: 111 residues processed: 455 average time/residue: 0.4902 time to fit residues: 373.3474 Evaluate side-chains 453 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 331 time to evaluate : 4.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 123 VAL Chi-restraints excluded: chain U residue 21 THR Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain V residue 96 VAL Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain Z residue 84 GLU Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 82 GLN Chi-restraints excluded: chain a residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 302 optimal weight: 0.5980 chunk 487 optimal weight: 8.9990 chunk 297 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 338 optimal weight: 8.9990 chunk 511 optimal weight: 10.0000 chunk 470 optimal weight: 0.0170 chunk 406 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 chunk 249 optimal weight: 0.8980 overall best weight: 1.5020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 165 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 14 GLN C 856 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 41122 Z= 0.263 Angle : 0.613 13.216 55896 Z= 0.318 Chirality : 0.045 0.184 6262 Planarity : 0.005 0.083 7225 Dihedral : 5.261 57.778 5642 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.14 % Favored : 92.78 % Rotamer: Outliers : 2.93 % Allowed : 17.44 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.88 (0.12), residues: 5140 helix: 0.69 (0.21), residues: 671 sheet: 0.07 (0.13), residues: 1454 loop : -1.25 (0.11), residues: 3015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 109 HIS 0.003 0.001 HIS A1048 PHE 0.046 0.002 PHE K 29 TYR 0.026 0.002 TYR I 54 ARG 0.007 0.000 ARG I 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10280 Ramachandran restraints generated. 5140 Oldfield, 0 Emsley, 5140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 337 time to evaluate : 4.456 Fit side-chains REVERT: A 370 ASN cc_start: 0.4655 (t0) cc_final: 0.4398 (t0) REVERT: A 408 ARG cc_start: 0.6660 (tmm160) cc_final: 0.6423 (ttp-110) REVERT: A 573 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8732 (m) REVERT: B 856 ASN cc_start: 0.7225 (OUTLIER) cc_final: 0.6604 (p0) REVERT: B 878 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8456 (mt) REVERT: B 973 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7407 (tp) REVERT: C 213 VAL cc_start: 0.5860 (OUTLIER) cc_final: 0.5482 (t) REVERT: C 233 ILE cc_start: 0.7775 (pt) cc_final: 0.7481 (pt) REVERT: C 535 LYS cc_start: 0.4925 (OUTLIER) cc_final: 0.3783 (tptm) REVERT: C 916 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8322 (tt) REVERT: C 1138 TYR cc_start: 0.7706 (t80) cc_final: 0.7361 (t80) REVERT: E 73 LEU cc_start: 0.2501 (OUTLIER) cc_final: 0.2097 (tt) REVERT: E 107 LYS cc_start: 0.2621 (OUTLIER) cc_final: 0.2340 (tptp) REVERT: J 27 GLN cc_start: 0.6902 (tm-30) cc_final: 0.6578 (tm-30) REVERT: J 40 TRP cc_start: 0.5605 (m100) cc_final: 0.5355 (m100) REVERT: K 19 ARG cc_start: 0.4554 (ttm170) cc_final: 0.4324 (ttm170) REVERT: K 82 GLN cc_start: 0.4835 (tm-30) cc_final: 0.4423 (mp10) REVERT: K 83 MET cc_start: 0.4549 (OUTLIER) cc_final: 0.3243 (mtm) REVERT: L 53 ARG cc_start: 0.7542 (ttm110) cc_final: 0.6990 (mtm-85) REVERT: M 34 MET cc_start: 0.7071 (mmm) cc_final: 0.6850 (mmm) REVERT: M 100 ARG cc_start: 0.5601 (OUTLIER) cc_final: 0.3829 (mtp85) REVERT: M 106 ASP cc_start: 0.5510 (m-30) cc_final: 0.4879 (m-30) REVERT: O 67 PHE cc_start: 0.1302 (m-10) cc_final: 0.1001 (m-10) REVERT: P 45 ASN cc_start: 0.3108 (m-40) cc_final: 0.2447 (p0) REVERT: U 34 TRP cc_start: 0.5125 (m100) cc_final: 0.4837 (m100) REVERT: Z 108 ARG cc_start: 0.4084 (OUTLIER) cc_final: 0.3739 (ttt180) REVERT: a 82 GLN cc_start: 0.5764 (OUTLIER) cc_final: 0.5033 (tp40) outliers start: 130 outliers final: 111 residues processed: 442 average time/residue: 0.5135 time to fit residues: 382.1243 Evaluate side-chains 448 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 324 time to evaluate : 4.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 123 VAL Chi-restraints excluded: chain U residue 21 THR Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain V residue 96 VAL Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain Z residue 108 ARG Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 82 GLN Chi-restraints excluded: chain a residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 323 optimal weight: 1.9990 chunk 433 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 375 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 407 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 418 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 14 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.153868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.122958 restraints weight = 85030.851| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.94 r_work: 0.3585 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 41122 Z= 0.243 Angle : 0.599 12.303 55896 Z= 0.312 Chirality : 0.045 0.186 6262 Planarity : 0.004 0.084 7225 Dihedral : 5.217 57.254 5642 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.65 % Favored : 93.27 % Rotamer: Outliers : 2.93 % Allowed : 17.51 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.85 (0.12), residues: 5140 helix: 0.70 (0.21), residues: 677 sheet: 0.10 (0.14), residues: 1433 loop : -1.22 (0.11), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP O 47 HIS 0.002 0.001 HIS T 103 PHE 0.040 0.002 PHE K 29 TYR 0.033 0.002 TYR a 80 ARG 0.007 0.000 ARG I 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9837.79 seconds wall clock time: 178 minutes 38.84 seconds (10718.84 seconds total)