Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 19 14:37:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8c_31014/10_2023/7e8c_31014_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8c_31014/10_2023/7e8c_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_31014/10_2023/7e8c_31014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8c_31014/10_2023/7e8c_31014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8c_31014/10_2023/7e8c_31014_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8c_31014/10_2023/7e8c_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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 19.64, per 1000 atoms: 0.49 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: 16.30 Conformation dependent library (CDL) restraints added in 5.8 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: 4.80 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: 21.47 Time building geometry restraints manager: 17.26 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: 4.630 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: 15.330 Check model and map are aligned: 0.590 Set scattering table: 0.330 Process input model: 106.690 Find NCS groups from input model: 2.970 Set up NCS constraints: 0.390 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:3.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.510 ------------------------------------------------------------------------------- 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 *********************** 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 : 4.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 410 outliers final: 49 residues processed: 856 average time/residue: 0.5149 time to fit residues: 725.6420 Evaluate side-chains 407 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 358 time to evaluate : 4.929 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.3986 time to fit residues: 42.9338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 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: 4.9990 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: 1.2362 ------------------------------------------------------------------------------- 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** C 978 ASN ** 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 ** 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 V 37 GLN a 3 GLN a 35 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 41122 Z= 0.266 Angle : 0.679 12.607 55896 Z= 0.359 Chirality : 0.047 0.200 6262 Planarity : 0.005 0.061 7225 Dihedral : 5.619 49.725 5632 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 1.80 % Allowed : 11.01 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.02 % Twisted Proline : 0.41 % 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: -1.42 (0.11), residues: 5140 helix: 0.19 (0.20), residues: 685 sheet: -0.36 (0.13), residues: 1474 loop : -1.57 (0.11), residues: 2981 *********************** 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 478 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 398 time to evaluate : 4.799 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 50 residues processed: 459 average time/residue: 0.5083 time to fit residues: 389.0578 Evaluate side-chains 374 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 324 time to evaluate : 4.345 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.3633 time to fit residues: 40.3768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 258 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 387 optimal weight: 4.9990 chunk 317 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 466 optimal weight: 0.4980 chunk 504 optimal weight: 10.0000 chunk 415 optimal weight: 10.0000 chunk 462 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 374 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 A 658 ASN B 658 ASN B 804 GLN B 957 GLN C 14 GLN C 762 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN E 3 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN K 3 GLN L 41 GLN L 68 ASN L 78 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 65 ASN Z 43 GLN a 39 GLN a 84 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 41122 Z= 0.244 Angle : 0.622 10.523 55896 Z= 0.328 Chirality : 0.045 0.186 6262 Planarity : 0.005 0.096 7225 Dihedral : 5.284 38.758 5632 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.67 % Favored : 93.25 % Rotamer: Outliers : 1.96 % Allowed : 13.35 % Favored : 84.70 % 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: -1.25 (0.11), residues: 5140 helix: 0.43 (0.20), residues: 683 sheet: -0.26 (0.13), residues: 1479 loop : -1.47 (0.11), residues: 2978 *********************** 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 457 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 370 time to evaluate : 4.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 35 residues processed: 445 average time/residue: 0.5316 time to fit residues: 391.8322 Evaluate side-chains 349 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 314 time to evaluate : 4.459 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3751 time to fit residues: 30.5758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 461 optimal weight: 0.9990 chunk 350 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 222 optimal weight: 7.9990 chunk 313 optimal weight: 0.2980 chunk 468 optimal weight: 10.0000 chunk 495 optimal weight: 7.9990 chunk 244 optimal weight: 0.8980 chunk 443 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 C 474 GLN ** 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** H 35 ASN 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 6 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 35 ASN ** T 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 41122 Z= 0.184 Angle : 0.568 9.860 55896 Z= 0.298 Chirality : 0.044 0.259 6262 Planarity : 0.004 0.071 7225 Dihedral : 4.976 36.203 5632 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.83 % Rotamer: Outliers : 1.46 % Allowed : 14.34 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % 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: -1.03 (0.11), residues: 5140 helix: 0.72 (0.21), residues: 681 sheet: -0.15 (0.13), residues: 1451 loop : -1.32 (0.11), residues: 3008 *********************** 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 420 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 355 time to evaluate : 4.744 Fit side-chains revert: symmetry clash outliers start: 65 outliers final: 29 residues processed: 407 average time/residue: 0.5243 time to fit residues: 355.7085 Evaluate side-chains 343 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 314 time to evaluate : 4.813 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3691 time to fit residues: 26.9717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 412 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 369 optimal weight: 20.0000 chunk 204 optimal weight: 0.8980 chunk 423 optimal weight: 0.8980 chunk 342 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 253 optimal weight: 7.9990 chunk 445 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN A 481 ASN A 658 ASN A 901 GLN B 955 ASN C 81 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 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 68 ASN ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 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** ** T 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 41122 Z= 0.407 Angle : 0.710 13.183 55896 Z= 0.369 Chirality : 0.049 0.315 6262 Planarity : 0.005 0.077 7225 Dihedral : 5.627 35.716 5632 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.32 % Rotamer: Outliers : 1.85 % Allowed : 16.27 % Favored : 81.88 % 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: -1.25 (0.11), residues: 5140 helix: 0.37 (0.20), residues: 680 sheet: -0.17 (0.13), residues: 1487 loop : -1.51 (0.11), residues: 2973 *********************** 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 433 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 351 time to evaluate : 4.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 44 residues processed: 423 average time/residue: 0.5268 time to fit residues: 377.4276 Evaluate side-chains 363 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 319 time to evaluate : 4.521 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.3664 time to fit residues: 37.3677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0470 chunk 98 optimal weight: 0.4980 chunk 291 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 496 optimal weight: 9.9990 chunk 412 optimal weight: 0.9980 chunk 229 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 165 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 901 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B 955 ASN C 856 ASN C 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 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 68 ASN ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN ** S 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.3492 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= 0.177 Angle : 0.569 9.082 55896 Z= 0.298 Chirality : 0.044 0.194 6262 Planarity : 0.004 0.081 7225 Dihedral : 5.018 31.938 5632 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 1.13 % Allowed : 17.35 % Favored : 81.52 % 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: -0.99 (0.11), residues: 5140 helix: 0.68 (0.21), residues: 680 sheet: -0.03 (0.13), residues: 1427 loop : -1.32 (0.11), residues: 3033 *********************** 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 404 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 354 time to evaluate : 4.531 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 25 residues processed: 390 average time/residue: 0.5465 time to fit residues: 350.5717 Evaluate side-chains 332 residues out of total 4461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 307 time to evaluate : 4.492 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3965 time to fit residues: 24.4034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.4283 > 50: distance: 30 - 36: 13.559 distance: 36 - 37: 17.333 distance: 37 - 38: 15.993 distance: 37 - 40: 14.203 distance: 38 - 39: 20.966 distance: 38 - 44: 22.542 distance: 40 - 41: 12.144 distance: 41 - 42: 23.429 distance: 41 - 43: 4.970 distance: 44 - 45: 27.753 distance: 45 - 46: 14.533 distance: 45 - 48: 16.282 distance: 46 - 47: 27.743 distance: 46 - 54: 25.872 distance: 48 - 49: 22.382 distance: 49 - 50: 25.591 distance: 49 - 51: 21.785 distance: 50 - 52: 15.836 distance: 51 - 53: 15.196 distance: 52 - 53: 9.180 distance: 54 - 55: 22.932 distance: 55 - 56: 25.300 distance: 55 - 58: 17.282 distance: 56 - 57: 20.585 distance: 56 - 60: 8.311 distance: 58 - 59: 33.941 distance: 60 - 61: 10.408 distance: 61 - 62: 21.495 distance: 61 - 64: 8.341 distance: 62 - 63: 11.348 distance: 62 - 68: 13.569 distance: 64 - 65: 7.928 distance: 65 - 66: 13.254 distance: 65 - 67: 15.657 distance: 68 - 69: 15.769 distance: 69 - 70: 33.617 distance: 70 - 71: 16.282 distance: 70 - 72: 19.752 distance: 72 - 73: 9.695 distance: 73 - 74: 12.227 distance: 73 - 76: 15.693 distance: 74 - 75: 13.352 distance: 74 - 84: 20.755 distance: 76 - 77: 17.174 distance: 77 - 78: 18.609 distance: 77 - 79: 6.224 distance: 78 - 80: 5.263 distance: 79 - 81: 3.578 distance: 80 - 82: 14.020 distance: 81 - 82: 12.266 distance: 82 - 83: 23.824 distance: 84 - 85: 15.978 distance: 85 - 86: 7.575 distance: 85 - 88: 14.407 distance: 86 - 87: 10.662 distance: 86 - 92: 30.511 distance: 88 - 89: 13.821 distance: 89 - 90: 22.146 distance: 89 - 91: 8.026 distance: 92 - 93: 6.921 distance: 93 - 94: 9.662 distance: 93 - 96: 8.746 distance: 94 - 95: 9.546 distance: 94 - 104: 15.650 distance: 96 - 97: 5.744 distance: 97 - 98: 4.040 distance: 97 - 99: 5.809 distance: 98 - 100: 4.068 distance: 99 - 101: 3.416 distance: 100 - 102: 4.509 distance: 102 - 103: 4.069 distance: 104 - 105: 7.493 distance: 105 - 106: 13.201 distance: 105 - 108: 6.970 distance: 106 - 112: 17.392 distance: 108 - 109: 5.261 distance: 109 - 110: 4.951 distance: 109 - 111: 4.785 distance: 112 - 113: 7.236 distance: 112 - 186: 7.390 distance: 113 - 114: 12.445 distance: 113 - 116: 13.616 distance: 114 - 115: 5.862 distance: 114 - 120: 15.120 distance: 115 - 183: 23.178 distance: 116 - 117: 6.441 distance: 117 - 118: 11.609 distance: 117 - 119: 16.842