Starting phenix.real_space_refine on Mon Mar 18 12:14:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o90_0660/03_2024/6o90_0660.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o90_0660/03_2024/6o90_0660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o90_0660/03_2024/6o90_0660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o90_0660/03_2024/6o90_0660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o90_0660/03_2024/6o90_0660.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o90_0660/03_2024/6o90_0660.pdb" } resolution = 3.49 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= 0.095 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4547 5.49 5 S 130 5.16 5 C 69195 2.51 5 N 25647 2.21 5 O 39009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "N ARG 119": "NH1" <-> "NH2" Residue "P ARG 103": "NH1" <-> "NH2" Residue "W ARG 15": "NH1" <-> "NH2" Residue "W TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 53": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 58": "NH1" <-> "NH2" Residue "1 ARG 61": "NH1" <-> "NH2" Residue "1 ARG 73": "NH1" <-> "NH2" Residue "1 PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 59": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 138532 Number of models: 1 Model: "" Number of chains: 53 Chain: "a" Number of atoms: 32746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32746 Classifications: {'RNA': 1528} Modifications used: {'rna2p_pur': 121, 'rna2p_pyr': 90, 'rna3p_pur': 736, 'rna3p_pyr': 581} Link IDs: {'rna2p': 211, 'rna3p': 1316} Chain breaks: 1 Chain: "c" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain: "d" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1620 Classifications: {'peptide': 201} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 190} Chain: "e" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1204 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "f" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "g" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1229 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain: "h" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 120} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 863 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 109} Chain: "l" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1065 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 126} Chain: "m" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 884 Classifications: {'peptide': 112} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 105} Chain: "n" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 741 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 708 Classifications: {'peptide': 89} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 83} Chain: "q" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 681 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "r" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 537 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "s" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 634 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "t" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "A" Number of atoms: 62302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62302 Classifications: {'RNA': 2903} Modifications used: {'rna2p_pur': 303, 'rna2p_pyr': 156, 'rna3p_pur': 1380, 'rna3p_pyr': 1058} Link IDs: {'rna2p': 459, 'rna3p': 2443} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 8 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 6 Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2478 Classifications: {'RNA': 116} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 54, 'rna3p_pyr': 49} Link IDs: {'rna2p': 11, 'rna3p': 104} Unresolved chain links: 1 Unresolved chain link angles: 5 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2114 Classifications: {'peptide': 275} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 257} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1577 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1573 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 8, 'TRANS': 197} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1391 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1344 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1129 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 7, 'TRANS': 137} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 922 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "M" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1094 Classifications: {'peptide': 146} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 140} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1117 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "O" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 898 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 897 Classifications: {'peptide': 112} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 106} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Unresolved chain links: 2 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 7 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 783 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 849 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "U" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 719 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "W" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 757 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "X" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 571 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 425 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "Z" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 504 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "0" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 434 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 673 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "2" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "3" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 418 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "5" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 522 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "6" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 303 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 4, 'TRANS': 33} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 45028 SG CYS n 24 57.486 135.371 120.356 1.00 98.96 S ATOM 45054 SG CYS n 27 60.971 136.248 120.122 1.00 98.32 S ATOM 45166 SG CYS n 40 60.569 135.528 123.702 1.00 97.98 S ATOM 45191 SG CYS n 43 60.541 138.953 122.690 1.00 96.80 S ATOM A0SBQ SG CYS 2 30 251.494 138.186 87.055 1.00 95.72 S ATOM A0SEY SG CYS 2 46 253.761 138.759 89.881 1.00 89.46 S ATOM A0SJB SG CYS 3 9 139.420 43.833 135.364 1.00120.76 S ATOM A0SJU SG CYS 3 12 142.847 43.417 136.236 1.00121.16 S ATOM A0SPQ SG CYS 3 36 142.419 42.042 132.912 1.00111.85 S ATOM A0TK6 SG CYS 6 11 143.447 125.477 50.204 1.00105.06 S ATOM A0TKU SG CYS 6 14 146.390 122.446 49.230 1.00105.59 S ATOM A0TNS SG CYS 6 27 147.890 125.464 48.331 1.00104.10 S Time building chain proxies: 51.78, per 1000 atoms: 0.37 Number of scatterers: 138532 At special positions: 0 Unit cell: (287.414, 276.444, 231.467, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 130 16.00 P 4547 15.00 O 39009 8.00 N 25647 7.00 C 69195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 52.95 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 101 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 46 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 30 " pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 12 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 36 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 9 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 27 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 11 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 14 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " Number of angles added : 6 10250 Ramachandran restraints generated. 5125 Oldfield, 0 Emsley, 5125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9578 Finding SS restraints... Warning! O6 atom is missing from residue G A2652 Was trying to link: A A2792 N6 with G A2652 O6, Saenger class: 8 Warning! O6 atom is missing from residue G A2652 Was trying to link: A A2792 N6 with G A2652 O6, Saenger class: 9 Warning! O6 atom is missing from residue G A2652 Was trying to link: A A2792 N6 with G A2652 O6, Saenger class: 8 Warning! O6 atom is missing from residue G A2652 Was trying to link: A A2792 N6 with G A2652 O6, Saenger class: 9 Secondary structure from input PDB file: 135 helices and 77 sheets defined 26.8% alpha, 14.5% beta 1422 base pairs and 2293 stacking pairs defined. Time for finding SS restraints: 46.03 Creating SS restraints... Processing helix chain 'c' and resid 7 through 12 Processing helix chain 'c' and resid 28 through 41 removed outlier: 3.919A pdb=" N ARG c 37 " --> pdb=" O HIS c 33 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE c 41 " --> pdb=" O ARG c 37 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 47 removed outlier: 3.743A pdb=" N ALA c 47 " --> pdb=" O ALA c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.685A pdb=" N LEU c 93 " --> pdb=" O GLU c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 111 removed outlier: 3.849A pdb=" N ASP c 111 " --> pdb=" O PRO c 108 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 124 Processing helix chain 'c' and resid 128 through 142 Processing helix chain 'd' and resid 9 through 16 removed outlier: 3.734A pdb=" N ARG d 14 " --> pdb=" O LYS d 10 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 62 removed outlier: 3.618A pdb=" N GLN d 50 " --> pdb=" O GLU d 46 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 74 removed outlier: 3.938A pdb=" N PHE d 68 " --> pdb=" O ASN d 64 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR d 70 " --> pdb=" O ARG d 66 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS d 74 " --> pdb=" O THR d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 75 through 78 removed outlier: 4.168A pdb=" N ILE d 78 " --> pdb=" O ALA d 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 75 through 78' Processing helix chain 'd' and resid 82 through 91 Processing helix chain 'd' and resid 94 through 101 Processing helix chain 'd' and resid 107 through 118 removed outlier: 4.012A pdb=" N HIS d 117 " --> pdb=" O GLN d 113 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY d 118 " --> pdb=" O LEU d 114 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 158 removed outlier: 4.043A pdb=" N LYS d 153 " --> pdb=" O ILE d 149 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU d 157 " --> pdb=" O LYS d 153 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA d 158 " --> pdb=" O GLU d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 192 through 199 removed outlier: 3.741A pdb=" N VAL d 196 " --> pdb=" O GLU d 192 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 68 Processing helix chain 'e' and resid 108 through 117 removed outlier: 3.505A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL e 114 " --> pdb=" O PRO e 110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU e 117 " --> pdb=" O ALA e 113 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 146 removed outlier: 3.586A pdb=" N GLN e 146 " --> pdb=" O GLU e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 157 removed outlier: 4.126A pdb=" N ARG e 157 " --> pdb=" O VAL e 153 " (cutoff:3.500A) Processing helix chain 'f' and resid 18 through 35 removed outlier: 3.609A pdb=" N THR f 23 " --> pdb=" O GLU f 19 " (cutoff:3.500A) Processing helix chain 'f' and resid 75 through 87 Processing helix chain 'g' and resid 20 through 29 Processing helix chain 'g' and resid 35 through 53 removed outlier: 3.980A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 68 Processing helix chain 'g' and resid 92 through 106 Processing helix chain 'g' and resid 107 through 111 removed outlier: 4.033A pdb=" N ARG g 111 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 120 through 127 Processing helix chain 'g' and resid 128 through 130 No H-bonds generated for 'chain 'g' and resid 128 through 130' Processing helix chain 'g' and resid 132 through 145 removed outlier: 4.290A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 20 removed outlier: 3.818A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 115 through 120 Processing helix chain 'i' and resid 44 through 49 removed outlier: 3.592A pdb=" N ILE i 48 " --> pdb=" O LEU i 44 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 78 Processing helix chain 'i' and resid 78 through 91 removed outlier: 3.770A pdb=" N GLY i 82 " --> pdb=" O ALA i 78 " (cutoff:3.500A) Processing helix chain 'i' and resid 94 through 102 removed outlier: 3.550A pdb=" N ALA i 101 " --> pdb=" O ALA i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 28 Processing helix chain 'j' and resid 81 through 88 removed outlier: 4.171A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 59 Processing helix chain 'k' and resid 60 through 77 removed outlier: 3.840A pdb=" N MET k 65 " --> pdb=" O PHE k 61 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL k 73 " --> pdb=" O ALA k 69 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS k 77 " --> pdb=" O VAL k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 101 removed outlier: 4.525A pdb=" N ALA k 95 " --> pdb=" O SER k 91 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ARG k 98 " --> pdb=" O GLU k 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 9 removed outlier: 3.601A pdb=" N ARG l 9 " --> pdb=" O ASN l 5 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 19 Processing helix chain 'm' and resid 20 through 22 No H-bonds generated for 'chain 'm' and resid 20 through 22' Processing helix chain 'm' and resid 27 through 38 removed outlier: 3.586A pdb=" N VAL m 37 " --> pdb=" O VAL m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 61 removed outlier: 3.651A pdb=" N ILE m 60 " --> pdb=" O ILE m 56 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 82 removed outlier: 3.739A pdb=" N ARG m 71 " --> pdb=" O GLY m 67 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU m 82 " --> pdb=" O LYS m 78 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 92 Processing helix chain 'n' and resid 3 through 10 removed outlier: 3.810A pdb=" N ALA n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) Processing helix chain 'n' and resid 42 through 50 removed outlier: 3.698A pdb=" N TYR n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS n 50 " --> pdb=" O GLU n 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 15 removed outlier: 3.848A pdb=" N LYS o 13 " --> pdb=" O ASN o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 25 through 46 removed outlier: 3.519A pdb=" N ILE o 29 " --> pdb=" O PRO o 25 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA o 30 " --> pdb=" O GLU o 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 72 removed outlier: 3.664A pdb=" N TYR o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG o 71 " --> pdb=" O LEU o 67 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS o 72 " --> pdb=" O ALA o 68 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 86 removed outlier: 3.565A pdb=" N GLY o 86 " --> pdb=" O ILE o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 56 through 64 removed outlier: 3.793A pdb=" N SER p 61 " --> pdb=" O LEU p 57 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS p 62 " --> pdb=" O ASP p 58 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA p 64 " --> pdb=" O LEU p 60 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 75 Processing helix chain 'p' and resid 78 through 86 Processing helix chain 'p' and resid 87 through 90 Processing helix chain 'r' and resid 32 through 37 removed outlier: 3.768A pdb=" N ILE r 37 " --> pdb=" O LYS r 34 " (cutoff:3.500A) Processing helix chain 'r' and resid 45 through 50 Processing helix chain 'r' and resid 52 through 67 removed outlier: 3.542A pdb=" N ARG r 57 " --> pdb=" O ALA r 53 " (cutoff:3.500A) Processing helix chain 't' and resid 7 through 40 removed outlier: 3.691A pdb=" N ARG t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) Processing helix chain 't' and resid 47 through 64 removed outlier: 3.675A pdb=" N LYS t 63 " --> pdb=" O MET t 59 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 80 removed outlier: 4.096A pdb=" N ASN t 72 " --> pdb=" O LYS t 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.543A pdb=" N ASP C 267 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS C 268 " --> pdb=" O LYS C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 268' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 57 through 61 removed outlier: 4.116A pdb=" N SER D 61 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 70 removed outlier: 3.605A pdb=" N ALA D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.692A pdb=" N VAL D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE D 102 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN D 103 " --> pdb=" O ASP D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.872A pdb=" N ARG D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N HIS D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 42 removed outlier: 4.008A pdb=" N VAL E 33 " --> pdb=" O ASN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 120 removed outlier: 3.524A pdb=" N GLU E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 146 Processing helix chain 'E' and resid 183 through 188 removed outlier: 3.653A pdb=" N SER E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.596A pdb=" N LEU E 199 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 205 " --> pdb=" O GLN E 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 11 through 21 Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 49 through 61 removed outlier: 4.458A pdb=" N GLU F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 106 Processing helix chain 'F' and resid 162 through 172 removed outlier: 3.798A pdb=" N SER F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 81 removed outlier: 3.830A pdb=" N GLY G 66 " --> pdb=" O LYS G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'K' and resid 25 through 37 removed outlier: 3.543A pdb=" N LEU K 29 " --> pdb=" O PRO K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 63 removed outlier: 4.160A pdb=" N VAL K 63 " --> pdb=" O ALA K 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 60 through 63' Processing helix chain 'K' and resid 90 through 95 removed outlier: 4.096A pdb=" N LEU K 93 " --> pdb=" O ALA K 90 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG K 94 " --> pdb=" O GLY K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 121 Processing helix chain 'K' and resid 133 through 137 removed outlier: 3.812A pdb=" N GLN K 137 " --> pdb=" O ALA K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 107 removed outlier: 3.888A pdb=" N LEU L 106 " --> pdb=" O ALA L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 118 Processing helix chain 'M' and resid 131 through 140 Processing helix chain 'N' and resid 44 through 56 Processing helix chain 'N' and resid 110 through 122 Processing helix chain 'O' and resid 9 through 21 removed outlier: 3.564A pdb=" N ARG O 13 " --> pdb=" O THR O 9 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR O 21 " --> pdb=" O LEU O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 52 removed outlier: 3.867A pdb=" N THR O 49 " --> pdb=" O GLU O 45 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU O 50 " --> pdb=" O LYS O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 63 Processing helix chain 'O' and resid 92 through 97 removed outlier: 4.014A pdb=" N PHE O 97 " --> pdb=" O LEU O 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 17 Processing helix chain 'P' and resid 68 through 85 removed outlier: 3.578A pdb=" N ALA P 72 " --> pdb=" O LYS P 68 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU P 85 " --> pdb=" O GLU P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 114 removed outlier: 3.765A pdb=" N ALA P 110 " --> pdb=" O ALA P 106 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU P 113 " --> pdb=" O GLU P 109 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN P 114 " --> pdb=" O ALA P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 9 Processing helix chain 'Q' and resid 97 through 101 removed outlier: 3.563A pdb=" N LEU Q 100 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG Q 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 97 through 101' Processing helix chain 'R' and resid 9 through 19 removed outlier: 3.852A pdb=" N ARG R 13 " --> pdb=" O VAL R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 50 removed outlier: 4.399A pdb=" N GLN R 38 " --> pdb=" O SER R 34 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 71 removed outlier: 3.990A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS R 59 " --> pdb=" O ARG R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 86 removed outlier: 3.612A pdb=" N HIS R 81 " --> pdb=" O SER R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 101 Processing helix chain 'R' and resid 102 through 117 removed outlier: 3.633A pdb=" N LEU R 117 " --> pdb=" O ALA R 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 22 through 27 removed outlier: 3.646A pdb=" N ILE T 26 " --> pdb=" O ALA T 22 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP T 27 " --> pdb=" O ARG T 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 22 through 27' Processing helix chain 'T' and resid 33 through 43 removed outlier: 3.623A pdb=" N ILE T 38 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER T 39 " --> pdb=" O ALA T 35 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE T 43 " --> pdb=" O SER T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 67 removed outlier: 4.257A pdb=" N ILE T 52 " --> pdb=" O SER T 48 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYS T 54 " --> pdb=" O GLY T 50 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE T 67 " --> pdb=" O ALA T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 74 removed outlier: 3.679A pdb=" N LEU T 74 " --> pdb=" O VAL T 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 20 Processing helix chain 'U' and resid 34 through 47 removed outlier: 4.019A pdb=" N VAL U 38 " --> pdb=" O ASN U 34 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP U 47 " --> pdb=" O GLU U 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 68 No H-bonds generated for 'chain 'V' and resid 66 through 68' Processing helix chain 'W' and resid 16 through 20 Processing helix chain 'W' and resid 44 through 46 No H-bonds generated for 'chain 'W' and resid 44 through 46' Processing helix chain 'W' and resid 47 through 55 removed outlier: 4.326A pdb=" N ILE W 51 " --> pdb=" O ASP W 47 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 55 removed outlier: 3.818A pdb=" N LYS Y 55 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 9 removed outlier: 3.553A pdb=" N LEU Z 9 " --> pdb=" O ILE Z 6 " (cutoff:3.500A) Processing helix chain 'Z' and resid 11 through 34 removed outlier: 3.743A pdb=" N LEU Z 15 " --> pdb=" O THR Z 11 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR Z 34 " --> pdb=" O PHE Z 30 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 61 removed outlier: 3.693A pdb=" N ALA Z 61 " --> pdb=" O LEU Z 57 " (cutoff:3.500A) Processing helix chain '0' and resid 16 through 27 removed outlier: 3.745A pdb=" N ALA 0 21 " --> pdb=" O GLN 0 17 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU 0 26 " --> pdb=" O THR 0 22 " (cutoff:3.500A) Processing helix chain '0' and resid 42 through 48 Processing helix chain '1' and resid 69 through 76 removed outlier: 3.892A pdb=" N PHE 1 74 " --> pdb=" O ARG 1 70 " (cutoff:3.500A) Processing helix chain '1' and resid 78 through 83 Processing helix chain '2' and resid 9 through 17 removed outlier: 4.008A pdb=" N LYS 2 13 " --> pdb=" O SER 2 9 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA 2 14 " --> pdb=" O LYS 2 10 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 20 No H-bonds generated for 'chain '2' and resid 18 through 20' Processing helix chain '4' and resid 26 through 36 removed outlier: 3.597A pdb=" N ARG 4 36 " --> pdb=" O ALA 4 32 " (cutoff:3.500A) Processing helix chain '5' and resid 37 through 44 removed outlier: 3.793A pdb=" N ARG 5 41 " --> pdb=" O THR 5 37 " (cutoff:3.500A) Processing helix chain '5' and resid 53 through 59 removed outlier: 4.370A pdb=" N ARG 5 57 " --> pdb=" O GLY 5 53 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 54 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 33 removed outlier: 4.119A pdb=" N HIS 6 33 " --> pdb=" O ASN 6 30 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 30 through 33' Processing sheet with id=AA1, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.729A pdb=" N THR c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN c 64 " --> pdb=" O GLU c 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 163 through 165 Processing sheet with id=AA3, first strand: chain 'c' and resid 163 through 165 removed outlier: 3.835A pdb=" N GLY c 147 " --> pdb=" O TYR c 202 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS c 149 " --> pdb=" O TRP c 200 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY c 196 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE c 201 " --> pdb=" O ASP c 182 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP c 182 " --> pdb=" O ILE c 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 120 through 122 removed outlier: 4.511A pdb=" N ILE d 120 " --> pdb=" O VAL d 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 166 through 169 Processing sheet with id=AA6, first strand: chain 'e' and resid 13 through 24 removed outlier: 5.261A pdb=" N ASP e 13 " --> pdb=" O GLY e 40 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLY e 40 " --> pdb=" O ASP e 13 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL e 38 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'e' and resid 13 through 24 removed outlier: 5.261A pdb=" N ASP e 13 " --> pdb=" O GLY e 40 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLY e 40 " --> pdb=" O ASP e 13 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL e 38 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'e' and resid 85 through 87 removed outlier: 3.502A pdb=" N LYS e 97 " --> pdb=" O THR e 124 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLY e 104 " --> pdb=" O ILE e 123 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N SER e 125 " --> pdb=" O GLY e 104 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA e 106 " --> pdb=" O SER e 125 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER e 127 " --> pdb=" O ALA e 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 7 through 9 removed outlier: 3.683A pdb=" N VAL f 96 " --> pdb=" O GLU f 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 39 through 40 Processing sheet with id=AB2, first strand: chain 'f' and resid 44 through 50 removed outlier: 5.060A pdb=" N ASP f 45 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE f 65 " --> pdb=" O ASP f 45 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU f 47 " --> pdb=" O TYR f 63 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'g' and resid 73 through 76 Processing sheet with id=AB4, first strand: chain 'h' and resid 24 through 27 Processing sheet with id=AB5, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.791A pdb=" N LYS h 78 " --> pdb=" O TYR h 130 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.791A pdb=" N LYS h 78 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU h 126 " --> pdb=" O SER h 107 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'i' and resid 6 through 12 Processing sheet with id=AB8, first strand: chain 'j' and resid 36 through 41 removed outlier: 3.659A pdb=" N ASP j 75 " --> pdb=" O SER j 37 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU j 73 " --> pdb=" O PRO j 39 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LYS j 71 " --> pdb=" O PRO j 41 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG j 7 " --> pdb=" O LYS j 101 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS j 11 " --> pdb=" O ASN j 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'j' and resid 46 through 48 Processing sheet with id=AC1, first strand: chain 'j' and resid 51 through 52 Processing sheet with id=AC2, first strand: chain 'k' and resid 17 through 18 removed outlier: 6.682A pdb=" N GLU k 17 " --> pdb=" O THR k 81 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N ASP k 83 " --> pdb=" O GLU k 17 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'k' and resid 17 through 18 removed outlier: 6.682A pdb=" N GLU k 17 " --> pdb=" O THR k 81 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N ASP k 83 " --> pdb=" O GLU k 17 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL k 107 " --> pdb=" O LYS k 80 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL k 82 " --> pdb=" O VAL k 107 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA k 109 " --> pdb=" O VAL k 82 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'l' and resid 75 through 79 removed outlier: 3.757A pdb=" N ARG l 49 " --> pdb=" O ARG l 67 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ARG l 69 " --> pdb=" O CYS l 47 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N CYS l 47 " --> pdb=" O ARG l 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'p' and resid 3 through 6 removed outlier: 3.616A pdb=" N ALA p 23 " --> pdb=" O LYS p 4 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N TYR p 18 " --> pdb=" O THR p 39 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR p 39 " --> pdb=" O TYR p 18 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE p 20 " --> pdb=" O VAL p 37 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU p 35 " --> pdb=" O VAL p 22 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'q' and resid 10 through 11 removed outlier: 7.654A pdb=" N ILE q 61 " --> pdb=" O VAL q 81 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL q 81 " --> pdb=" O ILE q 61 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS q 63 " --> pdb=" O LEU q 79 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA q 49 " --> pdb=" O ILE q 24 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'q' and resid 14 through 15 Processing sheet with id=AC8, first strand: chain 'q' and resid 29 through 33 removed outlier: 4.015A pdb=" N THR q 30 " --> pdb=" O TYR q 43 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR q 43 " --> pdb=" O THR q 30 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 's' and resid 48 through 52 Processing sheet with id=AD1, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.884A pdb=" N SER C 18 " --> pdb=" O LYS C 4 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AD3, first strand: chain 'C' and resid 65 through 66 removed outlier: 4.929A pdb=" N LEU C 105 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C 102 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C 93 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS C 79 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AD5, first strand: chain 'C' and resid 163 through 167 removed outlier: 7.027A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 247 through 248 Processing sheet with id=AD7, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.681A pdb=" N THR D 201 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 12 through 16 removed outlier: 3.584A pdb=" N ILE D 188 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS D 189 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL D 176 " --> pdb=" O LYS D 189 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 34 through 39 removed outlier: 6.613A pdb=" N VAL D 35 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLY D 52 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AE2, first strand: chain 'E' and resid 6 through 7 removed outlier: 3.524A pdb=" N PHE E 7 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA E 194 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU E 153 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL E 152 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL E 176 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 88 through 89 removed outlier: 6.818A pdb=" N VAL F 157 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE F 34 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL F 155 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE F 156 " --> pdb=" O TYR F 128 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 9 through 10 removed outlier: 3.840A pdb=" N VAL G 9 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 16 through 17 removed outlier: 4.055A pdb=" N GLU G 16 " --> pdb=" O LYS G 27 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 96 through 98 Processing sheet with id=AE7, first strand: chain 'G' and resid 122 through 124 removed outlier: 3.834A pdb=" N THR G 122 " --> pdb=" O LYS G 134 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS G 134 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 123 through 126 removed outlier: 6.813A pdb=" N VAL K 55 " --> pdb=" O ASN K 124 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N TYR K 126 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL K 57 " --> pdb=" O TYR K 126 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP K 16 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 77 through 78 Processing sheet with id=AF1, first strand: chain 'L' and resid 16 through 23 removed outlier: 6.734A pdb=" N ALA L 16 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA L 46 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU L 18 " --> pdb=" O LYS L 44 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 77 through 78 removed outlier: 3.607A pdb=" N VAL Q 70 " --> pdb=" O LYS Q 63 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 110 through 111 removed outlier: 3.633A pdb=" N VAL M 111 " --> pdb=" O LYS M 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'M' and resid 122 through 125 removed outlier: 3.509A pdb=" N GLU M 144 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA M 125 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 63 through 66 removed outlier: 3.722A pdb=" N ALA N 107 " --> pdb=" O LYS N 63 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N PHE N 104 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 40 through 42 Processing sheet with id=AF7, first strand: chain 'O' and resid 30 through 33 removed outlier: 4.496A pdb=" N GLU O 111 " --> pdb=" O MET O 120 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL O 122 " --> pdb=" O LYS O 109 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS O 109 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLU O 124 " --> pdb=" O ILE O 107 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ILE O 107 " --> pdb=" O GLU O 124 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 34 through 35 removed outlier: 6.795A pdb=" N ILE P 40 " --> pdb=" O SER P 57 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER P 57 " --> pdb=" O ILE P 40 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ALA P 42 " --> pdb=" O SER P 55 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N SER P 55 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL P 44 " --> pdb=" O LEU P 53 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 37 through 40 removed outlier: 4.066A pdb=" N ARG Q 37 " --> pdb=" O GLU Q 34 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL Q 28 " --> pdb=" O PHE Q 43 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE Q 43 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 37 through 40 removed outlier: 4.066A pdb=" N ARG Q 37 " --> pdb=" O GLU Q 34 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG Q 27 " --> pdb=" O ILE Q 84 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE Q 84 " --> pdb=" O ARG Q 27 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N HIS Q 29 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.538A pdb=" N ILE S 4 " --> pdb=" O ILE S 39 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL S 41 " --> pdb=" O LYS S 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 19 through 22 removed outlier: 3.642A pdb=" N LYS S 94 " --> pdb=" O LYS S 64 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS S 64 " --> pdb=" O LYS S 94 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N MET S 96 " --> pdb=" O VAL S 62 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL S 62 " --> pdb=" O MET S 96 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'T' and resid 11 through 15 removed outlier: 5.804A pdb=" N THR T 11 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL T 110 " --> pdb=" O THR T 11 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LYS T 13 " --> pdb=" O ILE T 108 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE T 108 " --> pdb=" O LYS T 13 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR T 109 " --> pdb=" O PHE T 80 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU T 78 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR T 113 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL T 76 " --> pdb=" O THR T 113 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 87 through 92 Processing sheet with id=AG6, first strand: chain 'U' and resid 7 through 10 removed outlier: 6.447A pdb=" N GLU U 28 " --> pdb=" O LYS U 8 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR U 26 " --> pdb=" O PRO U 10 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'V' and resid 23 through 27 removed outlier: 6.561A pdb=" N ILE V 34 " --> pdb=" O LEU V 24 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ALA V 26 " --> pdb=" O LYS V 32 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LYS V 32 " --> pdb=" O ALA V 26 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'V' and resid 40 through 44 Processing sheet with id=AG9, first strand: chain 'V' and resid 70 through 71 removed outlier: 4.299A pdb=" N VAL V 70 " --> pdb=" O THR V 79 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR V 79 " --> pdb=" O VAL V 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'V' and resid 92 through 93 removed outlier: 4.377A pdb=" N ARG V 92 " --> pdb=" O LEU V 101 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'W' and resid 8 through 9 removed outlier: 4.004A pdb=" N LYS W 8 " --> pdb=" O TYR W 42 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA W 29 " --> pdb=" O ILE W 41 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'W' and resid 61 through 63 removed outlier: 3.984A pdb=" N ILE W 61 " --> pdb=" O THR W 72 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'X' and resid 31 through 32 removed outlier: 3.631A pdb=" N ARG X 48 " --> pdb=" O GLY X 31 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'X' and resid 54 through 56 Processing sheet with id=AH6, first strand: chain 'Y' and resid 34 through 36 Processing sheet with id=AH7, first strand: chain 'Y' and resid 39 through 40 Processing sheet with id=AH8, first strand: chain '0' and resid 34 through 38 removed outlier: 3.580A pdb=" N THR 0 7 " --> pdb=" O ASP 0 55 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP 0 55 " --> pdb=" O THR 0 7 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '2' and resid 27 through 28 Processing sheet with id=AI1, first strand: chain '2' and resid 48 through 49 Processing sheet with id=AI2, first strand: chain '3' and resid 15 through 22 removed outlier: 6.700A pdb=" N ARG 3 15 " --> pdb=" O CYS 3 9 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N CYS 3 9 " --> pdb=" O ARG 3 15 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR 3 17 " --> pdb=" O LEU 3 7 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS 3 41 " --> pdb=" O CYS 3 36 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain '5' and resid 14 through 16 removed outlier: 3.691A pdb=" N LYS 5 15 " --> pdb=" O LYS 5 23 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain '6' and resid 2 through 4 removed outlier: 6.490A pdb=" N LYS 6 2 " --> pdb=" O ARG 6 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain '6' and resid 15 through 17 removed outlier: 3.663A pdb=" N LYS 6 15 " --> pdb=" O ILE 6 26 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE 6 26 " --> pdb=" O LYS 6 15 " (cutoff:3.500A) 1138 hydrogen bonds defined for protein. 3168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3576 hydrogen bonds 5788 hydrogen bond angles 0 basepair planarities 1422 basepair parallelities 2293 stacking parallelities Total time for adding SS restraints: 224.52 Time building geometry restraints manager: 57.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 16348 1.32 - 1.44: 65305 1.44 - 1.57: 59788 1.57 - 1.69: 9084 1.69 - 1.81: 241 Bond restraints: 150766 Sorted by residual: bond pdb=" C SER C 248 " pdb=" N PRO C 249 " ideal model delta sigma weight residual 1.334 1.377 -0.044 8.40e-03 1.42e+04 2.69e+01 bond pdb=" C LEU F 108 " pdb=" N PRO F 109 " ideal model delta sigma weight residual 1.331 1.358 -0.027 7.90e-03 1.60e+04 1.15e+01 bond pdb=" CB ARG R 13 " pdb=" CG ARG R 13 " ideal model delta sigma weight residual 1.520 1.428 0.092 3.00e-02 1.11e+03 9.48e+00 bond pdb=" C PHE s 41 " pdb=" N PRO s 42 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.45e+00 bond pdb=" CB ARG Q 62 " pdb=" CG ARG Q 62 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.19e+00 ... (remaining 150761 not shown) Histogram of bond angle deviations from ideal: 94.94 - 103.74: 13108 103.74 - 112.53: 95028 112.53 - 121.32: 78879 121.32 - 130.11: 36686 130.11 - 138.91: 2343 Bond angle restraints: 226044 Sorted by residual: angle pdb=" C ILE V 71 " pdb=" N ASP V 72 " pdb=" CA ASP V 72 " ideal model delta sigma weight residual 121.80 138.68 -16.88 2.44e+00 1.68e-01 4.78e+01 angle pdb=" N ILE G 4 " pdb=" CA ILE G 4 " pdb=" C ILE G 4 " ideal model delta sigma weight residual 112.96 106.19 6.77 1.00e+00 1.00e+00 4.58e+01 angle pdb=" CA ARG O 41 " pdb=" CB ARG O 41 " pdb=" CG ARG O 41 " ideal model delta sigma weight residual 114.10 126.59 -12.49 2.00e+00 2.50e-01 3.90e+01 angle pdb=" C HIS k 38 " pdb=" N GLY k 39 " pdb=" CA GLY k 39 " ideal model delta sigma weight residual 121.70 132.62 -10.92 1.80e+00 3.09e-01 3.68e+01 angle pdb=" C VAL M 15 " pdb=" N ARG M 16 " pdb=" CA ARG M 16 " ideal model delta sigma weight residual 121.54 132.90 -11.36 1.91e+00 2.74e-01 3.54e+01 ... (remaining 226039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 85539 35.98 - 71.95: 9724 71.95 - 107.93: 1101 107.93 - 143.90: 20 143.90 - 179.88: 27 Dihedral angle restraints: 96411 sinusoidal: 81522 harmonic: 14889 Sorted by residual: dihedral pdb=" C4' C A2531 " pdb=" C3' C A2531 " pdb=" C2' C A2531 " pdb=" C1' C A2531 " ideal model delta sinusoidal sigma weight residual 36.34 -31.89 68.23 1 3.10e+00 1.04e-01 6.28e+02 dihedral pdb=" O4' C A2531 " pdb=" C4' C A2531 " pdb=" C3' C A2531 " pdb=" C2' C A2531 " ideal model delta sinusoidal sigma weight residual -35.15 16.89 -52.04 1 4.00e+00 6.25e-02 2.31e+02 dihedral pdb=" CA GLY G 47 " pdb=" C GLY G 47 " pdb=" N ASN G 48 " pdb=" CA ASN G 48 " ideal model delta harmonic sigma weight residual -180.00 -108.84 -71.16 0 5.00e+00 4.00e-02 2.03e+02 ... (remaining 96408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 26483 0.090 - 0.179: 2320 0.179 - 0.269: 149 0.269 - 0.359: 20 0.359 - 0.449: 7 Chirality restraints: 28979 Sorted by residual: chirality pdb=" CB VAL l 38 " pdb=" CA VAL l 38 " pdb=" CG1 VAL l 38 " pdb=" CG2 VAL l 38 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" C3' C A 963 " pdb=" C4' C A 963 " pdb=" O3' C A 963 " pdb=" C2' C A 963 " both_signs ideal model delta sigma weight residual False -2.48 -2.04 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CB ILE r 22 " pdb=" CA ILE r 22 " pdb=" CG1 ILE r 22 " pdb=" CG2 ILE r 22 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.25e+00 ... (remaining 28976 not shown) Planarity restraints: 11720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP V 72 " 0.080 5.00e-02 4.00e+02 1.21e-01 2.36e+01 pdb=" N PRO V 73 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO V 73 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO V 73 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G A 940 " 0.048 2.00e-02 2.50e+03 2.10e-02 1.32e+01 pdb=" N9 G A 940 " -0.051 2.00e-02 2.50e+03 pdb=" C8 G A 940 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G A 940 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G A 940 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 940 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G A 940 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G A 940 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G A 940 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G A 940 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G A 940 " -0.007 2.00e-02 2.50e+03 pdb=" C4 G A 940 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G a 6 " -0.047 2.00e-02 2.50e+03 2.10e-02 1.32e+01 pdb=" N9 G a 6 " 0.052 2.00e-02 2.50e+03 pdb=" C8 G a 6 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G a 6 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G a 6 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G a 6 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G a 6 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G a 6 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G a 6 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G a 6 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G a 6 " 0.009 2.00e-02 2.50e+03 pdb=" C4 G a 6 " 0.007 2.00e-02 2.50e+03 ... (remaining 11717 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 20914 2.74 - 3.28: 112479 3.28 - 3.82: 275710 3.82 - 4.36: 325581 4.36 - 4.90: 448446 Nonbonded interactions: 1183130 Sorted by model distance: nonbonded pdb=" O2' C A2361 " pdb=" OH TYR 3 17 " model vdw 2.204 2.440 nonbonded pdb=" C2 A A2893 " pdb=" C4 A A2893 " model vdw 2.205 3.560 nonbonded pdb=" O2' G A 900 " pdb=" O6 G A 957 " model vdw 2.208 2.440 nonbonded pdb=" O2' A A2047 " pdb=" OP2 G A2049 " model vdw 2.211 2.440 nonbonded pdb=" O2' A A1421 " pdb=" O2 U A1432 " model vdw 2.215 2.440 ... (remaining 1183125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 22.660 Check model and map are aligned: 1.600 Set scattering table: 0.930 Process input model: 489.300 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.320 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: 0.020 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 523.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.007 0.092 150766 Z= 0.447 Angle : 1.037 16.877 226044 Z= 0.513 Chirality : 0.052 0.449 28979 Planarity : 0.007 0.121 11720 Dihedral : 22.757 179.875 86833 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.80 % Favored : 85.93 % Rotamer: Outliers : 0.46 % Allowed : 2.86 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 2.07 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.68 (0.09), residues: 5125 helix: -3.18 (0.10), residues: 1352 sheet: -2.62 (0.15), residues: 910 loop : -3.33 (0.10), residues: 2863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP R 61 HIS 0.019 0.003 HIS O 57 PHE 0.052 0.004 PHE K 45 TYR 0.047 0.004 TYR R 76 ARG 0.015 0.001 ARG M 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10250 Ramachandran restraints generated. 5125 Oldfield, 0 Emsley, 5125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10250 Ramachandran restraints generated. 5125 Oldfield, 0 Emsley, 5125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1678 residues out of total 4389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1658 time to evaluate : 5.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE K 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN S 75 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 135 GLN cc_start: 0.7029 (pt0) cc_final: 0.6710 (pt0) REVERT: d 74 LYS cc_start: 0.9221 (mttt) cc_final: 0.9020 (mtpp) REVERT: d 88 MET cc_start: 0.6807 (tpp) cc_final: 0.6445 (mmt) REVERT: d 132 TYR cc_start: 0.7150 (t80) cc_final: 0.6822 (t80) REVERT: e 12 GLU cc_start: 0.8118 (tt0) cc_final: 0.7538 (mt-10) REVERT: e 52 LYS cc_start: 0.8247 (ptpt) cc_final: 0.7954 (ptmt) REVERT: f 5 THR cc_start: 0.7566 (p) cc_final: 0.7112 (p) REVERT: f 8 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7647 (tm-30) REVERT: f 10 MET cc_start: 0.7529 (ttm) cc_final: 0.7279 (tmm) REVERT: f 20 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8025 (pm20) REVERT: f 27 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8818 (tp30) REVERT: f 31 THR cc_start: 0.8700 (p) cc_final: 0.8448 (p) REVERT: f 47 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7837 (mt-10) REVERT: f 50 ARG cc_start: 0.8552 (ptm-80) cc_final: 0.8299 (tmt-80) REVERT: f 56 ASN cc_start: 0.7848 (m110) cc_final: 0.7374 (m110) REVERT: f 69 THR cc_start: 0.9439 (p) cc_final: 0.9127 (t) REVERT: f 94 MET cc_start: 0.8283 (ttm) cc_final: 0.7094 (ttp) REVERT: h 43 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8349 (mm-30) REVERT: j 42 LEU cc_start: 0.8866 (mt) cc_final: 0.8494 (mp) REVERT: j 49 TYR cc_start: 0.8491 (m-80) cc_final: 0.8243 (m-80) REVERT: k 13 LYS cc_start: 0.6685 (mttt) cc_final: 0.5913 (tppt) REVERT: k 81 THR cc_start: 0.8001 (p) cc_final: 0.7372 (p) REVERT: k 86 VAL cc_start: 0.7667 (t) cc_final: 0.6029 (t) REVERT: k 93 ARG cc_start: 0.8210 (pmt100) cc_final: 0.7810 (ptp90) REVERT: k 111 ARG cc_start: 0.7468 (mtm110) cc_final: 0.6912 (mtt-85) REVERT: l 42 GLN cc_start: 0.7633 (pt0) cc_final: 0.7087 (pm20) REVERT: l 124 LYS cc_start: 0.7913 (mttt) cc_final: 0.7604 (tppt) REVERT: m 69 LEU cc_start: 0.7987 (tp) cc_final: 0.7617 (tp) REVERT: o 12 ILE cc_start: 0.9025 (pt) cc_final: 0.8702 (pt) REVERT: o 13 LYS cc_start: 0.9385 (mttt) cc_final: 0.8874 (mppt) REVERT: o 38 GLN cc_start: 0.8720 (mt0) cc_final: 0.8410 (tt0) REVERT: o 40 ASN cc_start: 0.9436 (t0) cc_final: 0.9006 (t0) REVERT: o 41 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8903 (mm-30) REVERT: o 44 ARG cc_start: 0.8958 (mtt180) cc_final: 0.8749 (ttm-80) REVERT: o 57 MET cc_start: 0.8762 (mmm) cc_final: 0.8255 (mmm) REVERT: o 67 LEU cc_start: 0.8995 (tp) cc_final: 0.8714 (tp) REVERT: o 85 LEU cc_start: 0.8309 (mt) cc_final: 0.7994 (mt) REVERT: p 35 GLU cc_start: 0.8308 (pt0) cc_final: 0.8099 (tm-30) REVERT: p 65 GLN cc_start: 0.7380 (mt0) cc_final: 0.7016 (mm-40) REVERT: p 68 ASP cc_start: 0.8384 (p0) cc_final: 0.7861 (p0) REVERT: q 7 GLN cc_start: 0.8925 (mt0) cc_final: 0.8602 (mp10) REVERT: q 31 LYS cc_start: 0.8760 (mttt) cc_final: 0.8390 (mtpp) REVERT: q 65 MET cc_start: 0.7390 (ttm) cc_final: 0.7155 (ttp) REVERT: q 76 PHE cc_start: 0.8645 (m-10) cc_final: 0.8164 (m-80) REVERT: r 42 LYS cc_start: 0.8719 (mttm) cc_final: 0.8287 (mmtm) REVERT: r 54 LYS cc_start: 0.9087 (ptmt) cc_final: 0.8749 (ptpt) REVERT: r 57 ARG cc_start: 0.9436 (mpp80) cc_final: 0.8979 (mtt90) REVERT: t 32 ILE cc_start: 0.8911 (mt) cc_final: 0.8698 (tp) REVERT: t 80 LYS cc_start: 0.9108 (mttt) cc_final: 0.8877 (mttp) REVERT: t 81 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7583 (pp) REVERT: C 273 ARG cc_start: 0.8095 (mtt90) cc_final: 0.7605 (mtp-110) REVERT: D 14 GLN cc_start: 0.8081 (mt0) cc_final: 0.7847 (mt0) REVERT: D 119 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.6835 (m-10) REVERT: E 13 GLN cc_start: 0.8270 (mt0) cc_final: 0.8058 (tm-30) REVERT: E 170 LEU cc_start: 0.8349 (mt) cc_final: 0.7775 (mt) REVERT: F 69 LYS cc_start: 0.7737 (mttt) cc_final: 0.7217 (mmtm) REVERT: F 83 MET cc_start: 0.8370 (mmm) cc_final: 0.8057 (mmm) REVERT: F 125 ARG cc_start: 0.7573 (mtt180) cc_final: 0.6651 (tpt90) REVERT: F 152 MET cc_start: 0.8831 (mmm) cc_final: 0.8006 (mmm) REVERT: F 162 THR cc_start: 0.8893 (p) cc_final: 0.8266 (p) REVERT: G 19 GLN cc_start: 0.8277 (mt0) cc_final: 0.7981 (pm20) REVERT: G 40 ASP cc_start: 0.8817 (m-30) cc_final: 0.8580 (m-30) REVERT: G 102 LYS cc_start: 0.8821 (mttt) cc_final: 0.8584 (mmmm) REVERT: G 104 THR cc_start: 0.8128 (p) cc_final: 0.7395 (p) REVERT: G 107 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8593 (p) REVERT: L 80 ASP cc_start: 0.8539 (m-30) cc_final: 0.8220 (m-30) REVERT: N 77 LYS cc_start: 0.7914 (mttt) cc_final: 0.7546 (mttp) REVERT: N 113 VAL cc_start: 0.9371 (t) cc_final: 0.8917 (t) REVERT: O 46 LYS cc_start: 0.8620 (mttt) cc_final: 0.8248 (tptp) REVERT: O 70 VAL cc_start: 0.8154 (t) cc_final: 0.7674 (p) REVERT: P 17 ARG cc_start: 0.7507 (mtt180) cc_final: 0.7001 (mtt90) REVERT: P 53 LEU cc_start: 0.8738 (mt) cc_final: 0.8533 (mp) REVERT: P 112 ARG cc_start: 0.7873 (mtt180) cc_final: 0.7398 (mtt90) REVERT: P 117 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7655 (mt-10) REVERT: Q 63 LYS cc_start: 0.8983 (mttt) cc_final: 0.8371 (mtmm) REVERT: R 32 PHE cc_start: 0.5505 (m-80) cc_final: 0.5258 (m-80) REVERT: R 52 GLN cc_start: 0.7536 (mt0) cc_final: 0.7298 (mt0) REVERT: S 1 MET cc_start: 0.7090 (mmm) cc_final: 0.6886 (mmt) REVERT: S 57 THR cc_start: 0.8392 (p) cc_final: 0.8174 (p) REVERT: S 92 TYR cc_start: 0.6021 (m-80) cc_final: 0.5710 (m-80) REVERT: V 1 MET cc_start: 0.6591 (tmt) cc_final: 0.5925 (tmm) REVERT: Z 8 GLU cc_start: 0.9258 (mt-10) cc_final: 0.9007 (mt-10) REVERT: 3 1 MET cc_start: 0.7926 (mmt) cc_final: 0.7494 (mmp) REVERT: 3 3 VAL cc_start: 0.9378 (t) cc_final: 0.9074 (m) REVERT: 3 39 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7867 (mp0) REVERT: 3 46 ARG cc_start: 0.7818 (mtp-110) cc_final: 0.7302 (ttm110) REVERT: 4 40 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7854 (mmtm) REVERT: 5 22 LEU cc_start: 0.8933 (mt) cc_final: 0.8706 (mt) REVERT: 5 24 ARG cc_start: 0.7939 (mtt180) cc_final: 0.6970 (ttp80) REVERT: 6 34 LYS cc_start: 0.8756 (mttt) cc_final: 0.8468 (mtpp) outliers start: 20 outliers final: 6 residues processed: 1672 average time/residue: 1.3482 time to fit residues: 3782.1825 Evaluate side-chains 980 residues out of total 4389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 971 time to evaluate : 5.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain Z residue 26 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 954 random chunks: chunk 805 optimal weight: 1.9990 chunk 723 optimal weight: 9.9990 chunk 401 optimal weight: 8.9990 chunk 247 optimal weight: 1.9990 chunk 487 optimal weight: 10.0000 chunk 386 optimal weight: 10.0000 chunk 747 optimal weight: 8.9990 chunk 289 optimal weight: 0.4980 chunk 454 optimal weight: 8.9990 chunk 556 optimal weight: 8.9990 chunk 866 optimal weight: 0.7980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 175 HIS d 35 GLN d 86 ASN e 135 ASN f 3 GLN f 64 HIS g 64 GLN ** g 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 14 ASN i 75 GLN k 64 GLN k 101 GLN l 42 GLN l 90 HIS l 125 GLN n 10 ASN n 38 HIS q 6 ASN q 50 HIS ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 22 GLN t 72 ASN C 73 ASN C 95 HIS C 128 ASN C 163 GLN C 177 ASN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 33 ASN D 37 GLN D 135 HIS E 29 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS F 27 GLN G 19 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN K 131 HIS L 13 ASN M 4 HIS ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS P 20 ASN P 32 ASN P 43 GLN P 101 HIS ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN R 81 HIS S 88 HIS ** V 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 HIS X 87 GLN Y 17 ASN Y 23 ASN Y 32 ASN Z 20 GLN ** 0 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 75 ASN 2 32 ASN 2 40 HIS 3 25 ASN 3 33 GLN 5 60 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 150766 Z= 0.190 Angle : 0.648 12.343 226044 Z= 0.334 Chirality : 0.037 0.357 28979 Planarity : 0.005 0.107 11720 Dihedral : 23.677 179.704 76379 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.87 % Favored : 89.91 % Rotamer: Outliers : 4.27 % Allowed : 13.80 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.26 % Twisted Proline : 1.04 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.10), residues: 5125 helix: -1.60 (0.13), residues: 1368 sheet: -2.23 (0.16), residues: 917 loop : -2.97 (0.10), residues: 2840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP c 200 HIS 0.006 0.001 HIS R 29 PHE 0.020 0.002 PHE G 123 TYR 0.021 0.002 TYR W 42 ARG 0.010 0.001 ARG q 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10250 Ramachandran restraints generated. 5125 Oldfield, 0 Emsley, 5125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10250 Ramachandran restraints generated. 5125 Oldfield, 0 Emsley, 5125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 4389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1118 time to evaluate : 5.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO G 112 " (corrupted residue). Skipping it. Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable