Starting phenix.real_space_refine on Mon Apr 15 14:11:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ifc_35412/04_2024/8ifc_35412_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ifc_35412/04_2024/8ifc_35412.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ifc_35412/04_2024/8ifc_35412_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ifc_35412/04_2024/8ifc_35412_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ifc_35412/04_2024/8ifc_35412_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ifc_35412/04_2024/8ifc_35412.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ifc_35412/04_2024/8ifc_35412.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ifc_35412/04_2024/8ifc_35412_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ifc_35412/04_2024/8ifc_35412_trim_updated.pdb" } resolution = 2.9 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4553 5.49 5 Mg 460 5.21 5 S 152 5.16 5 C 71384 2.51 5 N 26522 2.21 5 O 39488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J ASP 63": "OD1" <-> "OD2" Residue "c ASP 66": "OD1" <-> "OD2" Residue "d ASP 43": "OD1" <-> "OD2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 11": "OE1" <-> "OE2" Residue "f ASP 56": "OD1" <-> "OD2" Residue "f ASP 147": "OD1" <-> "OD2" Residue "k GLU 115": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 142560 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 32612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32612 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 120, 'rna2p_pyr': 82, 'rna3p': 10, 'rna3p_pur': 742, 'rna3p_pyr': 564} Link IDs: {'rna2p': 203, 'rna3p': 1315} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1203 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'IAS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "S" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "a" Number of atoms: 59130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 59130 Classifications: {'RNA': 2753} Modifications used: {'rna2p': 7, 'rna2p_pur': 268, 'rna2p_pyr': 139, 'rna3p': 16, 'rna3p_pur': 1317, 'rna3p_pyr': 1005} Link IDs: {'rna2p': 413, 'rna3p': 2339} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "i" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "l" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'peptide': 135, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 l 81 " pdbres="MS6 l 82 " Not linked: pdbres="MS6 l 82 " pdbres="GLY l 83 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "r" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "s" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "u" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "v" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 586 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "x" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "3" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "5" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1632 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p': 6, 'rna3p_pur': 31, 'rna3p_pyr': 30} Link IDs: {'rna2p': 9, 'rna3p': 66} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Chain: "6" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1645 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p': 5, 'rna3p_pur': 34, 'rna3p_pyr': 30} Link IDs: {'rna2p': 7, 'rna3p': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "7" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'RNA': 10} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "A" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 322 Unusual residues: {' MG': 188, '84G': 3, 'SPD': 2} Classifications: {'undetermined': 193} Link IDs: {None: 192} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' MG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 653 Unusual residues: {' MG': 233, '84G': 7, 'SPD': 14, 'SPM': 1} Classifications: {'undetermined': 255} Link IDs: {None: 254} Chain: "b" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0STU SG CYS 3 11 152.308 162.348 184.445 1.00 97.71 S ATOM A0SUJ SG CYS 3 14 154.236 163.467 181.373 1.00 88.24 S ATOM A0SXE SG CYS 3 27 156.010 161.589 184.155 1.00100.44 S Time building chain proxies: 55.98, per 1000 atoms: 0.39 Number of scatterers: 142560 At special positions: 0 Unit cell: (250.584, 237.976, 248.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 152 16.00 P 4553 15.00 Mg 460 11.99 O 39488 8.00 N 26522 7.00 C 71384 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 59.15 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " Number of angles added : 3 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10260 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 173 helices and 68 sheets defined 39.3% alpha, 19.9% beta 1556 base pairs and 2434 stacking pairs defined. Time for finding SS restraints: 75.26 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 24 through 32 removed outlier: 4.109A pdb=" N LYS B 28 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Proline residue: B 29 - end of helix removed outlier: 5.626A pdb=" N PHE B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 32' Processing helix chain 'B' and resid 42 through 64 Proline residue: B 48 - end of helix removed outlier: 3.644A pdb=" N ARG B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 103 through 124 removed outlier: 4.439A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 removed outlier: 4.495A pdb=" N LEU B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 125 through 130' Processing helix chain 'B' and resid 131 through 148 removed outlier: 4.795A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 6 through 12 removed outlier: 3.926A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 48 removed outlier: 4.320A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 113 removed outlier: 3.982A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 113' Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 129 through 145 removed outlier: 3.565A pdb=" N GLY C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.251A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 4.275A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 27 through 32' Processing helix chain 'D' and resid 49 through 66 removed outlier: 4.312A pdb=" N GLN D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 83 removed outlier: 5.075A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.719A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.566A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.800A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.990A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 4.745A pdb=" N SER D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.923A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 4.243A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 147 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 14 through 33 removed outlier: 3.815A pdb=" N VAL F 18 " --> pdb=" O GLN F 14 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 3.768A pdb=" N ALA F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'G' and resid 20 through 31 removed outlier: 6.279A pdb=" N ALA G 24 " --> pdb=" O SER G 20 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS G 25 " --> pdb=" O GLU G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 55 Processing helix chain 'G' and resid 57 through 70 Processing helix chain 'G' and resid 92 through 111 Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 132 through 149 Processing helix chain 'H' and resid 5 through 21 Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 112 through 120 Processing helix chain 'I' and resid 34 through 40 removed outlier: 4.204A pdb=" N GLY I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 56 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 93 through 102 removed outlier: 5.048A pdb=" N GLU I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 Processing helix chain 'J' and resid 80 through 90 Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.011A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.888A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 54 through 59' Processing helix chain 'K' and resid 60 through 75 Processing helix chain 'K' and resid 92 through 104 removed outlier: 3.977A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY K 104 " --> pdb=" O LEU K 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 11 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.848A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.760A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 64 removed outlier: 3.932A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 21 Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 52 Proline residue: N 52 - end of helix Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 44 removed outlier: 4.033A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 74 removed outlier: 3.849A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 80 removed outlier: 3.903A pdb=" N LYS P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.264A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N THR R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 66 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 70 through 76 removed outlier: 4.363A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA S 75 " --> pdb=" O LEU S 71 " (cutoff:3.500A) Proline residue: S 76 - end of helix No H-bonds generated for 'chain 'S' and resid 70 through 76' Processing helix chain 'T' and resid 4 through 41 Processing helix chain 'T' and resid 44 through 65 removed outlier: 3.787A pdb=" N GLN T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 removed outlier: 4.010A pdb=" N ALA T 87 " --> pdb=" O ILE T 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 27 Processing helix chain 'U' and resid 28 through 37 removed outlier: 4.683A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 68 removed outlier: 4.220A pdb=" N ARG U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 17 removed outlier: 4.785A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N VAL c 16 " --> pdb=" O GLY c 12 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL c 17 " --> pdb=" O ARG c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 3.775A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLU c 35 " --> pdb=" O ALA c 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 30 through 35' Processing helix chain 'c' and resid 131 through 136 Proline residue: c 136 - end of helix Processing helix chain 'c' and resid 207 through 215 removed outlier: 3.672A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY c 215 " --> pdb=" O ALA c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.788A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 221 through 226' Processing helix chain 'c' and resid 260 through 268 removed outlier: 5.080A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 5.797A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 72 removed outlier: 3.517A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 103 removed outlier: 3.916A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 98 through 103' Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.717A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 53 removed outlier: 6.385A pdb=" N THR e 53 " --> pdb=" O ARG e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 Processing helix chain 'e' and resid 130 through 142 Processing helix chain 'e' and resid 154 through 163 removed outlier: 4.525A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 removed outlier: 3.646A pdb=" N PHE e 183 " --> pdb=" O SER e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 21 removed outlier: 4.761A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 47 removed outlier: 3.739A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 62 removed outlier: 3.525A pdb=" N ASN f 52 " --> pdb=" O LYS f 48 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 111 removed outlier: 3.575A pdb=" N ALA f 107 " --> pdb=" O LEU f 103 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 removed outlier: 3.897A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP f 174 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 Proline residue: f 139 - end of helix Processing helix chain 'g' and resid 2 through 8 Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 60 through 81 removed outlier: 4.984A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.199A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 28 Processing helix chain 'h' and resid 29 through 34 Processing helix chain 'i' and resid 24 through 38 removed outlier: 4.004A pdb=" N GLU i 31 " --> pdb=" O ARG i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 96 Processing helix chain 'i' and resid 97 through 110 removed outlier: 4.214A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) Proline residue: i 110 - end of helix Processing helix chain 'i' and resid 112 through 122 removed outlier: 3.811A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 109 removed outlier: 4.523A pdb=" N ARG j 108 " --> pdb=" O THR j 104 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER j 109 " --> pdb=" O ARG j 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 104 through 109' Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 37 through 42 removed outlier: 5.389A pdb=" N SER k 42 " --> pdb=" O GLN k 38 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 62 Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 4.139A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 85 removed outlier: 3.950A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL k 85 " --> pdb=" O ASP k 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 78 through 85' Processing helix chain 'k' and resid 91 through 99 Processing helix chain 'k' and resid 128 through 139 Processing helix chain 'l' and resid 42 through 58 Processing helix chain 'l' and resid 109 through 125 removed outlier: 3.929A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Proline residue: l 125 - end of helix Processing helix chain 'm' and resid 13 through 32 Processing helix chain 'm' and resid 38 through 57 removed outlier: 4.209A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.393A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 4.447A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 5.174A pdb=" N GLY m 84 " --> pdb=" O PHE m 80 " (cutoff:3.500A) Proline residue: m 85 - end of helix Processing helix chain 'n' and resid 2 through 22 removed outlier: 4.532A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 4.711A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 86 Processing helix chain 'n' and resid 101 through 114 Processing helix chain 'o' and resid 2 through 13 removed outlier: 3.836A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.722A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N THR o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 104' Processing helix chain 'p' and resid 6 through 22 Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.716A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 3.884A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.801A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 87 Processing helix chain 'p' and resid 91 through 102 Processing helix chain 'p' and resid 103 through 118 Processing helix chain 'r' and resid 13 through 25 removed outlier: 3.658A pdb=" N LEU r 19 " --> pdb=" O GLN r 15 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.643A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 65 through 70 removed outlier: 3.646A pdb=" N LEU r 69 " --> pdb=" O ASP r 65 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS r 70 " --> pdb=" O ILE r 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 65 through 70' Processing helix chain 's' and resid 3 through 11 removed outlier: 4.162A pdb=" N LEU s 11 " --> pdb=" O LEU s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 27 Processing helix chain 's' and resid 39 through 51 Processing helix chain 't' and resid 66 through 71 removed outlier: 3.964A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ALA t 71 " --> pdb=" O VAL t 67 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 66 through 71' Processing helix chain 'u' and resid 13 through 24 Processing helix chain 'u' and resid 43 through 53 removed outlier: 4.155A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 4.197A pdb=" N SER u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) Processing helix chain 'w' and resid 52 through 63 Processing helix chain 'w' and resid 64 through 75 Processing helix chain 'x' and resid 2 through 9 removed outlier: 4.054A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) Processing helix chain 'x' and resid 10 through 35 removed outlier: 3.636A pdb=" N GLY x 35 " --> pdb=" O GLN x 31 " (cutoff:3.500A) Processing helix chain 'x' and resid 40 through 62 removed outlier: 4.404A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 18 Processing helix chain '0' and resid 26 through 31 Proline residue: 0 31 - end of helix No H-bonds generated for 'chain '0' and resid 26 through 31' Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.153A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 Processing helix chain '2' and resid 32 through 37 removed outlier: 4.422A pdb=" N LYS 2 36 " --> pdb=" O ILE 2 32 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 32 through 37' Processing helix chain '2' and resid 38 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.357A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Proline residue: 2 63 - end of helix Processing helix chain '4' and resid 41 through 46 Processing helix chain '4' and resid 55 through 64 Processing sheet with id= 1, first strand: chain 'B' and resid 15 through 18 removed outlier: 5.714A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 89 through 93 Processing sheet with id= 3, first strand: chain 'C' and resid 53 through 59 Processing sheet with id= 4, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.859A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 141 through 145 removed outlier: 6.974A pdb=" N MET D 178 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 11 through 16 removed outlier: 6.772A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 84 through 88 removed outlier: 3.879A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 33 through 41 removed outlier: 6.881A pdb=" N ARG E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 38 through 42 removed outlier: 5.730A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 43 through 47 removed outlier: 7.078A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 73 through 79 Processing sheet with id= 12, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.179A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.692A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 5 through 11 removed outlier: 3.836A pdb=" N LYS I 27 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'J' and resid 39 through 42 removed outlier: 4.484A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'J' and resid 44 through 52 Processing sheet with id= 17, first strand: chain 'K' and resid 30 through 35 removed outlier: 6.897A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 29 through 32 removed outlier: 5.064A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 36 through 41 removed outlier: 3.623A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'P' and resid 4 through 11 removed outlier: 3.544A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Q' and resid 7 through 11 removed outlier: 6.684A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N SER Q 72 " --> pdb=" O CYS Q 64 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'S' and resid 30 through 34 removed outlier: 4.352A pdb=" N LEU S 47 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'c' and resid 80 through 83 removed outlier: 6.718A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'c' and resid 138 through 142 removed outlier: 3.979A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'c' and resid 90 through 96 removed outlier: 5.265A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'd' and resid 3 through 6 Processing sheet with id= 28, first strand: chain 'd' and resid 10 through 16 removed outlier: 3.706A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'd' and resid 36 through 40 removed outlier: 3.872A pdb=" N LEU d 40 " --> pdb=" O TYR d 45 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR d 45 " --> pdb=" O LEU d 40 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'd' and resid 46 through 51 removed outlier: 5.801A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.508A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'e' and resid 1 through 6 removed outlier: 3.806A pdb=" N MET e 1 " --> pdb=" O VAL e 14 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.495A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'f' and resid 65 through 69 removed outlier: 5.920A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'g' and resid 15 through 20 removed outlier: 6.122A pdb=" N GLN g 22 " --> pdb=" O LEU g 37 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU g 33 " --> pdb=" O ILE g 26 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY g 28 " --> pdb=" O GLY g 31 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY g 31 " --> pdb=" O GLY g 28 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'g' and resid 41 through 46 removed outlier: 4.580A pdb=" N ALA g 46 " --> pdb=" O THR g 49 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR g 49 " --> pdb=" O ALA g 46 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'g' and resid 94 through 99 removed outlier: 6.898A pdb=" N ASN g 101 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'g' and resid 121 through 125 removed outlier: 5.951A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'h' and resid 17 through 21 removed outlier: 4.475A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN h 2 " --> pdb=" O ALA h 39 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LYS h 35 " --> pdb=" O LEU h 6 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'i' and resid 14 through 19 Processing sheet with id= 41, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.437A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'j' and resid 18 through 21 removed outlier: 4.170A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU j 86 " --> pdb=" O ALA j 11 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS j 59 " --> pdb=" O LEU j 87 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP j 37 " --> pdb=" O VAL j 62 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'l' and resid 37 through 40 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'l' and resid 62 through 65 removed outlier: 6.616A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'l' and resid 30 through 36 removed outlier: 8.028A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'm' and resid 33 through 37 removed outlier: 4.697A pdb=" N ARG m 103 " --> pdb=" O ASN m 107 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLY m 101 " --> pdb=" O PRO m 109 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA m 111 " --> pdb=" O LYS m 99 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS m 99 " --> pdb=" O ALA m 111 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE m 113 " --> pdb=" O ILE m 97 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE m 97 " --> pdb=" O ILE m 113 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU m 115 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR m 95 " --> pdb=" O LEU m 115 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'n' and resid 49 through 52 Processing sheet with id= 48, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.275A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.638A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'q' and resid 11 through 15 removed outlier: 7.017A pdb=" N LEU q 39 " --> pdb=" O GLY q 50 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU q 46 " --> pdb=" O ASN q 43 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'q' and resid 18 through 23 removed outlier: 4.016A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU q 31 " --> pdb=" O VAL q 63 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 53, first strand: chain 'q' and resid 65 through 68 Processing sheet with id= 54, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.029A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'r' and resid 2 through 8 removed outlier: 4.759A pdb=" N THR r 100 " --> pdb=" O GLY r 79 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 's' and resid 12 through 15 removed outlier: 5.264A pdb=" N VAL s 31 " --> pdb=" O HIS s 15 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS s 81 " --> pdb=" O VAL s 34 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 't' and resid 40 through 45 removed outlier: 4.894A pdb=" N ASN t 40 " --> pdb=" O ALA t 63 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 't' and resid 82 through 86 removed outlier: 5.010A pdb=" N ARG t 82 " --> pdb=" O LYS t 97 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ARG t 94 " --> pdb=" O ILE t 103 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'u' and resid 69 through 72 removed outlier: 3.656A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'v' and resid 66 through 71 Processing sheet with id= 61, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.389A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'w' and resid 34 through 41 Processing sheet with id= 63, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.168A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'z' and resid 29 through 32 removed outlier: 4.519A pdb=" N GLU z 36 " --> pdb=" O ASP z 31 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '0' and resid 19 through 24 removed outlier: 6.075A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '2' and resid 22 through 25 removed outlier: 5.661A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '3' and resid 1 through 5 removed outlier: 6.703A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER 3 28 " --> pdb=" O ASN 3 13 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ASN 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '4' and resid 20 through 25 removed outlier: 4.039A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) 1962 hydrogen bonds defined for protein. 5787 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3921 hydrogen bonds 6148 hydrogen bond angles 0 basepair planarities 1556 basepair parallelities 2434 stacking parallelities Total time for adding SS restraints: 259.23 Time building geometry restraints manager: 64.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 13675 1.31 - 1.44: 68309 1.44 - 1.57: 63069 1.57 - 1.71: 9098 1.71 - 1.84: 268 Bond restraints: 154419 Sorted by residual: bond pdb=" N PRO h 38 " pdb=" CD PRO h 38 " ideal model delta sigma weight residual 1.473 1.793 -0.320 1.40e-02 5.10e+03 5.24e+02 bond pdb=" C4 5MU a1939 " pdb=" C5 5MU a1939 " ideal model delta sigma weight residual 1.802 1.442 0.360 2.00e-02 2.50e+03 3.24e+02 bond pdb=" C4 5MU 6 55 " pdb=" C5 5MU 6 55 " ideal model delta sigma weight residual 1.802 1.443 0.359 2.00e-02 2.50e+03 3.22e+02 bond pdb=" C4 5MU a 747 " pdb=" C5 5MU a 747 " ideal model delta sigma weight residual 1.802 1.443 0.359 2.00e-02 2.50e+03 3.22e+02 bond pdb=" C4 5MU 5 54 " pdb=" C5 5MU 5 54 " ideal model delta sigma weight residual 1.802 1.445 0.357 2.00e-02 2.50e+03 3.18e+02 ... (remaining 154414 not shown) Histogram of bond angle deviations from ideal: 89.64 - 102.65: 7448 102.65 - 115.66: 124871 115.66 - 128.68: 93031 128.68 - 141.69: 5616 141.69 - 154.70: 5 Bond angle restraints: 230971 Sorted by residual: angle pdb=" C D2T L 89 " pdb=" N LEU L 90 " pdb=" CA LEU L 90 " ideal model delta sigma weight residual 121.70 154.70 -33.00 1.80e+00 3.09e-01 3.36e+02 angle pdb=" O D2T L 89 " pdb=" C D2T L 89 " pdb=" N LEU L 90 " ideal model delta sigma weight residual 123.00 99.40 23.60 1.60e+00 3.91e-01 2.18e+02 angle pdb=" CA D2T L 89 " pdb=" C D2T L 89 " pdb=" N LEU L 90 " ideal model delta sigma weight residual 116.20 139.68 -23.48 2.00e+00 2.50e-01 1.38e+02 angle pdb=" C VAL h 37 " pdb=" N PRO h 38 " pdb=" CA PRO h 38 " ideal model delta sigma weight residual 119.76 109.67 10.09 1.03e+00 9.43e-01 9.60e+01 angle pdb=" N PRO h 38 " pdb=" CD PRO h 38 " pdb=" CG PRO h 38 " ideal model delta sigma weight residual 103.20 89.64 13.56 1.50e+00 4.44e-01 8.18e+01 ... (remaining 230966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 86873 35.81 - 71.62: 11132 71.62 - 107.43: 1268 107.43 - 143.24: 30 143.24 - 179.06: 13 Dihedral angle restraints: 99316 sinusoidal: 83411 harmonic: 15905 Sorted by residual: dihedral pdb=" O4' C 5 74 " pdb=" C1' C 5 74 " pdb=" N1 C 5 74 " pdb=" C2 C 5 74 " ideal model delta sinusoidal sigma weight residual -160.00 9.94 -169.94 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U 5 45 " pdb=" C1' U 5 45 " pdb=" N1 U 5 45 " pdb=" C2 U 5 45 " ideal model delta sinusoidal sigma weight residual 200.00 31.47 168.53 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 49.33 150.67 1 1.50e+01 4.44e-03 7.99e+01 ... (remaining 99313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 27426 0.073 - 0.147: 1878 0.147 - 0.220: 135 0.220 - 0.293: 6 0.293 - 0.367: 4 Chirality restraints: 29449 Sorted by residual: chirality pdb=" C1* PSU a2580 " pdb=" O4* PSU a2580 " pdb=" C2* PSU a2580 " pdb=" C5 PSU a2580 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C2' 3TD a1915 " pdb=" C3' 3TD a1915 " pdb=" O2' 3TD a1915 " pdb=" C1' 3TD a1915 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C1* PSU A 516 " pdb=" O4* PSU A 516 " pdb=" C2* PSU A 516 " pdb=" C5 PSU A 516 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 29446 not shown) Planarity restraints: 12260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " -0.077 2.00e-02 2.50e+03 6.12e-01 8.44e+03 pdb=" C4' 5MC A1407 " -0.438 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " -0.619 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " 0.601 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " 0.674 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " 0.158 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " -1.014 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " -0.221 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " 0.936 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.063 2.00e-02 2.50e+03 5.89e-01 7.80e+03 pdb=" C4' 2MG A1516 " -0.432 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.585 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.632 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.168 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -0.974 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.236 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.897 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC a2498 " 0.076 2.00e-02 2.50e+03 5.89e-01 7.80e+03 pdb=" C4' OMC a2498 " 0.429 2.00e-02 2.50e+03 pdb=" O4' OMC a2498 " 0.558 2.00e-02 2.50e+03 pdb=" C3' OMC a2498 " -0.596 2.00e-02 2.50e+03 pdb=" O3' OMC a2498 " -0.650 2.00e-02 2.50e+03 pdb=" C2' OMC a2498 " -0.163 2.00e-02 2.50e+03 pdb=" O2' OMC a2498 " 0.992 2.00e-02 2.50e+03 pdb=" C1' OMC a2498 " 0.234 2.00e-02 2.50e+03 pdb=" N1 OMC a2498 " -0.880 2.00e-02 2.50e+03 ... (remaining 12257 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 437 2.32 - 2.96: 64299 2.96 - 3.61: 231889 3.61 - 4.25: 457550 4.25 - 4.90: 598657 Nonbonded interactions: 1352832 Sorted by model distance: nonbonded pdb=" O2 C a2000 " pdb="MG MG a6220 " model vdw 1.672 2.170 nonbonded pdb=" OP1 G a1026 " pdb="MG MG a6118 " model vdw 1.723 2.170 nonbonded pdb=" O PRO B 48 " pdb=" OE1 GLU B 52 " model vdw 1.756 3.040 nonbonded pdb=" OP2 G a1186 " pdb="MG MG a6068 " model vdw 1.758 2.170 nonbonded pdb=" OP1 C a 948 " pdb="MG MG a6028 " model vdw 1.768 2.170 ... (remaining 1352827 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=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: 5.790 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: 0.110 Extract box with map and model: 32.400 Check model and map are aligned: 1.570 Set scattering table: 0.990 Process input model: 578.190 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.330 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:14.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 636.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 : 0.008 0.360 154419 Z= 0.443 Angle : 0.643 33.004 230971 Z= 0.319 Chirality : 0.039 0.367 29449 Planarity : 0.021 0.612 12260 Dihedral : 23.412 179.055 89056 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.37 % Allowed : 28.24 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.11), residues: 5474 helix: 1.62 (0.12), residues: 1879 sheet: -0.14 (0.15), residues: 1124 loop : -0.72 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP c 248 HIS 0.005 0.001 HIS u 88 PHE 0.017 0.002 PHE p 57 TYR 0.017 0.002 TYR r 38 ARG 0.005 0.000 ARG U 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 636 time to evaluate : 6.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 14 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.5995 (tm-30) REVERT: c 100 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: w 22 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7937 (mp) outliers start: 154 outliers final: 146 residues processed: 784 average time/residue: 2.2243 time to fit residues: 2464.2310 Evaluate side-chains 785 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 636 time to evaluate : 6.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 136 ARG Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 90 ARG Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain c residue 5 LYS Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 100 GLU Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain d residue 35 THR Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 74 LYS Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 136 ILE Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 17 ASP Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 136 GLN Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain i residue 142 ILE Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 114 LYS Chi-restraints excluded: chain j residue 123 LEU Chi-restraints excluded: chain k residue 92 LEU Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 15 SER Chi-restraints excluded: chain n residue 25 ARG Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain o residue 32 VAL Chi-restraints excluded: chain o residue 37 LYS Chi-restraints excluded: chain q residue 51 VAL Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 52 LEU Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain t residue 79 LYS Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain v residue 16 SER Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 81 SER Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain w residue 22 LEU Chi-restraints excluded: chain w residue 51 VAL Chi-restraints excluded: chain x residue 6 LEU Chi-restraints excluded: chain x residue 58 ASN Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain 0 residue 5 ILE Chi-restraints excluded: chain 0 residue 43 VAL Chi-restraints excluded: chain 1 residue 15 SER Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 26 ILE Chi-restraints excluded: chain 4 residue 21 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 834 optimal weight: 1.9990 chunk 748 optimal weight: 4.9990 chunk 415 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 505 optimal weight: 8.9990 chunk 400 optimal weight: 0.8980 chunk 774 optimal weight: 7.9990 chunk 299 optimal weight: 7.9990 chunk 470 optimal weight: 40.0000 chunk 576 optimal weight: 6.9990 chunk 897 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 HIS B 177 ASN ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 GLN N 62 ASN R 54 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 13 GLN ** c 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN e 195 GLN j 29 HIS k 4 ASN o 66 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.0552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 154419 Z= 0.289 Angle : 0.651 15.651 230971 Z= 0.352 Chirality : 0.039 0.375 29449 Planarity : 0.007 0.138 12260 Dihedral : 23.093 179.136 78273 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.58 % Allowed : 24.98 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.11), residues: 5474 helix: 1.53 (0.12), residues: 1892 sheet: -0.07 (0.15), residues: 1108 loop : -0.59 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 201 HIS 0.005 0.001 HIS F 11 PHE 0.017 0.002 PHE B 198 TYR 0.019 0.002 TYR r 38 ARG 0.005 0.000 ARG s 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 660 time to evaluate : 6.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.5699 (mtt-85) REVERT: B 52 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6530 (mp0) REVERT: B 133 GLU cc_start: 0.5084 (OUTLIER) cc_final: 0.4334 (tm-30) REVERT: B 135 LEU cc_start: 0.4671 (OUTLIER) cc_final: 0.4321 (tm) REVERT: D 44 ARG cc_start: 0.5432 (mtm110) cc_final: 0.4220 (mmm160) REVERT: D 197 GLU cc_start: 0.5740 (OUTLIER) cc_final: 0.3966 (mp0) REVERT: D 206 LYS cc_start: 0.6174 (OUTLIER) cc_final: 0.5399 (ptpp) REVERT: F 9 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6485 (mtm) REVERT: F 14 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6729 (mm-40) REVERT: F 17 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.6172 (mp10) REVERT: G 63 GLU cc_start: 0.5857 (mt-10) cc_final: 0.5650 (mt-10) REVERT: G 138 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.5718 (tmm160) REVERT: H 108 LYS cc_start: 0.7993 (mmpt) cc_final: 0.6910 (mttt) REVERT: I 119 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6883 (mtm180) REVERT: K 13 ARG cc_start: 0.4404 (OUTLIER) cc_final: 0.4154 (tpm170) REVERT: K 17 SER cc_start: 0.6970 (OUTLIER) cc_final: 0.6594 (t) REVERT: K 94 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.5884 (mp0) REVERT: L 40 THR cc_start: 0.7819 (m) cc_final: 0.7470 (p) REVERT: L 56 ARG cc_start: 0.7255 (ttp-110) cc_final: 0.6911 (ttm-80) REVERT: M 75 MET cc_start: 0.6174 (tpp) cc_final: 0.5886 (tpt) REVERT: O 14 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.5921 (tm-30) REVERT: O 80 GLN cc_start: 0.6341 (mt0) cc_final: 0.6084 (tt0) REVERT: S 23 VAL cc_start: 0.6750 (OUTLIER) cc_final: 0.6480 (t) REVERT: T 15 GLU cc_start: 0.6570 (tp30) cc_final: 0.6288 (tp30) REVERT: U 4 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6269 (mp) REVERT: c 251 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.6853 (tm-30) REVERT: d 30 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: d 86 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6116 (mp0) REVERT: d 88 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7157 (mt-10) REVERT: g 99 LYS cc_start: 0.5693 (mtmt) cc_final: 0.5270 (mmtm) REVERT: i 129 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: j 45 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6847 (tp30) REVERT: n 116 GLN cc_start: 0.6726 (mm-40) cc_final: 0.6246 (mp10) REVERT: p 9 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7539 (mp) REVERT: q 6 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: q 48 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7407 (mtpm) REVERT: w 22 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7845 (mp) REVERT: w 45 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6533 (ttm170) REVERT: 0 27 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.6773 (mmtp) outliers start: 255 outliers final: 135 residues processed: 845 average time/residue: 2.3079 time to fit residues: 2743.7117 Evaluate side-chains 804 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 640 time to evaluate : 6.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 138 ARG Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 119 ARG Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain c residue 251 GLN Chi-restraints excluded: chain d residue 30 GLU Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 110 SER Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 168 ASP Chi-restraints excluded: chain e residue 179 SER Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 128 GLN Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 17 ASP Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 129 GLU Chi-restraints excluded: chain i residue 136 GLN Chi-restraints excluded: chain j residue 45 GLU Chi-restraints excluded: chain j residue 53 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 123 LEU Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain n residue 25 ARG Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain o residue 7 GLN Chi-restraints excluded: chain o residue 32 VAL Chi-restraints excluded: chain o residue 37 LYS Chi-restraints excluded: chain p residue 9 ILE Chi-restraints excluded: chain p residue 77 SER Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 48 LYS Chi-restraints excluded: chain q residue 49 ILE Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 52 LEU Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain w residue 22 LEU Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 45 ARG Chi-restraints excluded: chain x residue 6 LEU Chi-restraints excluded: chain x residue 30 MET Chi-restraints excluded: chain x residue 58 ASN Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 0 residue 27 LYS Chi-restraints excluded: chain 0 residue 43 VAL Chi-restraints excluded: chain 1 residue 15 SER Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 3 residue 6 SER Chi-restraints excluded: chain 4 residue 22 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 498 optimal weight: 8.9990 chunk 278 optimal weight: 2.9990 chunk 746 optimal weight: 0.0000 chunk 610 optimal weight: 8.9990 chunk 247 optimal weight: 3.9990 chunk 898 optimal weight: 7.9990 chunk 970 optimal weight: 2.9990 chunk 800 optimal weight: 0.5980 chunk 891 optimal weight: 8.9990 chunk 306 optimal weight: 1.9990 chunk 721 optimal weight: 4.9990 overall best weight: 1.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 ASN L 112 GLN N 62 ASN R 54 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 13 GLN ** c 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN e 195 GLN i 58 ASN o 66 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 154419 Z= 0.164 Angle : 0.611 15.072 230971 Z= 0.335 Chirality : 0.035 0.378 29449 Planarity : 0.006 0.132 12260 Dihedral : 23.099 178.539 78146 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.10 % Allowed : 25.50 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.11), residues: 5474 helix: 1.67 (0.12), residues: 1887 sheet: -0.06 (0.15), residues: 1111 loop : -0.50 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 HIS 0.004 0.001 HIS F 11 PHE 0.016 0.001 PHE B 198 TYR 0.016 0.001 TYR r 38 ARG 0.005 0.000 ARG G 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 668 time to evaluate : 6.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.5661 (mtt-85) REVERT: B 9 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5350 (mtt) REVERT: B 52 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6555 (mp0) REVERT: B 135 LEU cc_start: 0.4680 (OUTLIER) cc_final: 0.4307 (tm) REVERT: C 147 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7334 (mttp) REVERT: D 44 ARG cc_start: 0.5413 (mtm110) cc_final: 0.4218 (mmm160) REVERT: D 197 GLU cc_start: 0.5737 (OUTLIER) cc_final: 0.3973 (mp0) REVERT: D 206 LYS cc_start: 0.6161 (OUTLIER) cc_final: 0.5415 (ptpp) REVERT: E 124 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7499 (mt) REVERT: F 9 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6470 (mtm) REVERT: F 14 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6741 (mm-40) REVERT: F 17 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.6183 (mp10) REVERT: F 63 ASN cc_start: 0.7331 (OUTLIER) cc_final: 0.6609 (m110) REVERT: G 63 GLU cc_start: 0.5829 (mt-10) cc_final: 0.5580 (mt-10) REVERT: G 137 LYS cc_start: 0.5594 (OUTLIER) cc_final: 0.5374 (tptp) REVERT: G 138 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5677 (tmm160) REVERT: H 43 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7424 (mm-30) REVERT: H 108 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.6877 (mttt) REVERT: K 13 ARG cc_start: 0.4377 (OUTLIER) cc_final: 0.4155 (tpm170) REVERT: K 94 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5896 (mp0) REVERT: L 40 THR cc_start: 0.7855 (m) cc_final: 0.7519 (p) REVERT: O 14 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.5936 (tm-30) REVERT: O 80 GLN cc_start: 0.6293 (mt0) cc_final: 0.6078 (mt0) REVERT: S 29 LYS cc_start: 0.6354 (OUTLIER) cc_final: 0.5705 (mttm) REVERT: T 15 GLU cc_start: 0.6517 (tp30) cc_final: 0.6011 (tp30) REVERT: T 69 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.5685 (mmtt) REVERT: c 251 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: d 30 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: d 86 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.6132 (mp0) REVERT: d 88 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7156 (mt-10) REVERT: d 183 GLU cc_start: 0.6967 (pm20) cc_final: 0.6264 (pp20) REVERT: f 135 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.5786 (pp30) REVERT: g 99 LYS cc_start: 0.5690 (mtmt) cc_final: 0.5274 (mmtm) REVERT: j 45 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6854 (tp30) REVERT: j 108 ARG cc_start: 0.7227 (ttm-80) cc_final: 0.6347 (ttm170) REVERT: n 104 GLN cc_start: 0.7646 (tt0) cc_final: 0.7353 (tt0) REVERT: n 116 GLN cc_start: 0.6699 (mm-40) cc_final: 0.6232 (mp10) REVERT: o 87 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7928 (mmmm) REVERT: p 9 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7520 (mp) REVERT: p 91 ASP cc_start: 0.8409 (p0) cc_final: 0.8066 (p0) REVERT: q 6 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.6925 (tm-30) REVERT: q 48 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7404 (mtpm) REVERT: w 22 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7938 (mp) outliers start: 233 outliers final: 135 residues processed: 831 average time/residue: 2.2581 time to fit residues: 2637.0797 Evaluate side-chains 821 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 655 time to evaluate : 6.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 136 ARG Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 138 ARG Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 29 LYS Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 69 LYS Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain c residue 251 GLN Chi-restraints excluded: chain d residue 30 GLU Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 135 GLN Chi-restraints excluded: chain f residue 136 ILE Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 77 ILE Chi-restraints excluded: chain g residue 128 GLN Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 17 ASP Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 136 GLN Chi-restraints excluded: chain i residue 142 ILE Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 45 GLU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 40 SER Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain n residue 25 ARG Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain o residue 7 GLN Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain o residue 32 VAL Chi-restraints excluded: chain o residue 37 LYS Chi-restraints excluded: chain o residue 87 LYS Chi-restraints excluded: chain p residue 9 ILE Chi-restraints excluded: chain p residue 77 SER Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 48 LYS Chi-restraints excluded: chain q residue 49 ILE Chi-restraints excluded: chain r residue 108 SER Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 52 LEU Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain w residue 22 LEU Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain x residue 6 LEU Chi-restraints excluded: chain x residue 30 MET Chi-restraints excluded: chain x residue 58 ASN Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 0 residue 43 VAL Chi-restraints excluded: chain 1 residue 15 SER Chi-restraints excluded: chain 1 residue 42 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 888 optimal weight: 4.9990 chunk 675 optimal weight: 5.9990 chunk 466 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 428 optimal weight: 7.9990 chunk 603 optimal weight: 10.0000 chunk 902 optimal weight: 10.0000 chunk 955 optimal weight: 6.9990 chunk 471 optimal weight: 40.0000 chunk 854 optimal weight: 4.9990 chunk 257 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: