Starting phenix.real_space_refine on Tue Mar 26 09:16:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/03_2024/7nwt_12635_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/03_2024/7nwt_12635.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/03_2024/7nwt_12635_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/03_2024/7nwt_12635_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/03_2024/7nwt_12635_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/03_2024/7nwt_12635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/03_2024/7nwt_12635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/03_2024/7nwt_12635_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/03_2024/7nwt_12635_updated.pdb" } resolution = 2.66 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= 0.021 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 2 6.06 5 P 4641 5.49 5 Mg 437 5.21 5 S 169 5.16 5 C 75752 2.51 5 N 27837 2.21 5 O 41094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149932 Number of models: 1 Model: "" Number of chains: 74 Chain: "B" 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: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "D" 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: "E" 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: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 984 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "J" 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: "K" 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: "L" 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: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "U" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "V" 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: "W" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "X" 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: "Y" 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: "Z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 289, 'rna2p_pyr': 165, 'rna3p': 16, 'rna3p_pur': 1378, 'rna3p_pyr': 1049} Link IDs: {'rna2p': 459, 'rna3p': 2443} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 118, 'rna2p_pyr': 89, 'rna3p': 10, 'rna3p_pur': 751, 'rna3p_pyr': 564} Link IDs: {'rna2p': 207, 'rna3p': 1326} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "5" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1622 Unusual residues: {'8AN': 1} Classifications: {'RNA': 75, 'undetermined': 1} Modifications used: {'rna2p': 2, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p': 3, 'rna3p_pur': 32, 'rna3p_pyr': 27} Link IDs: {'p': 1, 'rna2p': 13, 'rna3p': 61} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 3 Chain: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" 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: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" 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: "e" 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: "f" 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: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" 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: "j" 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: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" 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: "n" 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: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" 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: "q" 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: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "s" 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: "t" 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: "u" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" 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: "x" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "y" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "z" 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: "XX" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "AA" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1067 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "BB" Number of atoms: 1111 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 130, 1089 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 7, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 130, 1089 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 7, 'TRANS': 122} bond proxies already assigned to first conformer: 1100 Chain: "CC" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1048 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 290 Unusual residues: {' MG': 290} Classifications: {'undetermined': 290} Link IDs: {None: 289} Chain: "2" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 128 Unusual residues: {' MG': 128} Classifications: {'undetermined': 128} Link IDs: {None: 127} Chain: "3" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "5" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 13 Unusual residues: {' MG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0KPG SG CYS f 11 60.519 143.409 129.674 1.00 57.54 S ATOM A0KQ5 SG CYS f 14 61.522 142.411 133.100 1.00 54.72 S ATOM A0KT0 SG CYS f 27 59.851 139.944 130.871 1.00 55.15 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARGBB 46 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARGBB 46 " occ=0.50 residue: pdb=" N AARGBB 100 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARGBB 100 " occ=0.50 residue: pdb="MG MG 13144 " occ=0.50 Time building chain proxies: 57.40, per 1000 atoms: 0.38 Number of scatterers: 149932 At special positions: 0 Unit cell: (243.96, 258.94, 273.92, 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 2 29.99 S 169 16.00 P 4641 15.00 Mg 437 11.99 O 41094 8.00 N 27837 7.00 C 75752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS a 18 " - pdb=" SG CYS a 37 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 57.17 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " Number of angles added : 3 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11714 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: 194 helices and 74 sheets defined 38.6% alpha, 19.6% beta 1490 base pairs and 2552 stacking pairs defined. Time for finding SS restraints: 74.71 Creating SS restraints... Processing helix chain 'B' and resid 10 through 17 removed outlier: 3.531A pdb=" N ARG B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 17' Processing helix chain 'B' and resid 30 through 35 removed outlier: 4.131A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLU B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 35' Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.659A pdb=" N ILE B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Proline residue: B 136 - end of helix No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.076A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 removed outlier: 3.750A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 268' Processing helix chain 'B' and resid 197 through 202 removed outlier: 4.008A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 6.011A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.578A pdb=" N HIS C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.144A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 103' Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 24 through 40 removed outlier: 3.805A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 removed outlier: 3.575A pdb=" N VAL D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.513A pdb=" N MET D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.635A pdb=" N ARG D 162 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.691A pdb=" N ILE D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 removed outlier: 3.609A pdb=" N LYS D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 5.503A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 removed outlier: 4.620A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 3.566A pdb=" N TRP E 97 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.827A pdb=" N GLY E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP E 174 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.599A pdb=" N ALA E 43 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE E 44 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.702A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Proline residue: E 139 - end of helix Processing helix chain 'F' and resid 2 through 8 removed outlier: 4.463A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 removed outlier: 3.615A pdb=" N SER F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.727A pdb=" N TYR F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 40 through 50 removed outlier: 4.518A pdb=" N GLU G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE G 46 " --> pdb=" O LYS G 42 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU G 48 " --> pdb=" O ILE G 44 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG G 50 " --> pdb=" O PHE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 73 removed outlier: 3.712A pdb=" N LEU G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 removed outlier: 3.522A pdb=" N ALA G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ALA G 105 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 21 removed outlier: 3.859A pdb=" N ALA H 10 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL H 12 " --> pdb=" O LYS H 8 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA H 19 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 removed outlier: 3.601A pdb=" N THR H 39 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU H 40 " --> pdb=" O ASP H 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU H 41 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG H 42 " --> pdb=" O MET H 38 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA H 44 " --> pdb=" O GLU H 40 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY H 45 " --> pdb=" O LEU H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 removed outlier: 5.649A pdb=" N GLY H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Proline residue: H 68 - end of helix No H-bonds generated for 'chain 'H' and resid 62 through 68' Processing helix chain 'H' and resid 74 through 79 removed outlier: 3.781A pdb=" N GLY H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Proline residue: H 79 - end of helix No H-bonds generated for 'chain 'H' and resid 74 through 79' Processing helix chain 'H' and resid 94 through 106 removed outlier: 4.502A pdb=" N GLU H 98 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA H 102 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN H 103 " --> pdb=" O PHE H 99 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ALA H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS H 105 " --> pdb=" O LYS H 101 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N PHE H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 removed outlier: 5.026A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 46 removed outlier: 3.778A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 removed outlier: 4.516A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 Processing helix chain 'I' and resid 101 through 113 removed outlier: 5.040A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE I 108 " --> pdb=" O GLN I 104 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 4.476A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR I 125 " --> pdb=" O ILE I 121 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.047A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.179A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.661A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.408A pdb=" N LYS J 72 " --> pdb=" O ASN J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 67 through 72' Processing helix chain 'K' and resid 104 through 109 removed outlier: 4.533A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N SER K 109 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.053A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.820A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.530A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY L 139 " --> pdb=" O ILE L 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.519A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.647A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 58 removed outlier: 4.325A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.619A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.807A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.656A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.551A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.578A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 2 through 14 removed outlier: 3.836A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS P 14 " --> pdb=" O GLN P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.582A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.519A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.712A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 removed outlier: 3.996A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.963A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.501A pdb=" N VAL Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.827A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 40 removed outlier: 3.882A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASN S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.799A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 3.815A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 65 through 70' Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.906A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.894A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.783A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.178A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 2 through 9 removed outlier: 4.067A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 3.535A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 62 removed outlier: 4.784A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 removed outlier: 3.539A pdb=" N VAL Z 51 " --> pdb=" O MET Z 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 51 removed outlier: 5.669A pdb=" N GLN a 48 " --> pdb=" O PHE a 44 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG a 49 " --> pdb=" O THR a 45 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP a 50 " --> pdb=" O GLY a 46 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL a 51 " --> pdb=" O LYS a 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 44 through 51' Processing helix chain 'a' and resid 55 through 64 removed outlier: 3.615A pdb=" N PHE a 64 " --> pdb=" O PHE a 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 19 removed outlier: 4.747A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 24 removed outlier: 4.329A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 38 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.858A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 37 removed outlier: 4.484A pdb=" N LYS e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ALA e 37 " --> pdb=" O LEU e 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 32 through 37' Processing helix chain 'e' and resid 38 through 46 removed outlier: 3.711A pdb=" N ARG e 45 " --> pdb=" O LYS e 41 " (cutoff:3.500A) Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 51 through 63 removed outlier: 4.675A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'e' and resid 26 through 31 removed outlier: 4.857A pdb=" N LEU e 29 " --> pdb=" O HIS e 26 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG e 30 " --> pdb=" O ALA e 27 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N HIS e 31 " --> pdb=" O ASN e 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 26 through 31' Processing helix chain 'g' and resid 5 through 13 removed outlier: 4.323A pdb=" N MET g 9 " --> pdb=" O SER g 5 " (cutoff:3.500A) Processing helix chain 'g' and resid 27 through 32 removed outlier: 3.638A pdb=" N ILE g 31 " --> pdb=" O MET g 27 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE g 32 " --> pdb=" O LYS g 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 27 through 32' Processing helix chain 'g' and resid 42 through 64 removed outlier: 3.571A pdb=" N VAL g 47 " --> pdb=" O LEU g 43 " (cutoff:3.500A) Proline residue: g 48 - end of helix removed outlier: 3.541A pdb=" N GLU g 52 " --> pdb=" O PRO g 48 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 88 removed outlier: 5.567A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP g 82 " --> pdb=" O GLU g 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 124 removed outlier: 4.276A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER g 110 " --> pdb=" O THR g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 125 through 130 removed outlier: 4.657A pdb=" N THR g 130 " --> pdb=" O PHE g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 148 removed outlier: 3.667A pdb=" N SER g 147 " --> pdb=" O LYS g 143 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 170 removed outlier: 3.525A pdb=" N HIS g 170 " --> pdb=" O ALA g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 180 Processing helix chain 'g' and resid 206 through 227 removed outlier: 3.574A pdb=" N SER g 226 " --> pdb=" O ARG g 222 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 12 removed outlier: 4.088A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 48 removed outlier: 4.389A pdb=" N ALA h 30 " --> pdb=" O THR h 26 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP h 31 " --> pdb=" O LYS h 27 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA h 48 " --> pdb=" O THR h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 Processing helix chain 'h' and resid 82 through 96 Processing helix chain 'h' and resid 108 through 113 removed outlier: 4.248A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 Processing helix chain 'h' and resid 129 through 145 Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.303A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU i 15 " --> pdb=" O LEU i 11 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 removed outlier: 3.738A pdb=" N LYS i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 66 removed outlier: 3.558A pdb=" N VAL i 61 " --> pdb=" O GLU i 57 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 5.651A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 3.761A pdb=" N LEU i 91 " --> pdb=" O GLY i 87 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG i 97 " --> pdb=" O LEU i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 106 removed outlier: 3.595A pdb=" N TYR i 103 " --> pdb=" O ASP i 99 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 121 removed outlier: 3.732A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 151 removed outlier: 4.763A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.640A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 3.550A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 187 through 192' Processing helix chain 'i' and resid 196 through 206 removed outlier: 4.070A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER i 205 " --> pdb=" O VAL i 201 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.578A pdb=" N ARG j 69 " --> pdb=" O GLU j 65 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 4.338A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU j 116 " --> pdb=" O ARG j 112 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY j 119 " --> pdb=" O LEU j 115 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 147 removed outlier: 4.051A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'j' and resid 160 through 165 Processing helix chain 'k' and resid 11 through 19 removed outlier: 3.711A pdb=" N SER k 15 " --> pdb=" O HIS k 11 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLU k 16 " --> pdb=" O PRO k 12 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN k 17 " --> pdb=" O ASP k 13 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL k 18 " --> pdb=" O GLN k 14 " (cutoff:3.500A) Proline residue: k 19 - end of helix No H-bonds generated for 'chain 'k' and resid 11 through 19' Processing helix chain 'k' and resid 20 through 33 removed outlier: 3.840A pdb=" N GLU k 33 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 81 removed outlier: 3.518A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU k 73 " --> pdb=" O GLU k 69 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR k 77 " --> pdb=" O GLU k 73 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 removed outlier: 3.575A pdb=" N PHE l 26 " --> pdb=" O LEU l 22 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.750A pdb=" N ARG l 53 " --> pdb=" O THR l 49 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER l 54 " --> pdb=" O LEU l 50 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.716A pdb=" N ASN l 68 " --> pdb=" O VAL l 64 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 112 removed outlier: 3.957A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA l 98 " --> pdb=" O VAL l 94 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG l 111 " --> pdb=" O ALA l 107 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLY l 112 " --> pdb=" O ALA l 108 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 Processing helix chain 'l' and resid 132 through 149 removed outlier: 3.501A pdb=" N ASN l 148 " --> pdb=" O MET l 144 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS l 149 " --> pdb=" O ALA l 145 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 30 through 44 Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 40 removed outlier: 4.352A pdb=" N GLY n 40 " --> pdb=" O GLU n 36 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 56 removed outlier: 3.510A pdb=" N VAL n 47 " --> pdb=" O THR n 43 " (cutoff:3.500A) Proline residue: n 51 - end of helix removed outlier: 4.031A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 92 Processing helix chain 'n' and resid 94 through 102 removed outlier: 3.630A pdb=" N LYS n 100 " --> pdb=" O SER n 96 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.743A pdb=" N ILE o 18 " --> pdb=" O ASP o 14 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU o 27 " --> pdb=" O ALA o 23 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 91 removed outlier: 3.921A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA o 86 " --> pdb=" O LYS o 82 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.267A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 4.051A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 54 through 59' Processing helix chain 'p' and resid 60 through 75 removed outlier: 3.510A pdb=" N ASP p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA p 73 " --> pdb=" O ARG p 69 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL p 74 " --> pdb=" O CYS p 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 93 through 104 removed outlier: 4.071A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 10 Processing helix chain 'q' and resid 113 through 118 removed outlier: 3.860A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.799A pdb=" N THR r 20 " --> pdb=" O VAL r 16 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 Processing helix chain 'r' and resid 49 through 64 removed outlier: 4.064A pdb=" N LYS r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.530A pdb=" N LEU r 80 " --> pdb=" O SER r 76 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 21 removed outlier: 3.724A pdb=" N VAL s 14 " --> pdb=" O GLU s 10 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 33 removed outlier: 3.652A pdb=" N LYS s 28 " --> pdb=" O ARG s 24 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA s 29 " --> pdb=" O ALA s 25 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 51 removed outlier: 3.756A pdb=" N GLN s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Processing helix chain 's' and resid 80 through 91 removed outlier: 3.566A pdb=" N ARG s 85 " --> pdb=" O ARG s 81 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU s 86 " --> pdb=" O ILE s 82 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 44 removed outlier: 3.568A pdb=" N GLN t 35 " --> pdb=" O LEU t 31 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 3.865A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 removed outlier: 3.683A pdb=" N GLU t 83 " --> pdb=" O THR t 79 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 64 Processing helix chain 'u' and resid 68 through 82 removed outlier: 3.563A pdb=" N LYS u 76 " --> pdb=" O ALA u 72 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA u 82 " --> pdb=" O VAL u 78 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 17 Processing helix chain 'w' and resid 25 through 34 removed outlier: 4.261A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE w 33 " --> pdb=" O LEU w 29 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 Processing helix chain 'w' and resid 48 through 66 removed outlier: 3.505A pdb=" N GLN w 54 " --> pdb=" O LYS w 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 removed outlier: 3.613A pdb=" N LYS x 18 " --> pdb=" O HIS x 14 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU x 24 " --> pdb=" O GLU x 20 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER x 25 " --> pdb=" O LYS x 21 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.501A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 70 through 76' Processing helix chain 'y' and resid 4 through 41 removed outlier: 3.521A pdb=" N ILE y 12 " --> pdb=" O LYS y 8 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 44 through 65 removed outlier: 3.504A pdb=" N GLU y 53 " --> pdb=" O LYS y 49 " (cutoff:3.500A) Proline residue: y 56 - end of helix removed outlier: 3.596A pdb=" N ARG y 60 " --> pdb=" O PRO y 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA y 63 " --> pdb=" O ASP y 59 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY y 65 " --> pdb=" O GLN y 61 " (cutoff:3.500A) Processing helix chain 'y' and resid 68 through 87 removed outlier: 3.542A pdb=" N LEU y 86 " --> pdb=" O GLN y 82 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ALA y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 removed outlier: 3.549A pdb=" N ARG z 18 " --> pdb=" O VAL z 14 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 37 removed outlier: 3.511A pdb=" N GLU z 36 " --> pdb=" O VAL z 32 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 66 removed outlier: 3.648A pdb=" N LYS z 58 " --> pdb=" O LYS z 54 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS z 59 " --> pdb=" O ARG z 55 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU z 63 " --> pdb=" O LYS z 59 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN z 64 " --> pdb=" O LEU z 60 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA z 65 " --> pdb=" O ALA z 61 " (cutoff:3.500A) Processing helix chain 'AA' and resid 47 through 58 Processing helix chain 'AA' and resid 114 through 127 removed outlier: 3.590A pdb=" N PHEAA 122 " --> pdb=" O LEUAA 118 " (cutoff:3.500A) Processing helix chain 'BB' and resid 47 through 58 Processing helix chain 'BB' and resid 114 through 127 Processing helix chain 'CC' and resid 47 through 58 Processing helix chain 'CC' and resid 114 through 127 Processing sheet with id= 1, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.601A pdb=" N ARG B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY B 127 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLN B 117 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.474A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 90 through 96 removed outlier: 5.582A pdb=" N ASN B 90 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 3 through 9 removed outlier: 4.480A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 10 through 16 removed outlier: 3.706A pdb=" N GLY C 10 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 79 through 84 removed outlier: 5.842A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN C 94 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 1 through 6 removed outlier: 3.869A pdb=" N VAL D 14 " --> pdb=" O MET D 1 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 42 through 46 removed outlier: 4.739A pdb=" N GLY D 42 " --> pdb=" O GLN D 90 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ARG D 44 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG D 88 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLN D 46 " --> pdb=" O ALA D 86 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ALA D 86 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.418A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 65 through 69 removed outlier: 3.562A pdb=" N LYS E 33 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 152 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 12, first strand: chain 'F' and resid 41 through 45 Processing sheet with id= 13, first strand: chain 'F' and resid 94 through 99 removed outlier: 6.945A pdb=" N ASN F 101 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL F 113 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 121 through 126 removed outlier: 6.677A pdb=" N GLU F 130 " --> pdb=" O PRO F 126 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 17 through 21 removed outlier: 4.210A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLN G 2 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 76 through 82 removed outlier: 5.453A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 18, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.599A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 56 through 60 removed outlier: 4.596A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.005A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.700A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 73 through 76 removed outlier: 6.781A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN M 88 " --> pdb=" O GLU M 75 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.944A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.882A pdb=" N ARG N 103 " --> pdb=" O ASN N 107 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLY N 101 " --> pdb=" O PRO N 109 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA N 111 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS N 99 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE N 113 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE N 97 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU N 115 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR N 95 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.717A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.261A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.691A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.627A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.038A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 32, first strand: chain 'R' and resid 65 through 68 Processing sheet with id= 33, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.101A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'S' and resid 2 through 8 Processing sheet with id= 35, first strand: chain 'T' and resid 29 through 33 removed outlier: 4.477A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'U' and resid 40 through 44 No H-bonds generated for sheet with id= 36 Processing sheet with id= 37, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 38, first strand: chain 'V' and resid 69 through 72 removed outlier: 6.614A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'W' and resid 51 through 54 removed outlier: 4.178A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'W' and resid 66 through 71 Processing sheet with id= 41, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.665A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'X' and resid 35 through 41 Processing sheet with id= 43, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.276A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'a' and resid 20 through 25 removed outlier: 4.168A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'b' and resid 29 through 32 removed outlier: 4.162A pdb=" N GLU b 36 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'c' and resid 19 through 26 removed outlier: 6.383A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE c 48 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.812A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.548A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'g' and resid 67 through 71 Processing sheet with id= 50, first strand: chain 'h' and resid 53 through 59 removed outlier: 3.581A pdb=" N ARG h 54 " --> pdb=" O HIS h 69 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.707A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY h 194 " --> pdb=" O THR h 191 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'i' and resid 141 through 145 removed outlier: 6.710A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.622A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.870A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'j' and resid 32 through 41 removed outlier: 7.073A pdb=" N ARG j 45 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'k' and resid 38 through 42 removed outlier: 5.552A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'k' and resid 43 through 47 removed outlier: 3.630A pdb=" N GLY k 43 " --> pdb=" O TYR k 59 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'l' and resid 72 through 79 removed outlier: 6.658A pdb=" N THR l 72 " --> pdb=" O VAL l 91 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.728A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'm' and resid 74 through 77 removed outlier: 3.620A pdb=" N SER m 74 " --> pdb=" O ALA m 130 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS m 127 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'n' and resid 5 through 11 removed outlier: 4.094A pdb=" N LYS n 27 " --> pdb=" O LEU n 61 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'o' and resid 36 through 40 removed outlier: 7.016A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG o 7 " --> pdb=" O SER o 101 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'o' and resid 44 through 52 Processing sheet with id= 64, first strand: chain 'p' and resid 30 through 35 Processing sheet with id= 65, first strand: chain 'q' and resid 29 through 32 removed outlier: 5.041A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'q' and resid 36 through 41 removed outlier: 5.036A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'u' and resid 4 through 10 removed outlier: 4.019A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLY u 49 " --> pdb=" O ASN u 40 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'v' and resid 7 through 11 removed outlier: 6.698A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER v 72 " --> pdb=" O CYS v 64 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'v' and resid 19 through 30 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 'x' and resid 30 through 33 removed outlier: 4.548A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'AA' and resid 24 through 30 removed outlier: 3.646A pdb=" N HISAA 15 " --> pdb=" O PHEAA 30 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THRAA 88 " --> pdb=" O ARGAA 81 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VALAA 87 " --> pdb=" O TRPAA 108 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYSAA 106 " --> pdb=" O METAA 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VALAA 91 " --> pdb=" O VALAA 104 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VALAA 104 " --> pdb=" O VALAA 91 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'AA' and resid 36 through 39 removed outlier: 6.370A pdb=" N TRPAA 36 " --> pdb=" O HISAA 136 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'BB' and resid 36 through 42 Processing sheet with id= 74, first strand: chain 'CC' and resid 104 through 109 removed outlier: 3.831A pdb=" N VALCC 104 " --> pdb=" O VALCC 91 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VALCC 91 " --> pdb=" O VALCC 104 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYSCC 106 " --> pdb=" O METCC 89 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N METCC 89 " --> pdb=" O LYSCC 106 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TRPCC 36 " --> pdb=" O HISCC 136 " (cutoff:3.500A) 2008 hydrogen bonds defined for protein. 5931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3700 hydrogen bonds 5750 hydrogen bond angles 0 basepair planarities 1490 basepair parallelities 2552 stacking parallelities Total time for adding SS restraints: 260.77 Time building geometry restraints manager: 62.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.51: 125404 1.51 - 1.88: 36772 1.88 - 2.25: 0 2.25 - 2.61: 0 2.61 - 2.98: 1 Bond restraints: 162177 Sorted by residual: bond pdb=" O3' G 21276 " pdb=" P C 21277 " ideal model delta sigma weight residual 1.607 2.978 -1.371 1.50e-02 4.44e+03 8.35e+03 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.438 -0.283 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C5 5MU 5 54 " pdb=" C6 5MU 5 54 " ideal model delta sigma weight residual 1.155 1.433 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.155 1.429 -0.274 2.00e-02 2.50e+03 1.87e+02 bond pdb=" C4 5MU 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.802 1.593 0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 162172 not shown) Histogram of bond angle deviations from ideal: 65.48 - 86.86: 2 86.86 - 108.25: 48155 108.25 - 129.64: 190444 129.64 - 151.03: 3363 151.03 - 172.41: 1 Bond angle restraints: 241965 Sorted by residual: angle pdb=" O3' G 21276 " pdb=" P C 21277 " pdb=" OP2 C 21277 " ideal model delta sigma weight residual 108.00 172.41 -64.41 3.00e+00 1.11e-01 4.61e+02 angle pdb=" O3' G 21276 " pdb=" P C 21277 " pdb=" O5' C 21277 " ideal model delta sigma weight residual 104.00 74.40 29.60 1.50e+00 4.44e-01 3.89e+02 angle pdb=" O3' G 21276 " pdb=" P C 21277 " pdb=" OP1 C 21277 " ideal model delta sigma weight residual 108.00 65.48 42.52 3.00e+00 1.11e-01 2.01e+02 angle pdb=" C3' G 21276 " pdb=" O3' G 21276 " pdb=" P C 21277 " ideal model delta sigma weight residual 120.20 99.20 21.00 1.50e+00 4.44e-01 1.96e+02 angle pdb=" C1' OMG 12251 " pdb=" N9 OMG 12251 " pdb=" C4 OMG 12251 " ideal model delta sigma weight residual 108.29 145.87 -37.58 3.00e+00 1.11e-01 1.57e+02 ... (remaining 241960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 91640 35.89 - 71.79: 10619 71.79 - 107.68: 1257 107.68 - 143.57: 10 143.57 - 179.46: 34 Dihedral angle restraints: 103560 sinusoidal: 85408 harmonic: 18152 Sorted by residual: dihedral pdb=" O4' U 2 632 " pdb=" C1' U 2 632 " pdb=" N1 U 2 632 " pdb=" C2 U 2 632 " ideal model delta sinusoidal sigma weight residual 200.00 27.26 172.74 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U 1 138 " pdb=" C1' U 1 138 " pdb=" N1 U 1 138 " pdb=" C2 U 1 138 " ideal model delta sinusoidal sigma weight residual 200.00 30.49 169.51 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' U 2 467 " pdb=" C1' U 2 467 " pdb=" N1 U 2 467 " pdb=" C2 U 2 467 " ideal model delta sinusoidal sigma weight residual 200.00 42.56 157.44 1 1.50e+01 4.44e-03 8.21e+01 ... (remaining 103557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 26702 0.070 - 0.141: 3698 0.141 - 0.211: 262 0.211 - 0.282: 37 0.282 - 0.352: 7 Chirality restraints: 30706 Sorted by residual: chirality pdb=" C1' G 1 748 " pdb=" O4' G 1 748 " pdb=" C2' G 1 748 " pdb=" N9 G 1 748 " both_signs ideal model delta sigma weight residual False 2.46 2.11 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C1' G 1 512 " pdb=" O4' G 1 512 " pdb=" C2' G 1 512 " pdb=" N9 G 1 512 " both_signs ideal model delta sigma weight residual False 2.44 2.10 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB 0TD q 89 " pdb=" CA 0TD q 89 " pdb=" SB 0TD q 89 " pdb=" CG 0TD q 89 " both_signs ideal model delta sigma weight residual False 3.04 2.71 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 30703 not shown) Planarity restraints: 13418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG 2 527 " 0.088 2.00e-02 2.50e+03 6.39e-01 9.20e+03 pdb=" C4' 7MG 2 527 " 0.471 2.00e-02 2.50e+03 pdb=" O4' 7MG 2 527 " 0.757 2.00e-02 2.50e+03 pdb=" C3' 7MG 2 527 " -0.590 2.00e-02 2.50e+03 pdb=" O3' 7MG 2 527 " -0.662 2.00e-02 2.50e+03 pdb=" C2' 7MG 2 527 " -0.190 2.00e-02 2.50e+03 pdb=" O2' 7MG 2 527 " 0.981 2.00e-02 2.50e+03 pdb=" C1' 7MG 2 527 " 0.175 2.00e-02 2.50e+03 pdb=" N9 7MG 2 527 " -1.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 12445 " 0.035 2.00e-02 2.50e+03 6.13e-01 8.45e+03 pdb=" C4' 2MG 12445 " 0.468 2.00e-02 2.50e+03 pdb=" O4' 2MG 12445 " 0.795 2.00e-02 2.50e+03 pdb=" C3' 2MG 12445 " -0.591 2.00e-02 2.50e+03 pdb=" O3' 2MG 12445 " -0.594 2.00e-02 2.50e+03 pdb=" C2' 2MG 12445 " -0.233 2.00e-02 2.50e+03 pdb=" O2' 2MG 12445 " 0.900 2.00e-02 2.50e+03 pdb=" C1' 2MG 12445 " 0.183 2.00e-02 2.50e+03 pdb=" N9 2MG 12445 " -0.963 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " 0.060 2.00e-02 2.50e+03 6.04e-01 8.21e+03 pdb=" C4' 2MG 21207 " 0.448 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " 0.676 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " -0.593 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " -0.628 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " -0.189 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " 0.955 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " 0.213 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " -0.940 2.00e-02 2.50e+03 ... (remaining 13415 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.90: 21 1.90 - 2.65: 6035 2.65 - 3.40: 175517 3.40 - 4.15: 510113 4.15 - 4.90: 696545 Nonbonded interactions: 1388231 Sorted by model distance: nonbonded pdb="MG MG 21713 " pdb="MG MG 21714 " model vdw 1.145 1.300 nonbonded pdb=" OP1 G 1 962 " pdb="MG MG 13024 " model vdw 1.829 2.170 nonbonded pdb=" OP1 C 12006 " pdb="MG MG 13029 " model vdw 1.833 2.170 nonbonded pdb=" OP1 A 11272 " pdb="MG MG 13030 " model vdw 1.837 2.170 nonbonded pdb=" OP1 U 12074 " pdb="MG MG 13187 " model vdw 1.850 2.170 ... (remaining 1388226 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'AA' and (resid 12 through 45 or resid 47 through 99 or resid 101 through \ 136)) selection = (chain 'BB' and (resid 12 through 45 or resid 47 through 99 or resid 101 through \ 136)) selection = (chain 'CC' and (resid 12 through 45 or resid 47 through 99 or resid 101 through \ 136)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.820 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: 0.140 Extract box with map and model: 22.440 Check model and map are aligned: 1.640 Set scattering table: 1.020 Process input model: 578.110 Find NCS groups from input model: 3.270 Set up NCS constraints: 0.400 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:14.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 626.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 : 0.011 1.371 162177 Z= 0.669 Angle : 0.843 64.412 241965 Z= 0.396 Chirality : 0.048 0.352 30706 Planarity : 0.019 0.639 13418 Dihedral : 22.594 179.464 91843 Min Nonbonded Distance : 1.145 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.58 % Favored : 97.41 % Rotamer: Outliers : 2.95 % Allowed : 8.60 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.09), residues: 6249 helix: -2.37 (0.09), residues: 1995 sheet: -0.69 (0.14), residues: 1292 loop : -1.21 (0.10), residues: 2962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 248 HIS 0.014 0.002 HISAA 22 PHE 0.032 0.003 PHEBB 99 TYR 0.031 0.003 TYR Q 32 ARG 0.021 0.001 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1181 time to evaluate : 6.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.9060 (mtm) cc_final: 0.8791 (mtm) REVERT: C 59 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8050 (mmt90) REVERT: C 97 SER cc_start: 0.8989 (p) cc_final: 0.8608 (p) REVERT: E 44 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8405 (pp) REVERT: E 47 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7534 (mmtt) REVERT: H 118 ILE cc_start: -0.1261 (OUTLIER) cc_final: -0.1554 (tp) REVERT: I 16 MET cc_start: 0.2782 (OUTLIER) cc_final: 0.2512 (tmt) REVERT: I 116 MET cc_start: -0.0215 (tpt) cc_final: -0.0459 (tpt) REVERT: J 1 MET cc_start: 0.6849 (ptt) cc_final: 0.6622 (ptt) REVERT: J 92 MET cc_start: 0.8557 (mmm) cc_final: 0.8242 (mmm) REVERT: J 96 ARG cc_start: 0.7514 (ttm170) cc_final: 0.7202 (ttp80) REVERT: J 103 ILE cc_start: 0.9143 (mt) cc_final: 0.8919 (mt) REVERT: J 136 GLN cc_start: 0.9190 (mt0) cc_final: 0.8892 (mt0) REVERT: N 5 LYS cc_start: 0.8870 (mttt) cc_final: 0.8666 (mttt) REVERT: P 7 GLN cc_start: 0.8413 (tm-30) cc_final: 0.7917 (tm-30) REVERT: P 11 GLU cc_start: 0.8001 (pt0) cc_final: 0.7694 (pt0) REVERT: Q 51 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.8784 (mtm-85) REVERT: Q 89 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: Q 117 LEU cc_start: 0.9221 (mt) cc_final: 0.9014 (mt) REVERT: T 21 SER cc_start: 0.8887 (m) cc_final: 0.8679 (m) REVERT: T 25 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: V 49 ASN cc_start: 0.8976 (m-40) cc_final: 0.8769 (m-40) REVERT: W 56 ASP cc_start: 0.8599 (p0) cc_final: 0.8207 (p0) REVERT: X 44 LYS cc_start: 0.8499 (mptp) cc_final: 0.8282 (mptp) REVERT: Z 54 MET cc_start: 0.9297 (ptm) cc_final: 0.9012 (ptm) REVERT: h 52 VAL cc_start: 0.9336 (OUTLIER) cc_final: 0.9134 (t) REVERT: h 185 ASN cc_start: 0.9291 (t0) cc_final: 0.9015 (t0) REVERT: i 73 ARG cc_start: 0.8328 (ttp-170) cc_final: 0.7857 (ttp-170) REVERT: j 96 MET cc_start: 0.8697 (mtm) cc_final: 0.8489 (mtm) REVERT: j 156 LYS cc_start: 0.9203 (ttpp) cc_final: 0.8995 (ttpp) REVERT: k 17 GLN cc_start: 0.8280 (mp10) cc_final: 0.8059 (mp10) REVERT: k 92 THR cc_start: 0.8991 (m) cc_final: 0.8788 (p) REVERT: r 78 LYS cc_start: 0.9139 (tmmt) cc_final: 0.8830 (tttp) REVERT: t 89 ARG cc_start: 0.7114 (ttp-110) cc_final: 0.6825 (ttp80) REVERT: x 43 ASN cc_start: 0.8976 (p0) cc_final: 0.8730 (p0) REVERT: z 40 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8266 (mtpt) REVERT: AA 74 SER cc_start: 0.8408 (p) cc_final: 0.8147 (p) REVERT: BB 54 PHE cc_start: 0.9235 (t80) cc_final: 0.8894 (t80) outliers start: 153 outliers final: 82 residues processed: 1303 average time/residue: 2.2329 time to fit residues: 4138.3429 Evaluate side-chains 1174 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1084 time to evaluate : 6.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 54 GLN Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain i residue 30 THR Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain k residue 76 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 76 ILE Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 52 VAL Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 39 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain z residue 6 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 905 optimal weight: 1.9990 chunk 812 optimal weight: 4.9990 chunk 450 optimal weight: 3.9990 chunk 277 optimal weight: 0.8980 chunk 548 optimal weight: 0.6980 chunk 434 optimal weight: 4.9990 chunk 840 optimal weight: 5.9990 chunk 325 optimal weight: 8.9990 chunk 510 optimal weight: 0.6980 chunk 625 optimal weight: 5.9990 chunk 973 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN D 195 GLN E 27 GLN E 127 ASN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN O 116 GLN P 41 GLN S 31 GLN T 28 ASN V 12 GLN Y 31 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN g 178 ASN h 3 GLN h 140 ASN i 71 GLN i 152 GLN k 52 ASN k 63 ASN l 142 HIS o 20 GLN o 64 GLN s 4 GLN w 31 ASN w 54 GLN w 74 HIS y 55 GLN y 84 ASN AA 19 GLN AA 40 HIS AA 105 GLN ** BB 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 51 GLN CC 105 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 162177 Z= 0.176 Angle : 0.615 13.682 241965 Z= 0.337 Chirality : 0.036 0.327 30706 Planarity : 0.006 0.136 13418 Dihedral : 23.152 178.758 79505 Min Nonbonded Distance : 1.142 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.95 % Allowed : 14.26 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.96 (0.10), residues: 6249 helix: -0.37 (0.11), residues: 2044 sheet: -0.30 (0.14), residues: 1309 loop : -0.86 (0.11), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 248 HIS 0.008 0.001 HISBB 15 PHE 0.014 0.001 PHE k 8 TYR 0.018 0.002 TYR g 213 ARG 0.008 0.000 ARG f 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1380 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1175 time to evaluate : 6.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7824 (mmt90) REVERT: C 97 SER cc_start: 0.8990 (p) cc_final: 0.8628 (p) REVERT: C 105 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8516 (mtpp) REVERT: D 136 GLN cc_start: 0.8314 (tp40) cc_final: 0.8113 (tp40) REVERT: E 44 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8496 (pp) REVERT: E 140 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: E 145 LYS cc_start: 0.8256 (mmtm) cc_final: 0.8008 (mmtm) REVERT: G 141 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7357 (mmtm) REVERT: H 118 ILE cc_start: -0.1254 (OUTLIER) cc_final: -0.1597 (tp) REVERT: I 116 MET cc_start: -0.0580 (tpt) cc_final: -0.0784 (tpt) REVERT: J 12 LYS cc_start: 0.8080 (tptp) cc_final: 0.7625 (ttpp) REVERT: J 136 GLN cc_start: 0.9178 (mt0) cc_final: 0.8890 (mt0) REVERT: M 78 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8198 (mp) REVERT: O 76 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8648 (ttmm) REVERT: P 11 GLU cc_start: 0.7954 (pt0) cc_final: 0.7734 (pt0) REVERT: Q 51 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8892 (mtm-85) REVERT: T 73 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6776 (ttp-110) REVERT: U 60 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: V 49 ASN cc_start: 0.8934 (m-40) cc_final: 0.8705 (m-40) REVERT: V 87 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8437 (mt0) REVERT: W 25 ARG cc_start: 0.8125 (mmp80) cc_final: 0.7810 (mmt-90) REVERT: W 56 ASP cc_start: 0.8548 (p0) cc_final: 0.8167 (p0) REVERT: X 41 GLU cc_start: 0.7515 (tp30) cc_final: 0.7055 (tp30) REVERT: Y 20 ASN cc_start: 0.8841 (m-40) cc_final: 0.8562 (m110) REVERT: Z 54 MET cc_start: 0.9239 (ptm) cc_final: 0.9036 (ptp) REVERT: a 65 ASN cc_start: 0.6473 (OUTLIER) cc_final: 0.6038 (t0) REVERT: i 73 ARG cc_start: 0.8229 (ttp-170) cc_final: 0.7864 (ttp-170) REVERT: j 156 LYS cc_start: 0.9139 (ttpp) cc_final: 0.8877 (ttpp) REVERT: l 68 ASN cc_start: 0.8867 (m-40) cc_final: 0.8597 (m-40) REVERT: l 116 MET cc_start: 0.8860 (tpt) cc_final: 0.8539 (tpp) REVERT: t 77 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.8060 (mtp180) REVERT: t 89 ARG cc_start: 0.7053 (ttp-110) cc_final: 0.6766 (ttp80) REVERT: u 2 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8491 (t) REVERT: x 43 ASN cc_start: 0.8897 (p0) cc_final: 0.8666 (p0) REVERT: x 69 HIS cc_start: 0.8780 (m-70) cc_final: 0.8524 (m-70) REVERT: z 40 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7892 (mtpt) REVERT: BB 54 PHE cc_start: 0.9201 (t80) cc_final: 0.8996 (t80) REVERT: BB 120 HIS cc_start: 0.7803 (m-70) cc_final: 0.7370 (m-70) outliers start: 205 outliers final: 107 residues processed: 1288 average time/residue: 2.2116 time to fit residues: 4101.8665 Evaluate side-chains 1234 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1114 time to evaluate : 6.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 141 LYS Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain U residue 54 GLN Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain i residue 30 THR Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 21 SER Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain x residue 6 LYS Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain AA residue 17 LEU Chi-restraints excluded: chain AA residue 96 ILE Chi-restraints excluded: chain BB residue 49 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 541 optimal weight: 10.0000 chunk 302 optimal weight: 3.9990 chunk 810 optimal weight: 7.9990 chunk 662 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 975 optimal weight: 20.0000 chunk 1053 optimal weight: 9.9990 chunk 868 optimal weight: 9.9990 chunk 967 optimal weight: 0.0980 chunk 332 optimal weight: 6.9990 chunk 782 optimal weight: 0.4980 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 GLN E 127 ASN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 41 GLN T 28 ASN V 12 GLN Y 31 GLN d 26 ASN d 29 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN h 140 ASN i 152 GLN k 63 ASN l 142 HIS o 64 GLN p 109 ASN ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 35 GLN u 63 GLN v 9 GLN w 74 HIS ** AA 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 40 HIS AA 93 HIS CC 51 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 162177 Z= 0.332 Angle : 0.687 14.820 241965 Z= 0.366 Chirality : 0.040 0.310 30706 Planarity : 0.007 0.144 13418 Dihedral : 23.133 179.705 79468 Min Nonbonded Distance : 1.085 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.75 % Allowed : 16.40 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.10), residues: 6249 helix: 0.36 (0.12), residues: 2028 sheet: -0.10 (0.14), residues: 1310 loop : -0.83 (0.11), residues: 2911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 248 HIS 0.007 0.001 HISBB 15 PHE 0.016 0.002 PHEAA 122 TYR 0.025 0.002 TYRBB 119 ARG 0.013 0.001 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1380 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1133 time to evaluate : 6.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7440 (pt0) REVERT: B 132 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8847 (mtm) REVERT: C 59 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7966 (mmt90) REVERT: C 97 SER cc_start: 0.8995 (p) cc_final: 0.8631 (p) REVERT: C 105 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8541 (mtpp) REVERT: D 136 GLN cc_start: 0.8463 (tp-100) cc_final: 0.8255 (tp40) REVERT: D 184 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7604 (m-30) REVERT: E 44 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8465 (pp) REVERT: E 145 LYS cc_start: 0.8266 (mmtm) cc_final: 0.8026 (mmtm) REVERT: H 118 ILE cc_start: -0.1616 (OUTLIER) cc_final: -0.1893 (tp) REVERT: I 124 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6722 (pmm) REVERT: J 12 LYS cc_start: 0.8064 (tptp) cc_final: 0.7642 (ttpp) REVERT: K 53 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8246 (mmtt) REVERT: L 86 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6914 (mm-30) REVERT: M 78 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8261 (mp) REVERT: O 76 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8686 (ttmm) REVERT: P 11 GLU cc_start: 0.8005 (pt0) cc_final: 0.7715 (pt0) REVERT: Q 51 ARG cc_start: 0.9353 (OUTLIER) cc_final: 0.8818 (mtm-85) REVERT: T 73 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.6693 (ttp-110) REVERT: U 10 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: U 60 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: V 41 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: V 87 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8497 (mt0) REVERT: W 25 ARG cc_start: 0.8135 (mmp80) cc_final: 0.7842 (mmt-90) REVERT: Y 20 ASN cc_start: 0.8736 (m-40) cc_final: 0.8415 (m110) REVERT: a 65 ASN cc_start: 0.6505 (OUTLIER) cc_final: 0.6092 (t0) REVERT: d 25 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7791 (ttpp) REVERT: h 59 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8652 (ptm160) REVERT: i 73 ARG cc_start: 0.8253 (ttp-170) cc_final: 0.7879 (ttp-170) REVERT: j 68 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7940 (mtt180) REVERT: j 156 LYS cc_start: 0.9153 (ttpp) cc_final: 0.8904 (ttpp) REVERT: l 68 ASN cc_start: 0.8893 (m-40) cc_final: 0.8561 (m-40) REVERT: m 85 ILE cc_start: 0.9237 (mm) cc_final: 0.9033 (mm) REVERT: o 40 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8529 (tp) REVERT: p 85 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.7683 (mtm) REVERT: r 75 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7337 (mmm) REVERT: r 78 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8655 (ttmt) REVERT: t 26 GLU cc_start: 0.8386 (mp0) cc_final: 0.8052 (mp0) REVERT: t 77 ARG cc_start: 0.8463 (mtm-85) cc_final: 0.8130 (mtp180) REVERT: t 89 ARG cc_start: 0.7030 (ttp-110) cc_final: 0.6695 (ttp80) REVERT: w 29 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8964 (mp) REVERT: x 43 ASN cc_start: 0.8935 (p0) cc_final: 0.8716 (p0) REVERT: x 69 HIS cc_start: 0.8844 (m-70) cc_final: 0.8548 (m-70) REVERT: z 24 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: BB 28 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8062 (mmm-85) REVERT: BB 54 PHE cc_start: 0.9221 (t80) cc_final: 0.9018 (t80) REVERT: CC 80 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8139 (mm) outliers start: 247 outliers final: 150 residues processed: 1270 average time/residue: 2.2336 time to fit residues: 4048.2068 Evaluate side-chains 1288 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1109 time to evaluate : 6.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 42 ARG Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 54 GLN Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain i residue 30 THR Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 6 ILE Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 76 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 41 SER Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain m residue 96 MET Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 85 MET Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 21 SER Chi-restraints excluded: chain r residue 46 SER Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 78 LYS Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 10 LYS Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 29 LEU Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain x residue 6 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 80 THR Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain z residue 24 GLU Chi-restraints excluded: chain AA residue 17 LEU Chi-restraints excluded: chain AA residue 47 SER Chi-restraints excluded: chain BB residue 28 ARG Chi-restraints excluded: chain BB residue 49 THR Chi-restraints excluded: chain CC residue 80 LEU Chi-restraints excluded: chain CC residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 963 optimal weight: 7.9990 chunk 733 optimal weight: 10.0000 chunk 506 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 465 optimal weight: 30.0000 chunk 654 optimal weight: 6.9990 chunk 978 optimal weight: 5.9990 chunk 1036 optimal weight: 9.9990 chunk 511 optimal weight: 5.9990 chunk 927 optimal weight: 5.9990 chunk 279 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 ASN D 195 GLN E 27 GLN F 104 ASN O 38 GLN S 31 GLN T 28 ASN V 12 GLN Y 31 GLN c 45 GLN d 29 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 140 ASN i 71 GLN i 152 GLN l 142 HIS o 64 GLN ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 63 GLN v 9 GLN w 54 GLN w 74 HIS ** AA 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 34 GLN AA 40 HIS AA 93 HIS ** BB 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 51 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 162177 Z= 0.464 Angle : 0.776 16.362 241965 Z= 0.404 Chirality : 0.045 0.315 30706 Planarity : 0.008 0.150 13418 Dihedral : 23.187 178.600 79465 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.31 % Allowed : 17.36 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.34 (0.10), residues: 6249 helix: 0.53 (0.12), residues: 2028 sheet: 0.03 (0.14), residues: 1249 loop : -0.81 (0.11), residues: 2972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPAA 36 HIS 0.008 0.001 HIS B 15 PHE 0.021 0.002 PHEAA 122 TYR 0.029 0.002 TYRBB 119 ARG 0.016 0.001 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1396 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1120 time to evaluate : 6.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7419 (pt0) REVERT: B 132 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8807 (mtm) REVERT: C 59 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7838 (mmt90) REVERT: C 97 SER cc_start: 0.8999 (p) cc_final: 0.8642 (p) REVERT: C 105 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8568 (mtpp) REVERT: D 136 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8559 (tp40) REVERT: D 184 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7727 (m-30) REVERT: E 44 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8406 (pp) REVERT: I 63 ASP cc_start: 0.4828 (OUTLIER) cc_final: 0.4571 (p0) REVERT: I 116 MET cc_start: -0.0325 (tpt) cc_final: -0.0548 (tpt) REVERT: I 124 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6738 (pmm) REVERT: J 12 LYS cc_start: 0.8111 (tptp) cc_final: 0.7668 (ttpp) REVERT: K 53 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8185 (mmtt) REVERT: L 86 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6914 (mm-30) REVERT: M 110 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: N 18 GLN cc_start: 0.8030 (tt0) cc_final: 0.7771 (tt0) REVERT: O 19 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: O 76 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8696 (ttmm) REVERT: Q 51 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.8934 (mtm-85) REVERT: T 73 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6559 (ttp-110) REVERT: U 10 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: U 60 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: V 41 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7447 (mt-10) REVERT: V 87 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8516 (mt0) REVERT: W 25 ARG cc_start: 0.8161 (mmp80) cc_final: 0.7879 (mmt-90) REVERT: Y 44 LYS cc_start: 0.9166 (ttmm) cc_final: 0.8960 (ttpt) REVERT: a 65 ASN cc_start: 0.6521 (OUTLIER) cc_final: 0.6179 (t0) REVERT: b 12 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7840 (mmmm) REVERT: c 53 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7439 (mttp) REVERT: d 25 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7971 (ttpp) REVERT: h 28 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: h 59 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8730 (ptm160) REVERT: i 73 ARG cc_start: 0.8268 (ttp-170) cc_final: 0.7796 (ttp-170) REVERT: i 178 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7859 (mtm) REVERT: j 156 LYS cc_start: 0.9190 (ttpp) cc_final: 0.8950 (ttpp) REVERT: l 68 ASN cc_start: 0.8942 (m-40) cc_final: 0.8611 (m-40) REVERT: r 75 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7364 (mmm) REVERT: r 78 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8688 (ttmt) REVERT: s 97 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8305 (pttt) REVERT: t 14 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7525 (tm-30) REVERT: t 26 GLU cc_start: 0.8421 (mp0) cc_final: 0.8069 (mp0) REVERT: t 77 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.8160 (mtp180) REVERT: t 84 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8383 (ttt-90) REVERT: t 89 ARG cc_start: 0.7060 (ttp-110) cc_final: 0.6775 (ttp80) REVERT: w 29 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9013 (mp) REVERT: x 43 ASN cc_start: 0.8996 (p0) cc_final: 0.8782 (p0) REVERT: z 24 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: z 34 ARG cc_start: 0.7700 (ptt90) cc_final: 0.7480 (ttp80) REVERT: AA 120 HIS cc_start: 0.7326 (m-70) cc_final: 0.6961 (m-70) REVERT: BB 54 PHE cc_start: 0.9259 (t80) cc_final: 0.9011 (t80) REVERT: BB 116 PHE cc_start: 0.7281 (t80) cc_final: 0.6550 (t80) REVERT: BB 120 HIS cc_start: 0.7600 (m-70) cc_final: 0.7352 (m-70) REVERT: CC 51 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7429 (mt0) REVERT: CC 80 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8097 (mm) outliers start: 276 outliers final: 165 residues processed: 1278 average time/residue: 2.2572 time to fit residues: 4113.8911 Evaluate side-chains 1300 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1102 time to evaluate : 6.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 42 ARG Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 54 GLN Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain a residue 64 PHE Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain b residue 12 LYS Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 28 GLU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain i residue 30 THR Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain i residue 178 MET Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 76 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 41 SER Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 57 LYS Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 21 SER Chi-restraints excluded: chain r residue 46 SER Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 78 LYS Chi-restraints excluded: chain s residue 97 LYS Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 10 LYS Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 84 ARG Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain u residue 77 GLU Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 29 LEU Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain x residue 6 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 80 THR Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain z residue 24 GLU Chi-restraints excluded: chain AA residue 17 LEU Chi-restraints excluded: chain AA residue 69 LEU Chi-restraints excluded: chain BB residue 9 LYS Chi-restraints excluded: chain BB residue 49 THR Chi-restraints excluded: chain CC residue 51 GLN Chi-restraints excluded: chain CC residue 80 LEU Chi-restraints excluded: chain CC residue 101 LEU Chi-restraints excluded: chain CC residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 862 optimal weight: 6.9990 chunk 588 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 771 optimal weight: 10.0000 chunk 427 optimal weight: 5.9990 chunk 884 optimal weight: 6.9990 chunk 716 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 529 optimal weight: 70.0000 chunk 930 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN F 104 ASN O 104 GLN S 31 GLN T 28 ASN V 12 GLN Y 31 GLN d 29 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 140 ASN i 71 GLN i 152 GLN l 142 HIS p 109 ASN ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 35 GLN v 9 GLN w 54 GLN w 74 HIS ** AA 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 93 HIS ** BB 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 51 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 162177 Z= 0.351 Angle : 0.698 14.637 241965 Z= 0.371 Chirality : 0.041 0.305 30706 Planarity : 0.007 0.144 13418 Dihedral : 23.150 179.360 79463 Min Nonbonded Distance : 1.086 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.87 % Allowed : 18.78 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.18 (0.10), residues: 6249 helix: 0.72 (0.12), residues: 2029 sheet: 0.07 (0.14), residues: 1274 loop : -0.75 (0.11), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPAA 36 HIS 0.007 0.001 HISBB 15 PHE 0.026 0.002 PHEAA 122 TYR 0.027 0.002 TYRBB 119 ARG 0.011 0.001 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1116 time to evaluate : 6.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7381 (pt0) REVERT: B 132 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8809 (mtm) REVERT: C 59 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7819 (mtt90) REVERT: C 97 SER cc_start: 0.9000 (p) cc_final: 0.8650 (p) REVERT: D 136 GLN cc_start: 0.8732 (tp-100) cc_final: 0.8517 (tp40) REVERT: D 184 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: E 44 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8457 (pp) REVERT: E 165 GLU cc_start: 0.8808 (mp0) cc_final: 0.8439 (mp0) REVERT: I 63 ASP cc_start: 0.4818 (OUTLIER) cc_final: 0.4560 (p0) REVERT: I 124 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6634 (pmm) REVERT: J 12 LYS cc_start: 0.8045 (tptp) cc_final: 0.7612 (ttpp) REVERT: K 53 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8179 (mmtt) REVERT: K 114 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7993 (ttpp) REVERT: L 86 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6907 (mm-30) REVERT: M 78 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8348 (mp) REVERT: N 18 GLN cc_start: 0.7976 (tt0) cc_final: 0.7734 (tt0) REVERT: O 19 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: O 76 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8672 (ttmm) REVERT: Q 51 ARG cc_start: 0.9353 (OUTLIER) cc_final: 0.8955 (mtm-85) REVERT: T 73 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6409 (mtp-110) REVERT: U 10 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: U 60 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: V 41 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: V 87 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8510 (mt0) REVERT: W 25 ARG cc_start: 0.8131 (mmp80) cc_final: 0.7873 (mmt-90) REVERT: a 65 ASN cc_start: 0.6514 (OUTLIER) cc_final: 0.6154 (t0) REVERT: b 12 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7870 (mmmm) REVERT: c 53 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7489 (mttp) REVERT: d 25 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7814 (ttpp) REVERT: h 28 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: h 59 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8698 (ptm160) REVERT: i 73 ARG cc_start: 0.8250 (ttp-170) cc_final: 0.7892 (ttp-170) REVERT: j 45 ARG cc_start: 0.8540 (mmm-85) cc_final: 0.8049 (mtp85) REVERT: l 68 ASN cc_start: 0.8908 (m-40) cc_final: 0.8604 (m-40) REVERT: p 85 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7682 (mtm) REVERT: r 75 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7403 (mmm) REVERT: r 78 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8681 (ttmt) REVERT: t 26 GLU cc_start: 0.8380 (mp0) cc_final: 0.8031 (mp0) REVERT: t 77 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8108 (mtp180) REVERT: t 89 ARG cc_start: 0.7055 (ttp-110) cc_final: 0.6801 (ttp80) REVERT: w 29 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9030 (mp) REVERT: x 43 ASN cc_start: 0.8973 (p0) cc_final: 0.8725 (p0) REVERT: z 24 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: z 46 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8858 (ttpm) REVERT: BB 54 PHE cc_start: 0.9243 (t80) cc_final: 0.9035 (t80) REVERT: BB 106 LYS cc_start: 0.8580 (mttp) cc_final: 0.8371 (mttp) REVERT: BB 116 PHE cc_start: 0.7312 (t80) cc_final: 0.6700 (t80) REVERT: BB 120 HIS cc_start: 0.7718 (m-70) cc_final: 0.7422 (m-70) REVERT: CC 80 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8125 (mm) outliers start: 253 outliers final: 162 residues processed: 1256 average time/residue: 2.2906 time to fit residues: 4095.2920 Evaluate side-chains 1294 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1101 time to evaluate : 6.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 166 LYS Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 42 ARG Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 54 GLN Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain a residue 64 PHE Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain b residue 12 LYS Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 28 GLU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain i residue 30 THR Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain j residue 71 MET Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 6 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 76 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 41 SER Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 96 MET Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 85 MET Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 21 SER Chi-restraints excluded: chain r residue 46 SER Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 78 LYS Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain u residue 77 GLU Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 29 LEU Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain x residue 6 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 24 GLU Chi-restraints excluded: chain z residue 46 LYS Chi-restraints excluded: chain BB residue 9 LYS Chi-restraints excluded: chain BB residue 29 ILE Chi-restraints excluded: chain BB residue 49 THR Chi-restraints excluded: chain CC residue 51 GLN Chi-restraints excluded: chain CC residue 80 LEU Chi-restraints excluded: chain CC residue 101 LEU Chi-restraints excluded: chain CC residue 104 VAL Chi-restraints excluded: chain CC residue 110 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 348 optimal weight: 20.0000 chunk 933 optimal weight: 2.9990 chunk 204 optimal weight: 0.3980 chunk 608 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 chunk 1037 optimal weight: 8.9990 chunk 861 optimal weight: 3.9990 chunk 480 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 343 optimal weight: 10.0000 chunk 544 optimal weight: 7.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN K 29 HIS O 104 GLN S 31 GLN S 60 HIS T 28 ASN V 12 GLN Y 31 GLN d 29 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 139 GLN h 140 ASN i 152 GLN l 142 HIS o 20 GLN p 28 ASN ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 9 GLN w 54 GLN w 74 HIS AA 93 HIS ** BB 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 51 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 162177 Z= 0.315 Angle : 0.675 13.729 241965 Z= 0.361 Chirality : 0.040 0.313 30706 Planarity : 0.007 0.142 13418 Dihedral : 23.118 179.934 79460 Min Nonbonded Distance : 1.094 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.12 % Allowed : 19.01 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.05 (0.10), residues: 6249 helix: 0.87 (0.12), residues: 2030 sheet: 0.13 (0.14), residues: 1284 loop : -0.69 (0.11), residues: 2935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 248 HIS 0.007 0.001 HISBB 15 PHE 0.026 0.002 PHEAA 122 TYR 0.025 0.002 TYRBB 119 ARG 0.012 0.001 ARG f 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1378 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1112 time to evaluate : 6.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7371 (pt0) REVERT: B 132 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8851 (mtm) REVERT: C 59 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7829 (mtt90) REVERT: C 97 SER cc_start: 0.8994 (p) cc_final: 0.8642 (p) REVERT: D 136 GLN cc_start: 0.8736 (tp-100) cc_final: 0.8514 (tp40) REVERT: D 184 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7604 (m-30) REVERT: E 44 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8435 (pp) REVERT: E 94 GLU cc_start: 0.7317 (tt0) cc_final: 0.6968 (tm-30) REVERT: E 98 GLU cc_start: 0.8151 (mt-10) cc_final: 0.6923 (mt-10) REVERT: E 165 GLU cc_start: 0.8678 (mp0) cc_final: 0.8194 (mp0) REVERT: I 63 ASP cc_start: 0.4781 (OUTLIER) cc_final: 0.4528 (p0) REVERT: J 12 LYS cc_start: 0.8041 (tptp) cc_final: 0.7603 (ttpp) REVERT: K 53 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8183 (mmtt) REVERT: L 86 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6909 (mm-30) REVERT: M 78 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8320 (mp) REVERT: M 110 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: N 18 GLN cc_start: 0.7968 (tt0) cc_final: 0.7714 (tt0) REVERT: O 19 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: O 76 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8205 (tmmm) REVERT: Q 51 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.8909 (mtm-85) REVERT: Q 59 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: T 73 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.6545 (ttp-110) REVERT: U 10 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: U 60 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: V 41 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: V 87 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8506 (mt0) REVERT: W 25 ARG cc_start: 0.8144 (mmp80) cc_final: 0.7865 (mmt-90) REVERT: a 65 ASN cc_start: 0.6435 (OUTLIER) cc_final: 0.6093 (t0) REVERT: b 12 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7838 (mmmm) REVERT: c 33 LYS cc_start: 0.8432 (mptt) cc_final: 0.8209 (tptt) REVERT: c 53 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7467 (mttp) REVERT: d 25 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7789 (ttpp) REVERT: h 28 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: h 59 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8696 (ptm160) REVERT: i 73 ARG cc_start: 0.8213 (ttp-170) cc_final: 0.7926 (ttp-170) REVERT: j 45 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8075 (mtp85) REVERT: l 68 ASN cc_start: 0.8902 (m-40) cc_final: 0.8609 (m-40) REVERT: l 116 MET cc_start: 0.8911 (tpt) cc_final: 0.8599 (tpp) REVERT: l 126 ASP cc_start: 0.8561 (m-30) cc_final: 0.8274 (m-30) REVERT: p 85 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7730 (mtm) REVERT: q 83 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7958 (ptt-90) REVERT: r 75 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7354 (mmm) REVERT: r 78 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8702 (ttmt) REVERT: s 97 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8315 (pttt) REVERT: t 26 GLU cc_start: 0.8370 (mp0) cc_final: 0.8029 (mp0) REVERT: t 77 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8032 (mtp180) REVERT: t 89 ARG cc_start: 0.7048 (ttp-110) cc_final: 0.6765 (ttp80) REVERT: v 40 ARG cc_start: 0.8370 (mmm160) cc_final: 0.8115 (mmm160) REVERT: w 29 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9025 (mp) REVERT: x 43 ASN cc_start: 0.8928 (p0) cc_final: 0.8698 (p0) REVERT: z 24 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: z 46 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8843 (ttpm) REVERT: BB 54 PHE cc_start: 0.9244 (t80) cc_final: 0.9025 (t80) REVERT: BB 116 PHE cc_start: 0.7254 (t80) cc_final: 0.6685 (t80) REVERT: BB 120 HIS cc_start: 0.7610 (m-70) cc_final: 0.7321 (m-70) outliers start: 266 outliers final: 175 residues processed: 1260 average time/residue: 2.2914 time to fit residues: 4134.2648 Evaluate side-chains 1311 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1103 time to evaluate : 6.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 166 LYS Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 42 ARG Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 59 GLN Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 36 LYS Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 54 GLN Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain a residue 49 ARG Chi-restraints excluded: chain a residue 64 PHE Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain b residue 12 LYS Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain h residue 28 GLU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 71 MET Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 6 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 76 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 41 SER Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 96 MET Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 85 MET Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 21 SER Chi-restraints excluded: chain r residue 46 SER Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 78 LYS Chi-restraints excluded: chain s residue 58 SER Chi-restraints excluded: chain s residue 97 LYS Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 77 ARG Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain u residue 77 GLU Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 29 LEU Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain x residue 6 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 80 THR Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 24 GLU Chi-restraints excluded: chain z residue 46 LYS Chi-restraints excluded: chain AA residue 17 LEU Chi-restraints excluded: chain AA residue 69 LEU Chi-restraints excluded: chain BB residue 9 LYS Chi-restraints excluded: chain BB residue 16 ILE Chi-restraints excluded: chain BB residue 49 THR Chi-restraints excluded: chain CC residue 101 LEU Chi-restraints excluded: chain CC residue 104 VAL Chi-restraints excluded: chain CC residue 110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 999 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 590 optimal weight: 8.9990 chunk 757 optimal weight: 10.0000 chunk 586 optimal weight: 10.0000 chunk 873 optimal weight: 7.9990 chunk 579 optimal weight: 6.9990 chunk 1033 optimal weight: 4.9990 chunk 646 optimal weight: 10.0000 chunk 629 optimal weight: 10.0000 chunk 477 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN K 29 HIS O 104 GLN S 31 GLN T 28 ASN V 12 GLN Y 31 GLN c 45 GLN d 29 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 140 ASN i 71 GLN i 152 GLN l 142 HIS o 20 GLN ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 35 GLN u 63 GLN v 9 GLN w 54 GLN w 74 HIS AA 40 HIS AA 93 HIS BB 32 HIS ** BB 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 125 HIS CC 105 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.105 162177 Z= 0.524 Angle : 0.821 17.347 241965 Z= 0.422 Chirality : 0.047 0.329 30706 Planarity : 0.008 0.153 13418 Dihedral : 23.194 179.512 79455 Min Nonbonded Distance : 1.037 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.19 % Allowed : 19.56 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.20 (0.10), residues: 6249 helix: 0.70 (0.12), residues: 2036 sheet: 0.11 (0.14), residues: 1249 loop : -0.77 (0.11), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 248 HIS 0.011 0.002 HISBB 32 PHE 0.027 0.002 PHEAA 122 TYR 0.030 0.003 TYRBB 119 ARG 0.019 0.001 ARGBB 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1375 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1105 time to evaluate : 5.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: B 132 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8814 (mtm) REVERT: C 59 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7717 (mtt90) REVERT: C 97 SER cc_start: 0.8998 (p) cc_final: 0.8647 (p) REVERT: C 105 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8547 (mtpp) REVERT: D 136 GLN cc_start: 0.8793 (tp-100) cc_final: 0.8555 (tp40) REVERT: D 184 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7724 (m-30) REVERT: E 44 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8391 (pp) REVERT: E 94 GLU cc_start: 0.7349 (tt0) cc_final: 0.7024 (tm-30) REVERT: E 98 GLU cc_start: 0.8169 (mt-10) cc_final: 0.6954 (mt-10) REVERT: E 165 GLU cc_start: 0.8803 (mp0) cc_final: 0.8121 (mp0) REVERT: I 63 ASP cc_start: 0.4674 (OUTLIER) cc_final: 0.4436 (p0) REVERT: K 53 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8147 (mmtt) REVERT: K 67 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.7860 (tmtt) REVERT: L 86 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6916 (mm-30) REVERT: M 78 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8309 (mp) REVERT: M 110 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: N 18 GLN cc_start: 0.8042 (tt0) cc_final: 0.7798 (tt0) REVERT: N 74 GLU cc_start: 0.7920 (tt0) cc_final: 0.7700 (tt0) REVERT: O 19 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: O 76 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8729 (ttmm) REVERT: Q 51 ARG cc_start: 0.9352 (OUTLIER) cc_final: 0.8804 (mtm-85) REVERT: S 62 ASP cc_start: 0.8395 (m-30) cc_final: 0.8184 (m-30) REVERT: T 73 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6395 (mtp-110) REVERT: U 10 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: U 60 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: V 41 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: V 87 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8487 (mt0) REVERT: W 25 ARG cc_start: 0.8188 (mmp80) cc_final: 0.7887 (mmt-90) REVERT: Y 15 ASN cc_start: 0.8921 (m-40) cc_final: 0.8622 (m110) REVERT: Y 44 LYS cc_start: 0.9189 (ttmm) cc_final: 0.8984 (ttpt) REVERT: Z 54 MET cc_start: 0.9321 (ptm) cc_final: 0.9081 (ptm) REVERT: a 65 ASN cc_start: 0.6567 (OUTLIER) cc_final: 0.6167 (t0) REVERT: b 12 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7892 (mmmm) REVERT: c 53 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7498 (mttp) REVERT: d 25 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7983 (ttpp) REVERT: h 3 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: h 28 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: h 59 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8774 (ptm160) REVERT: i 73 ARG cc_start: 0.8246 (ttp-170) cc_final: 0.7666 (ttp-170) REVERT: l 68 ASN cc_start: 0.8985 (m-40) cc_final: 0.8626 (m-40) REVERT: o 31 ARG cc_start: 0.8041 (tmm160) cc_final: 0.7787 (ptt90) REVERT: o 64 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8462 (mt0) REVERT: p 85 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.7661 (mtm) REVERT: q 83 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8108 (ptt-90) REVERT: r 75 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7372 (mmm) REVERT: r 78 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8718 (ttmt) REVERT: s 97 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8314 (pttt) REVERT: t 14 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7294 (tm-30) REVERT: t 26 GLU cc_start: 0.8421 (mp0) cc_final: 0.8112 (mp0) REVERT: t 77 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8187 (mtp180) REVERT: t 84 ARG cc_start: 0.8608 (tpp80) cc_final: 0.8250 (ttt-90) REVERT: t 89 ARG cc_start: 0.6931 (ttp-110) cc_final: 0.6570 (ttp80) REVERT: w 29 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9008 (mp) REVERT: x 43 ASN cc_start: 0.8880 (p0) cc_final: 0.8646 (p0) REVERT: z 24 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: z 46 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8777 (ttpm) REVERT: AA 120 HIS cc_start: 0.7306 (m-70) cc_final: 0.7081 (m-70) REVERT: BB 89 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8112 (ttp) REVERT: BB 116 PHE cc_start: 0.7322 (t80) cc_final: 0.6630 (t80) REVERT: BB 120 HIS cc_start: 0.7738 (m-70) cc_final: 0.7456 (m-70) REVERT: CC 80 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8074 (mm) outliers start: 270 outliers final: 189 residues processed: 1256 average time/residue: 2.2488 time to fit residues: 4022.0344 Evaluate side-chains 1328 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1101 time to evaluate : 6.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 42 ARG Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 36 LYS Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 54 GLN Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 45 ARG Chi-restraints excluded: chain a residue 49 ARG Chi-restraints excluded: chain a residue 64 PHE Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain b residue 12 LYS Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 31 LEU Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain h residue 3 GLN Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 28 GLU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain i residue 30 THR Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 6 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 76 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 41 SER Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 113 ASP Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 101 ILE Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 64 GLN Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 85 MET Chi-restraints excluded: chain p residue 126 LYS Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 21 SER Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 78 LYS Chi-restraints excluded: chain r residue 83 LEU Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 58 SER Chi-restraints excluded: chain s residue 97 LYS Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 10 LYS Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 77 ARG Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain u residue 77 GLU Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 29 LEU Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain x residue 6 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 80 THR Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 24 GLU Chi-restraints excluded: chain z residue 46 LYS Chi-restraints excluded: chain AA residue 17 LEU Chi-restraints excluded: chain AA residue 69 LEU Chi-restraints excluded: chain BB residue 9 LYS Chi-restraints excluded: chain BB residue 16 ILE Chi-restraints excluded: chain BB residue 19 GLN Chi-restraints excluded: chain BB residue 29 ILE Chi-restraints excluded: chain BB residue 49 THR Chi-restraints excluded: chain BB residue 89 MET Chi-restraints excluded: chain CC residue 80 LEU Chi-restraints excluded: chain CC residue 101 LEU Chi-restraints excluded: chain CC residue 104 VAL Chi-restraints excluded: chain CC residue 110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 639 optimal weight: 6.9990 chunk 412 optimal weight: 2.9990 chunk 617 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 656 optimal weight: 5.9990 chunk 703 optimal weight: 10.0000 chunk 510 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 812 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN G 73 ASN K 29 HIS O 38 GLN O 104 GLN Q 20 GLN S 31 GLN T 28 ASN V 12 GLN Y 31 GLN a 33 ASN d 29 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 140 ASN i 152 GLN l 142 HIS ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 63 GLN v 9 GLN w 54 GLN w 74 HIS ** AA 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 93 HIS ** BB 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 125 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 162177 Z= 0.248 Angle : 0.637 14.829 241965 Z= 0.345 Chirality : 0.038 0.320 30706 Planarity : 0.006 0.138 13418 Dihedral : 23.094 179.506 79453 Min Nonbonded Distance : 1.114 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.41 % Allowed : 21.12 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: 0.06 (0.10), residues: 6249 helix: 1.00 (0.12), residues: 2027 sheet: 0.16 (0.14), residues: 1267 loop : -0.64 (0.11), residues: 2955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRPAA 36 HIS 0.007 0.001 HISBB 15 PHE 0.027 0.001 PHEAA 122 TYR 0.033 0.002 TYR E 83 ARG 0.018 0.001 ARGBB 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1126 time to evaluate : 6.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: B 132 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8885 (mtm) REVERT: C 59 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7832 (mtt90) REVERT: C 97 SER cc_start: 0.8975 (p) cc_final: 0.8629 (p) REVERT: D 136 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8496 (tp40) REVERT: D 152 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7907 (pp20) REVERT: D 184 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: E 44 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8442 (pp) REVERT: E 94 GLU cc_start: 0.7294 (tt0) cc_final: 0.6927 (tm-30) REVERT: E 98 GLU cc_start: 0.8119 (mt-10) cc_final: 0.6829 (mt-10) REVERT: E 165 GLU cc_start: 0.8747 (mp0) cc_final: 0.8158 (mp0) REVERT: G 57 LYS cc_start: 0.8249 (mmpt) cc_final: 0.8039 (mmtt) REVERT: G 66 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7197 (t0) REVERT: I 63 ASP cc_start: 0.4559 (OUTLIER) cc_final: 0.4324 (p0) REVERT: J 12 LYS cc_start: 0.8024 (tptp) cc_final: 0.7592 (ttpp) REVERT: L 86 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6878 (mm-30) REVERT: M 78 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8304 (mp) REVERT: M 110 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: N 18 GLN cc_start: 0.7952 (tt0) cc_final: 0.7715 (tt0) REVERT: O 19 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: Q 51 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.8924 (mtm-85) REVERT: T 73 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.6500 (ttp-110) REVERT: U 10 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: U 29 LEU cc_start: 0.8415 (mt) cc_final: 0.8122 (mp) REVERT: U 60 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: V 41 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: V 87 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8516 (mt0) REVERT: W 25 ARG cc_start: 0.8131 (mmp80) cc_final: 0.7858 (mmt-90) REVERT: Y 9 LYS cc_start: 0.8989 (mmtp) cc_final: 0.8669 (mmtp) REVERT: Z 54 MET cc_start: 0.9250 (ptm) cc_final: 0.8941 (ptm) REVERT: a 65 ASN cc_start: 0.6416 (OUTLIER) cc_final: 0.6094 (t0) REVERT: b 12 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7830 (mmmm) REVERT: c 33 LYS cc_start: 0.8451 (mptt) cc_final: 0.8204 (tptt) REVERT: d 25 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7734 (ttpp) REVERT: h 3 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7825 (mt0) REVERT: h 28 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: h 59 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8676 (ptm160) REVERT: i 73 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.7908 (ttp-170) REVERT: k 79 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.7830 (ttm110) REVERT: l 68 ASN cc_start: 0.8904 (m-40) cc_final: 0.8613 (m-40) REVERT: l 110 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8790 (ptpp) REVERT: l 116 MET cc_start: 0.8916 (tpt) cc_final: 0.8627 (tpp) REVERT: l 126 ASP cc_start: 0.8504 (m-30) cc_final: 0.8261 (m-30) REVERT: p 85 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7694 (mtm) REVERT: q 83 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7674 (ptt-90) REVERT: r 75 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7359 (mmm) REVERT: r 78 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8689 (ttmt) REVERT: s 97 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8313 (pttt) REVERT: t 14 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7268 (tm-30) REVERT: t 26 GLU cc_start: 0.8353 (mp0) cc_final: 0.8012 (mp0) REVERT: t 77 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8045 (mtp180) REVERT: t 84 ARG cc_start: 0.8626 (tpp80) cc_final: 0.8096 (ttt-90) REVERT: t 89 ARG cc_start: 0.6974 (ttp-110) cc_final: 0.6646 (ttp80) REVERT: w 29 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9024 (mp) REVERT: y 80 THR cc_start: 0.9022 (m) cc_final: 0.8743 (m) REVERT: z 24 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: z 46 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8835 (ttpm) REVERT: AA 116 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6961 (t80) REVERT: AA 120 HIS cc_start: 0.7256 (m-70) cc_final: 0.5947 (m-70) REVERT: BB 50 LYS cc_start: 0.8825 (mmtm) cc_final: 0.8465 (mptp) REVERT: BB 116 PHE cc_start: 0.7187 (t80) cc_final: 0.6509 (t80) REVERT: BB 120 HIS cc_start: 0.7751 (m-70) cc_final: 0.7113 (m-70) outliers start: 229 outliers final: 160 residues processed: 1260 average time/residue: 2.2841 time to fit residues: 4107.9886 Evaluate side-chains 1303 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1110 time to evaluate : 6.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 42 ARG Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 36 LYS Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 54 GLN Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain a residue 49 ARG Chi-restraints excluded: chain a residue 64 PHE Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain b residue 12 LYS Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain h residue 3 GLN Chi-restraints excluded: chain h residue 28 GLU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain i residue 30 THR Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 76 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 110 LYS Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 101 ILE Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 85 MET Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 21 SER Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 78 LYS Chi-restraints excluded: chain r residue 83 LEU Chi-restraints excluded: chain s residue 58 SER Chi-restraints excluded: chain s residue 97 LYS Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain u residue 77 GLU Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 29 LEU Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain x residue 6 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain z residue 24 GLU Chi-restraints excluded: chain z residue 46 LYS Chi-restraints excluded: chain AA residue 17 LEU Chi-restraints excluded: chain AA residue 69 LEU Chi-restraints excluded: chain AA residue 116 PHE Chi-restraints excluded: chain BB residue 16 ILE Chi-restraints excluded: chain BB residue 19 GLN Chi-restraints excluded: chain BB residue 49 THR Chi-restraints excluded: chain CC residue 101 LEU Chi-restraints excluded: chain CC residue 104 VAL Chi-restraints excluded: chain CC residue 110 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 939 optimal weight: 8.9990 chunk 989 optimal weight: 0.8980 chunk 903 optimal weight: 7.9990 chunk 962 optimal weight: 4.9990 chunk 579 optimal weight: 7.9990 chunk 419 optimal weight: 50.0000 chunk 756 optimal weight: 10.0000 chunk 295 optimal weight: 5.9990 chunk 870 optimal weight: 10.0000 chunk 910 optimal weight: 6.9990 chunk 959 optimal weight: 2.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN K 29 HIS O 104 GLN Q 20 GLN S 31 GLN T 28 ASN V 12 GLN Y 31 GLN d 29 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 140 ASN i 71 GLN i 152 GLN k 37 HIS l 142 HIS p 109 ASN ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 35 GLN v 9 GLN w 54 GLN w 74 HIS ** AA 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 93 HIS BB 32 HIS ** BB 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 125 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 162177 Z= 0.368 Angle : 0.709 14.616 241965 Z= 0.375 Chirality : 0.041 0.306 30706 Planarity : 0.007 0.145 13418 Dihedral : 23.120 179.625 79453 Min Nonbonded Distance : 1.079 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.31 % Allowed : 21.33 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: 0.03 (0.10), residues: 6249 helix: 0.94 (0.12), residues: 2037 sheet: 0.15 (0.14), residues: 1268 loop : -0.64 (0.11), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRPAA 36 HIS 0.007 0.001 HISBB 15 PHE 0.028 0.002 PHEAA 122 TYR 0.027 0.002 TYR h 42 ARG 0.019 0.001 ARGBB 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1103 time to evaluate : 6.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7390 (pt0) REVERT: B 132 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8860 (mtm) REVERT: C 59 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7922 (mtt90) REVERT: C 97 SER cc_start: 0.8994 (p) cc_final: 0.8647 (p) REVERT: D 136 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8541 (tp40) REVERT: D 184 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: E 44 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8411 (pp) REVERT: E 165 GLU cc_start: 0.8768 (mp0) cc_final: 0.8115 (mp0) REVERT: G 66 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.7013 (t0) REVERT: I 63 ASP cc_start: 0.4597 (OUTLIER) cc_final: 0.4372 (p0) REVERT: J 12 LYS cc_start: 0.8068 (tptp) cc_final: 0.7631 (ttpp) REVERT: K 53 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8190 (mmtt) REVERT: K 114 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8105 (ttpp) REVERT: L 86 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6913 (mm-30) REVERT: M 78 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8333 (mp) REVERT: M 110 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: M 136 MET cc_start: 0.7408 (ttm) cc_final: 0.7102 (ttp) REVERT: N 18 GLN cc_start: 0.7967 (tt0) cc_final: 0.7723 (tt0) REVERT: O 19 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: Q 51 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8865 (mtm-85) REVERT: S 1 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6495 (ttm) REVERT: T 73 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6458 (ttp-110) REVERT: U 10 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: U 60 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7236 (tm-30) REVERT: V 41 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: V 87 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8516 (mt0) REVERT: W 25 ARG cc_start: 0.8167 (mmp80) cc_final: 0.7909 (mmt-90) REVERT: Y 15 ASN cc_start: 0.8908 (m-40) cc_final: 0.8638 (m110) REVERT: Z 54 MET cc_start: 0.9307 (ptm) cc_final: 0.8968 (ptm) REVERT: a 65 ASN cc_start: 0.6492 (OUTLIER) cc_final: 0.6156 (t0) REVERT: b 12 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7865 (mmmm) REVERT: d 25 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7849 (ttpp) REVERT: h 3 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7779 (mt0) REVERT: h 28 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: i 73 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.7796 (ttp-170) REVERT: k 88 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8581 (ttm) REVERT: l 68 ASN cc_start: 0.8946 (m-40) cc_final: 0.8616 (m-40) REVERT: l 116 MET cc_start: 0.8949 (tpt) cc_final: 0.8673 (tpp) REVERT: l 126 ASP cc_start: 0.8410 (m-30) cc_final: 0.8202 (m-30) REVERT: p 85 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7717 (mtm) REVERT: q 83 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8019 (ptt-90) REVERT: r 75 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7373 (mmm) REVERT: r 78 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8694 (ttmt) REVERT: s 97 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8314 (pttt) REVERT: t 14 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7333 (tm-30) REVERT: t 26 GLU cc_start: 0.8384 (mp0) cc_final: 0.8039 (mp0) REVERT: t 77 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8121 (mtp180) REVERT: t 84 ARG cc_start: 0.8626 (tpp80) cc_final: 0.8018 (ttt-90) REVERT: t 89 ARG cc_start: 0.6918 (ttp-110) cc_final: 0.6568 (ttp80) REVERT: w 29 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9032 (mp) REVERT: z 24 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: z 46 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8873 (ttpm) REVERT: AA 116 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6976 (t80) REVERT: AA 120 HIS cc_start: 0.7419 (m-70) cc_final: 0.6168 (m-70) REVERT: BB 116 PHE cc_start: 0.7203 (t80) cc_final: 0.6568 (t80) REVERT: BB 120 HIS cc_start: 0.7794 (m-70) cc_final: 0.7536 (m-70) outliers start: 224 outliers final: 165 residues processed: 1234 average time/residue: 2.2838 time to fit residues: 4008.9160 Evaluate side-chains 1299 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1099 time to evaluate : 6.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 36 LYS Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 94 ASP Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 54 GLN Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 45 ARG Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 49 ARG Chi-restraints excluded: chain a residue 64 PHE Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain b residue 12 LYS Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain h residue 3 GLN Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 28 GLU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain i residue 30 THR Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 76 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 101 ILE Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 85 MET Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 21 SER Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 78 LYS Chi-restraints excluded: chain s residue 58 SER Chi-restraints excluded: chain s residue 97 LYS Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 77 ARG Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain u residue 77 GLU Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 29 LEU Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain x residue 6 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain z residue 24 GLU Chi-restraints excluded: chain z residue 46 LYS Chi-restraints excluded: chain AA residue 17 LEU Chi-restraints excluded: chain AA residue 69 LEU Chi-restraints excluded: chain AA residue 116 PHE Chi-restraints excluded: chain BB residue 16 ILE Chi-restraints excluded: chain BB residue 19 GLN Chi-restraints excluded: chain BB residue 49 THR Chi-restraints excluded: chain CC residue 101 LEU Chi-restraints excluded: chain CC residue 104 VAL Chi-restraints excluded: chain CC residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 632 optimal weight: 6.9990 chunk 1018 optimal weight: 5.9990 chunk 621 optimal weight: 10.0000 chunk 483 optimal weight: 10.0000 chunk 707 optimal weight: 8.9990 chunk 1067 optimal weight: 30.0000 chunk 982 optimal weight: 8.9990 chunk 850 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 656 optimal weight: 7.9990 chunk 521 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN K 29 HIS O 104 GLN Q 20 GLN S 31 GLN T 28 ASN Y 31 GLN d 29 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 140 ASN k 37 HIS l 142 HIS ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 9 GLN w 54 GLN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 93 HIS ** BB 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 125 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 162177 Z= 0.493 Angle : 0.799 16.385 241965 Z= 0.413 Chirality : 0.046 0.318 30706 Planarity : 0.008 0.152 13418 Dihedral : 23.169 179.454 79453 Min Nonbonded Distance : 1.048 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.29 % Allowed : 21.50 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.09 (0.10), residues: 6249 helix: 0.80 (0.12), residues: 2039 sheet: 0.11 (0.14), residues: 1257 loop : -0.69 (0.11), residues: 2953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRPAA 36 HIS 0.010 0.001 HIS B 15 PHE 0.028 0.002 PHEAA 122 TYR 0.044 0.003 TYR E 83 ARG 0.019 0.001 ARGBB 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1324 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1101 time to evaluate : 6.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7438 (pt0) REVERT: B 132 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8820 (mtm) REVERT: C 59 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7884 (mtt90) REVERT: C 97 SER cc_start: 0.8999 (p) cc_final: 0.8653 (p) REVERT: D 136 GLN cc_start: 0.8794 (tp-100) cc_final: 0.8556 (tp40) REVERT: D 184 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7718 (m-30) REVERT: E 44 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8405 (pp) REVERT: E 98 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7096 (mt-10) REVERT: E 165 GLU cc_start: 0.8792 (mp0) cc_final: 0.8103 (mp0) REVERT: G 66 ASN cc_start: 0.7572 (OUTLIER) cc_final: 0.7049 (t0) REVERT: I 63 ASP cc_start: 0.4699 (OUTLIER) cc_final: 0.4470 (p0) REVERT: K 53 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8155 (mmtt) REVERT: K 114 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8126 (ttpp) REVERT: L 86 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6923 (mm-30) REVERT: M 78 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8333 (mp) REVERT: M 110 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7397 (tt0) REVERT: M 136 MET cc_start: 0.7427 (ttm) cc_final: 0.7137 (ttp) REVERT: N 18 GLN cc_start: 0.8016 (tt0) cc_final: 0.7772 (tt0) REVERT: O 19 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: Q 51 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8853 (mtm-85) REVERT: S 1 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6407 (ttm) REVERT: T 73 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6383 (mtp-110) REVERT: U 10 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7329 (tm-30) REVERT: V 41 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: V 87 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8512 (mt0) REVERT: W 25 ARG cc_start: 0.8195 (mmp80) cc_final: 0.7919 (mmt-90) REVERT: Y 15 ASN cc_start: 0.8913 (m-40) cc_final: 0.8637 (m110) REVERT: Y 44 LYS cc_start: 0.9182 (ttmm) cc_final: 0.8978 (ttpt) REVERT: Z 54 MET cc_start: 0.9335 (ptm) cc_final: 0.9016 (ptm) REVERT: a 65 ASN cc_start: 0.6496 (OUTLIER) cc_final: 0.6147 (t0) REVERT: b 12 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7904 (mmmm) REVERT: d 25 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7960 (ttpp) REVERT: h 3 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7691 (mt0) REVERT: h 28 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: h 59 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8721 (ptm160) REVERT: i 73 ARG cc_start: 0.8229 (ttp-170) cc_final: 0.7753 (ttp-170) REVERT: i 203 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9173 (tt) REVERT: l 68 ASN cc_start: 0.9001 (m-40) cc_final: 0.8638 (m-40) REVERT: l 126 ASP cc_start: 0.8438 (m-30) cc_final: 0.8191 (m-30) REVERT: o 31 ARG cc_start: 0.8053 (tmm160) cc_final: 0.7761 (ptt90) REVERT: p 85 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.7658 (mtm) REVERT: q 83 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8086 (ptt-90) REVERT: r 75 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7383 (mmm) REVERT: r 78 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8719 (ttmt) REVERT: s 97 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8307 (pttt) REVERT: t 14 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7371 (tm-30) REVERT: t 26 GLU cc_start: 0.8415 (mp0) cc_final: 0.8055 (mp0) REVERT: t 77 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8162 (mtp180) REVERT: t 84 ARG cc_start: 0.8612 (tpp80) cc_final: 0.8003 (ttt-90) REVERT: t 89 ARG cc_start: 0.6935 (ttp-110) cc_final: 0.6582 (ttp80) REVERT: w 29 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9037 (mp) REVERT: z 24 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: z 46 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8774 (ttpm) REVERT: AA 116 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.7099 (t80) REVERT: AA 120 HIS cc_start: 0.7415 (m-70) cc_final: 0.6144 (m-70) REVERT: BB 116 PHE cc_start: 0.7237 (t80) cc_final: 0.6622 (t80) REVERT: BB 120 HIS cc_start: 0.7912 (m-70) cc_final: 0.7526 (m-70) outliers start: 223 outliers final: 172 residues processed: 1235 average time/residue: 2.2726 time to fit residues: 4004.4894 Evaluate side-chains 1299 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1092 time to evaluate : 6.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 36 LYS Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 94 ASP Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 54 GLN Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 45 ARG Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 49 ARG Chi-restraints excluded: chain a residue 64 PHE Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain b residue 12 LYS Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain h residue 3 GLN Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 28 GLU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain i residue 30 THR Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain i residue 203 LEU Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 76 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 130 ASN Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 101 ILE Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 85 MET Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 21 SER Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 78 LYS Chi-restraints excluded: chain s residue 58 SER Chi-restraints excluded: chain s residue 97 LYS Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 77 ARG Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain u residue 77 GLU Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 29 LEU Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain x residue 6 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain z residue 24 GLU Chi-restraints excluded: chain z residue 46 LYS Chi-restraints excluded: chain AA residue 17 LEU Chi-restraints excluded: chain AA residue 69 LEU Chi-restraints excluded: chain AA residue 116 PHE Chi-restraints excluded: chain BB residue 16 ILE Chi-restraints excluded: chain BB residue 19 GLN Chi-restraints excluded: chain BB residue 49 THR Chi-restraints excluded: chain CC residue 101 LEU Chi-restraints excluded: chain CC residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 675 optimal weight: 5.9990 chunk 905 optimal weight: 8.9990 chunk 260 optimal weight: 0.9990 chunk 784 optimal weight: 0.9990 chunk 125 optimal weight: 0.0170 chunk 236 optimal weight: 0.9980 chunk 851 optimal weight: 0.9990 chunk 356 optimal weight: 4.9990 chunk 874 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN K 29 HIS O 104 GLN Q 20 GLN S 31 GLN T 28 ASN V 12 GLN Y 31 GLN d 26 ASN d 29 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 140 ASN i 71 GLN k 37 HIS l 142 HIS o 56 HIS p 109 ASN t 35 GLN v 9 GLN w 31 ASN w 54 GLN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 93 HIS ** BB 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 125 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.110435 restraints weight = 183702.028| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 0.36 r_work: 0.3062 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work: 0.2899 rms_B_bonded: 4.36 restraints_weight: 0.1250 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 162177 Z= 0.123 Angle : 0.578 13.484 241965 Z= 0.320 Chirality : 0.034 0.337 30706 Planarity : 0.006 0.125 13418 Dihedral : 23.022 178.309 79453 Min Nonbonded Distance : 1.177 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.16 % Allowed : 22.74 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: 0.27 (0.11), residues: 6249 helix: 1.19 (0.12), residues: 2057 sheet: 0.21 (0.14), residues: 1306 loop : -0.50 (0.11), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.001 TRPAA 36 HIS 0.006 0.001 HIS w 74 PHE 0.026 0.001 PHEAA 122 TYR 0.030 0.001 TYR h 42 ARG 0.025 0.000 ARGAA 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 54426.34 seconds wall clock time: 942 minutes 42.47 seconds (56562.47 seconds total)