Starting phenix.real_space_refine on Sat Mar 23 00:18:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha8_0177/03_2024/6ha8_0177_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha8_0177/03_2024/6ha8_0177.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha8_0177/03_2024/6ha8_0177_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha8_0177/03_2024/6ha8_0177_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha8_0177/03_2024/6ha8_0177_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha8_0177/03_2024/6ha8_0177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha8_0177/03_2024/6ha8_0177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha8_0177/03_2024/6ha8_0177_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha8_0177/03_2024/6ha8_0177_updated.pdb" } resolution = 3.5 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= 0.003 sd= 0.027 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: 5 Type Number sf(0) Gaussians P 4612 5.49 5 S 145 5.16 5 C 73887 2.51 5 N 27134 2.21 5 O 40626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "F ARG 125": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 172": "NH1" <-> "NH2" Residue "J ARG 77": "NH1" <-> "NH2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "K ARG 70": "NH1" <-> "NH2" Residue "K TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 108": "NH1" <-> "NH2" Residue "O ARG 97": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "P ARG 14": "NH1" <-> "NH2" Residue "P PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 39": "NH1" <-> "NH2" Residue "P ARG 93": "NH1" <-> "NH2" Residue "P TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R ARG 75": "NH1" <-> "NH2" Residue "R ARG 89": "NH1" <-> "NH2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 86": "NH1" <-> "NH2" Residue "V ARG 99": "NH1" <-> "NH2" Residue "V ARG 113": "NH1" <-> "NH2" Residue "V ARG 160": "NH1" <-> "NH2" Residue "V PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 278": "NH1" <-> "NH2" Residue "V ARG 290": "NH1" <-> "NH2" Residue "V ARG 383": "NH1" <-> "NH2" Residue "V ARG 391": "NH1" <-> "NH2" Residue "V ARG 442": "NH1" <-> "NH2" Residue "W ARG 28": "NH1" <-> "NH2" Residue "W TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "3 TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 17": "NH1" <-> "NH2" Residue "8 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 47": "NH1" <-> "NH2" Residue "8 ARG 129": "NH1" <-> "NH2" Residue "b ARG 22": "NH1" <-> "NH2" Residue "b ARG 29": "NH1" <-> "NH2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ARG 143": "NH1" <-> "NH2" Residue "b ARG 167": "NH1" <-> "NH2" Residue "b ARG 170": "NH1" <-> "NH2" Residue "b ARG 177": "NH1" <-> "NH2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "d TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "d TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 146": "NH1" <-> "NH2" Residue "d PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 20": "NH1" <-> "NH2" Residue "e ARG 32": "NH1" <-> "NH2" Residue "e ARG 112": "NH1" <-> "NH2" Residue "f ARG 11": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 77": "NH1" <-> "NH2" Residue "g ARG 78": "NH1" <-> "NH2" Residue "g ARG 79": "NH1" <-> "NH2" Residue "g ARG 92": "NH1" <-> "NH2" Residue "g ARG 111": "NH1" <-> "NH2" Residue "g ARG 119": "NH1" <-> "NH2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "h ARG 61": "NH1" <-> "NH2" Residue "h ARG 96": "NH1" <-> "NH2" Residue "h ARG 119": "NH1" <-> "NH2" Residue "i ARG 12": "NH1" <-> "NH2" Residue "i ARG 20": "NH1" <-> "NH2" Residue "i TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "i ARG 109": "NH1" <-> "NH2" Residue "i ARG 113": "NH1" <-> "NH2" Residue "i TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 7": "NH1" <-> "NH2" Residue "j ARG 9": "NH1" <-> "NH2" Residue "j ARG 53": "NH1" <-> "NH2" Residue "k ARG 26": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l ARG 63": "NH1" <-> "NH2" Residue "l ARG 96": "NH1" <-> "NH2" Residue "l ARG 123": "NH1" <-> "NH2" Residue "m ARG 3": "NH1" <-> "NH2" Residue "m ARG 11": "NH1" <-> "NH2" Residue "m PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 27": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 79": "NH1" <-> "NH2" Residue "m ARG 93": "NH1" <-> "NH2" Residue "m ARG 107": "NH1" <-> "NH2" Residue "m ARG 109": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "o ARG 54": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 19": "NH1" <-> "NH2" Residue "p ARG 29": "NH1" <-> "NH2" Residue "p ARG 32": "NH1" <-> "NH2" Residue "p ARG 71": "NH1" <-> "NH2" Residue "q ARG 39": "NH1" <-> "NH2" Residue "q ARG 67": "NH1" <-> "NH2" Residue "r ARG 48": "NH1" <-> "NH2" Residue "t ARG 18": "NH1" <-> "NH2" Residue "t ARG 78": "NH1" <-> "NH2" 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: 146404 Number of models: 1 Model: "" Number of chains: 55 Chain: "A" Number of atoms: 61997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2887, 61997 Inner-chain residues flagged as termini: ['pdbres=" G A 328 "', 'pdbres=" G A1220 "'] Classifications: {'RNA': 2887} Modifications used: {'5*END': 3, 'rna2p_pur': 294, 'rna2p_pyr': 159, 'rna3p_pur': 1383, 'rna3p_pyr': 1050} Link IDs: {'rna2p': 453, 'rna3p': 2433} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2392 Classifications: {'RNA': 112} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 46} Link IDs: {'rna2p': 14, 'rna3p': 97} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1569 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "E" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "F" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1386 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "G" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "J" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1123 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1081 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "M" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1076 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "O" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "P" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 944 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "S" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "T" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 725 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "U" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 762 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "V" Number of atoms: 4177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4177 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 13, 'TRANS': 527} Chain: "W" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 630 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "X" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "Y" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "Z" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "0" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "1" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "3" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "4" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 499 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "7" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "8" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1599 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 9, 'TRANS': 202} Chain: "a" Number of atoms: 32891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1533, 32891 Classifications: {'RNA': 1533} Modifications used: {'rna2p_pur': 117, 'rna2p_pyr': 86, 'rna3p_pur': 753, 'rna3p_pyr': 577} Link IDs: {'rna2p': 202, 'rna3p': 1330} Chain: "b" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1757 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 3, 'TRANS': 202} Chain: "d" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1568 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "e" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1218 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain: "f" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 755 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "g" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1181 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "h" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1036 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "i" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "j" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 761 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "k" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 838 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "l" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1052 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "m" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 868 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "n" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 497 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 710 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "p" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "q" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 691 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "r" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "s" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 633 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "t" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 637 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain: "x" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1603 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 29, 'rna3p_pyr': 30} Link IDs: {'rna2p': 15, 'rna3p': 59} Chain breaks: 1 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'TEL': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 56.00, per 1000 atoms: 0.38 Number of scatterers: 146404 At special positions: 0 Unit cell: (269.494, 276.921, 223.871, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 145 16.00 P 4612 15.00 O 40626 8.00 N 27134 7.00 C 73887 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 0 30 " - pdb=" SG CYS 0 43 " distance=2.02 Simple disulfide: pdb=" SG CYS 0 33 " - pdb=" SG CYS 0 46 " distance=2.02 Simple disulfide: pdb=" SG CYS n 27 " - pdb=" SG CYS n 43 " distance=2.02 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 63.82 Conformation dependent library (CDL) restraints added in 7.0 seconds 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11106 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: 178 helices and 76 sheets defined 38.3% alpha, 18.5% beta 1460 base pairs and 2609 stacking pairs defined. Time for finding SS restraints: 77.22 Creating SS restraints... Processing helix chain 'C' and resid 131 through 136 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.376A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.946A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.266A pdb=" N ILE C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 271' Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.625A pdb=" N SER D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASN D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 62' Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.526A pdb=" N TYR D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU D 92 " --> pdb=" O MET D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 92' Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'E' and resid 29 through 46 removed outlier: 3.671A pdb=" N ARG E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLN E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 Processing helix chain 'E' and resid 135 through 147 removed outlier: 3.890A pdb=" N MET E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 168 removed outlier: 4.521A pdb=" N ALA E 167 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 4.281A pdb=" N VAL E 186 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'F' and resid 2 through 21 Proline residue: F 14 - end of helix Processing helix chain 'F' and resid 48 through 62 removed outlier: 4.258A pdb=" N SER F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU F 56 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR F 58 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY F 62 " --> pdb=" O THR F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 removed outlier: 4.547A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 147 removed outlier: 5.299A pdb=" N THR F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 removed outlier: 4.216A pdb=" N ALA F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.486A pdb=" N ALA F 47 " --> pdb=" O ASP F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 42 through 47' Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.822A pdb=" N ALA G 64 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG G 70 " --> pdb=" O HIS G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 154 removed outlier: 4.095A pdb=" N ALA G 144 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 39 removed outlier: 3.796A pdb=" N GLU J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 97 removed outlier: 3.701A pdb=" N ASN J 96 " --> pdb=" O GLU J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 111 Proline residue: J 111 - end of helix Processing helix chain 'J' and resid 113 through 124 removed outlier: 3.850A pdb=" N LYS J 122 " --> pdb=" O GLN J 118 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU J 123 " --> pdb=" O MET J 119 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ASN J 124 " --> pdb=" O PHE J 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 4.079A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASN K 110 " --> pdb=" O LEU K 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 110' Processing helix chain 'K' and resid 111 through 119 removed outlier: 3.623A pdb=" N LEU K 117 " --> pdb=" O LYS K 113 " (cutoff:3.500A) Proline residue: K 119 - end of helix Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 78 through 85 removed outlier: 6.553A pdb=" N LEU L 82 " --> pdb=" O ASN L 78 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE L 85 " --> pdb=" O LYS L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 92 through 100 Processing helix chain 'L' and resid 129 through 140 removed outlier: 3.548A pdb=" N GLU L 134 " --> pdb=" O ALA L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 59 removed outlier: 3.722A pdb=" N ILE M 47 " --> pdb=" O THR M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 126 removed outlier: 4.138A pdb=" N LYS M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Proline residue: M 126 - end of helix Processing helix chain 'N' and resid 9 through 28 Processing helix chain 'N' and resid 34 through 54 removed outlier: 4.409A pdb=" N SER N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL N 43 " --> pdb=" O GLU N 39 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG N 53 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY N 54 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 66 removed outlier: 3.773A pdb=" N ARG N 59 " --> pdb=" O ASP N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 92 Processing helix chain 'O' and resid 6 through 22 removed outlier: 3.612A pdb=" N VAL O 18 " --> pdb=" O ARG O 14 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA O 20 " --> pdb=" O ALA O 16 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYS O 21 " --> pdb=" O ARG O 17 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU O 22 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 89 removed outlier: 4.032A pdb=" N GLY O 89 " --> pdb=" O ALA O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 117 Processing helix chain 'P' and resid 1 through 14 removed outlier: 4.943A pdb=" N GLU P 11 " --> pdb=" O ASP P 7 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLN P 12 " --> pdb=" O ILE P 8 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG P 14 " --> pdb=" O LYS P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.671A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ARG P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 22 removed outlier: 5.019A pdb=" N THR Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG Q 11 " --> pdb=" O GLY Q 7 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 31 removed outlier: 4.899A pdb=" N HIS Q 29 " --> pdb=" O PHE Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.614A pdb=" N ARG Q 51 " --> pdb=" O PHE Q 47 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N MET Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.727A pdb=" N GLY Q 87 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 103 removed outlier: 3.509A pdb=" N ASP Q 102 " --> pdb=" O LEU Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 118 removed outlier: 3.566A pdb=" N GLN Q 108 " --> pdb=" O THR Q 104 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN Q 118 " --> pdb=" O LYS Q 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.701A pdb=" N ALA S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 40 removed outlier: 4.003A pdb=" N LEU S 38 " --> pdb=" O SER S 34 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR S 39 " --> pdb=" O ILE S 35 " (cutoff:3.500A) Proline residue: S 40 - end of helix Processing helix chain 'S' and resid 41 through 61 Proline residue: S 45 - end of helix Processing helix chain 'S' and resid 65 through 70 removed outlier: 4.281A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL S 70 " --> pdb=" O ALA 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 9 removed outlier: 4.049A pdb=" N VAL T 7 " --> pdb=" O ASP T 3 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU T 8 " --> pdb=" O PRO T 4 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LYS T 9 " --> pdb=" O ARG T 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 3 through 9' Processing helix chain 'T' and resid 14 through 24 removed outlier: 3.515A pdb=" N ALA T 18 " --> pdb=" O THR T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 47 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.355A pdb=" N VAL U 68 " --> pdb=" O HIS U 64 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N MET U 69 " --> pdb=" O VAL U 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 64 through 69' Processing helix chain 'V' and resid 42 through 52 removed outlier: 4.510A pdb=" N LEU V 47 " --> pdb=" O LYS V 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 95 removed outlier: 3.739A pdb=" N LYS V 89 " --> pdb=" O PRO V 85 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU V 90 " --> pdb=" O ALA V 86 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N HIS V 95 " --> pdb=" O LEU V 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 105 through 121 removed outlier: 3.760A pdb=" N LYS V 109 " --> pdb=" O SER V 105 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU V 110 " --> pdb=" O GLY V 106 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS V 111 " --> pdb=" O GLY V 107 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA V 115 " --> pdb=" O LYS V 111 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS V 116 " --> pdb=" O ALA V 112 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER V 119 " --> pdb=" O ALA V 115 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU V 120 " --> pdb=" O LYS V 116 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP V 121 " --> pdb=" O GLY V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 149 removed outlier: 3.573A pdb=" N PHE V 141 " --> pdb=" O LYS V 137 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE V 143 " --> pdb=" O LEU V 139 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN V 144 " --> pdb=" O GLN V 140 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS V 148 " --> pdb=" O GLN V 144 " (cutoff:3.500A) Processing helix chain 'V' and resid 159 through 166 removed outlier: 3.731A pdb=" N LEU V 163 " --> pdb=" O ASP V 159 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP V 164 " --> pdb=" O ARG V 160 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU V 165 " --> pdb=" O TYR V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 185 through 231 removed outlier: 3.690A pdb=" N LYS V 190 " --> pdb=" O SER V 186 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU V 220 " --> pdb=" O GLN V 216 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS V 226 " --> pdb=" O SER V 222 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER V 231 " --> pdb=" O ALA V 227 " (cutoff:3.500A) Processing helix chain 'V' and resid 238 through 267 removed outlier: 3.759A pdb=" N ARG V 242 " --> pdb=" O LYS V 238 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS V 244 " --> pdb=" O TYR V 240 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA V 245 " --> pdb=" O HIS V 241 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN V 251 " --> pdb=" O ARG V 247 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS V 253 " --> pdb=" O ASP V 249 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN V 256 " --> pdb=" O ILE V 252 " (cutoff:3.500A) Processing helix chain 'V' and resid 329 through 339 removed outlier: 3.725A pdb=" N LEU V 334 " --> pdb=" O LYS V 330 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN V 335 " --> pdb=" O THR V 331 " (cutoff:3.500A) Processing helix chain 'V' and resid 370 through 376 removed outlier: 5.218A pdb=" N GLU V 376 " --> pdb=" O GLU V 372 " (cutoff:3.500A) Processing helix chain 'V' and resid 379 through 385 removed outlier: 5.119A pdb=" N ARG V 383 " --> pdb=" O THR V 379 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY V 384 " --> pdb=" O PHE V 380 " (cutoff:3.500A) Processing helix chain 'V' and resid 386 through 395 removed outlier: 3.934A pdb=" N MET V 390 " --> pdb=" O VAL V 386 " (cutoff:3.500A) Processing helix chain 'V' and resid 403 through 408 removed outlier: 5.313A pdb=" N SER V 408 " --> pdb=" O ILE V 404 " (cutoff:3.500A) Processing helix chain 'V' and resid 409 through 422 removed outlier: 5.050A pdb=" N VAL V 413 " --> pdb=" O MET V 409 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LYS V 414 " --> pdb=" O GLY V 410 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ILE V 415 " --> pdb=" O GLU V 411 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS V 416 " --> pdb=" O ARG V 412 " (cutoff:3.500A) Processing helix chain 'V' and resid 433 through 438 removed outlier: 4.425A pdb=" N LEU V 437 " --> pdb=" O PRO V 433 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASP V 438 " --> pdb=" O THR V 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 433 through 438' Processing helix chain 'V' and resid 439 through 452 removed outlier: 3.972A pdb=" N GLU V 443 " --> pdb=" O LEU V 439 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN V 444 " --> pdb=" O PRO V 440 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU V 445 " --> pdb=" O SER V 441 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER V 450 " --> pdb=" O GLU V 446 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN V 451 " --> pdb=" O GLU V 447 " (cutoff:3.500A) Processing helix chain 'V' and resid 462 through 470 removed outlier: 4.645A pdb=" N LEU V 466 " --> pdb=" O ASP V 462 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU V 467 " --> pdb=" O ARG V 463 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS V 468 " --> pdb=" O TYR V 464 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR V 469 " --> pdb=" O PHE V 465 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 518 removed outlier: 3.541A pdb=" N ALA V 498 " --> pdb=" O ALA V 494 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA V 517 " --> pdb=" O ALA V 513 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA V 518 " --> pdb=" O ALA V 514 " (cutoff:3.500A) Processing helix chain 'V' and resid 523 through 542 removed outlier: 3.818A pdb=" N ALA V 527 " --> pdb=" O ALA V 523 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA V 542 " --> pdb=" O ALA V 538 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 55 removed outlier: 4.118A pdb=" N LYS X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 8 removed outlier: 4.430A pdb=" N ASP Y 8 " --> pdb=" O ASN Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 35 Processing helix chain 'Y' and resid 39 through 65 removed outlier: 4.134A pdb=" N ILE Y 43 " --> pdb=" O ASN Y 39 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG Y 44 " --> pdb=" O THR Y 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE Y 57 " --> pdb=" O MET Y 53 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.546A pdb=" N LEU Z 26 " --> pdb=" O THR Z 22 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY Z 27 " --> pdb=" O VAL Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 Processing helix chain '0' and resid 9 through 21 removed outlier: 5.174A pdb=" N HIS 0 19 " --> pdb=" O LEU 0 15 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS 0 21 " --> pdb=" O ARG 0 17 " (cutoff:3.500A) Processing helix chain '1' and resid 22 through 27 Proline residue: 1 27 - end of helix No H-bonds generated for 'chain '1' and resid 22 through 27' Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.130A pdb=" N SER 2 24 " --> pdb=" O SER 2 20 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 removed outlier: 3.792A pdb=" N GLY 2 38 " --> pdb=" O ARG 2 34 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 14 Processing helix chain '3' and resid 32 through 37 removed outlier: 4.521A pdb=" N LYS 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N SER 3 37 " --> pdb=" O PHE 3 33 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 32 through 37' Processing helix chain '3' and resid 38 through 46 removed outlier: 4.109A pdb=" N LYS 3 46 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 63 removed outlier: 5.631A pdb=" N GLN 3 60 " --> pdb=" O LYS 3 56 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N MET 3 61 " --> pdb=" O ARG 3 57 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU 3 62 " --> pdb=" O ILE 3 58 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA 3 63 " --> pdb=" O LYS 3 59 " (cutoff:3.500A) Processing helix chain '6' and resid 40 through 45 removed outlier: 3.910A pdb=" N THR 6 44 " --> pdb=" O HIS 6 40 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY 6 45 " --> pdb=" O PRO 6 41 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 40 through 45' Processing helix chain '6' and resid 48 through 55 removed outlier: 4.552A pdb=" N ARG 6 55 " --> pdb=" O SER 6 51 " (cutoff:3.500A) Processing helix chain '8' and resid 22 through 34 removed outlier: 4.395A pdb=" N ALA 8 28 " --> pdb=" O SER 8 24 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS 8 31 " --> pdb=" O VAL 8 27 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS 8 32 " --> pdb=" O ALA 8 28 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN 8 34 " --> pdb=" O VAL 8 30 " (cutoff:3.500A) Processing helix chain '8' and resid 81 through 91 removed outlier: 4.857A pdb=" N LYS 8 85 " --> pdb=" O GLY 8 81 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU 8 86 " --> pdb=" O GLU 8 82 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA 8 89 " --> pdb=" O LYS 8 85 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA 8 90 " --> pdb=" O GLU 8 86 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY 8 91 " --> pdb=" O ALA 8 87 " (cutoff:3.500A) Processing helix chain '8' and resid 100 through 107 removed outlier: 5.303A pdb=" N GLN 8 106 " --> pdb=" O ASN 8 102 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLY 8 107 " --> pdb=" O LYS 8 103 " (cutoff:3.500A) Processing helix chain '8' and resid 120 through 128 removed outlier: 4.047A pdb=" N ILE 8 127 " --> pdb=" O GLU 8 123 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY 8 128 " --> pdb=" O VAL 8 124 " (cutoff:3.500A) Processing helix chain '8' and resid 129 through 135 Proline residue: 8 133 - end of helix No H-bonds generated for 'chain '8' and resid 129 through 135' Processing helix chain '8' and resid 148 through 159 removed outlier: 3.520A pdb=" N GLY 8 154 " --> pdb=" O GLU 8 150 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU 8 155 " --> pdb=" O LYS 8 151 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE 8 156 " --> pdb=" O ALA 8 152 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA 8 158 " --> pdb=" O GLY 8 154 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY 8 159 " --> pdb=" O GLU 8 155 " (cutoff:3.500A) Processing helix chain '8' and resid 181 through 200 removed outlier: 4.163A pdb=" N LEU 8 185 " --> pdb=" O GLU 8 181 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL 8 186 " --> pdb=" O ASP 8 182 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU 8 187 " --> pdb=" O GLU 8 183 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS 8 200 " --> pdb=" O ILE 8 196 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 removed outlier: 4.799A pdb=" N LYS b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ARG b 29 " --> pdb=" O PRO b 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 24 through 29' Processing helix chain 'b' and resid 42 through 64 removed outlier: 4.111A pdb=" N LYS b 48 " --> pdb=" O GLN b 44 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS b 49 " --> pdb=" O LYS b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 88 removed outlier: 4.847A pdb=" N ASP b 78 " --> pdb=" O LYS b 74 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER b 79 " --> pdb=" O GLN b 75 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 123 removed outlier: 3.645A pdb=" N ILE b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN b 121 " --> pdb=" O ILE b 117 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU b 122 " --> pdb=" O GLU b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 148 removed outlier: 4.567A pdb=" N LYS b 139 " --> pdb=" O VAL b 135 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG b 143 " --> pdb=" O LYS b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 155 removed outlier: 5.339A pdb=" N MET b 154 " --> pdb=" O GLY b 150 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS b 155 " --> pdb=" O ILE b 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 150 through 155' Processing helix chain 'b' and resid 165 through 170 removed outlier: 3.535A pdb=" N GLU b 169 " --> pdb=" O ASP b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 192 through 197 removed outlier: 3.915A pdb=" N ILE b 196 " --> pdb=" O ASP b 192 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP b 197 " --> pdb=" O PRO b 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 192 through 197' Processing helix chain 'b' and resid 206 through 225 removed outlier: 3.906A pdb=" N ALA b 224 " --> pdb=" O ALA b 220 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS b 225 " --> pdb=" O ILE b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.580A pdb=" N ILE c 12 " --> pdb=" O VAL c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 50 removed outlier: 4.683A pdb=" N ASP c 48 " --> pdb=" O LYS c 44 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA c 49 " --> pdb=" O ARG c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 76 removed outlier: 4.764A pdb=" N VAL c 75 " --> pdb=" O LYS c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 78 through 95 removed outlier: 6.353A pdb=" N GLU c 82 " --> pdb=" O LYS c 78 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL c 83 " --> pdb=" O GLY c 79 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA c 89 " --> pdb=" O ALA c 85 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU c 90 " --> pdb=" O LEU c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 Processing helix chain 'c' and resid 128 through 144 removed outlier: 4.181A pdb=" N GLN c 133 " --> pdb=" O PHE c 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 6.359A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER d 12 " --> pdb=" O SER d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 62 Processing helix chain 'd' and resid 64 through 79 removed outlier: 4.916A pdb=" N ALA d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 94 removed outlier: 6.391A pdb=" N LEU d 94 " --> pdb=" O LEU d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 95 through 102 Processing helix chain 'd' and resid 106 through 116 removed outlier: 3.853A pdb=" N ALA d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 158 removed outlier: 5.148A pdb=" N ASN d 158 " --> pdb=" O SER d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 186 removed outlier: 3.576A pdb=" N LEU d 185 " --> pdb=" O GLU d 181 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA d 186 " --> pdb=" O ARG d 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 181 through 186' Processing helix chain 'd' and resid 190 through 200 removed outlier: 4.595A pdb=" N ILE d 194 " --> pdb=" O ASN d 190 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL d 195 " --> pdb=" O GLU d 191 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU d 196 " --> pdb=" O ALA d 192 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG d 200 " --> pdb=" O GLU d 196 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 71 removed outlier: 3.843A pdb=" N ALA e 59 " --> pdb=" O GLU e 55 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 119 removed outlier: 3.807A pdb=" N GLY e 119 " --> pdb=" O LEU e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 147 removed outlier: 3.533A pdb=" N GLU e 146 " --> pdb=" O GLN e 142 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU e 147 " --> pdb=" O GLY e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 158 removed outlier: 3.707A pdb=" N GLY e 158 " --> pdb=" O ALA e 154 " (cutoff:3.500A) Processing helix chain 'e' and resid 160 through 166 Processing helix chain 'f' and resid 15 through 34 removed outlier: 3.705A pdb=" N SER f 32 " --> pdb=" O ASN f 28 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN f 33 " --> pdb=" O VAL f 29 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY f 34 " --> pdb=" O LEU f 30 " (cutoff:3.500A) Processing helix chain 'f' and resid 69 through 82 removed outlier: 4.717A pdb=" N GLN f 73 " --> pdb=" O ALA f 69 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.840A pdb=" N SER g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET g 30 " --> pdb=" O LEU g 26 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N MET g 31 " --> pdb=" O ILE g 27 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.636A pdb=" N SER g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR g 54 " --> pdb=" O ILE g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.737A pdb=" N VAL g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 4.194A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.526A pdb=" N ASN g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN g 130 " --> pdb=" O ASP g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 149 removed outlier: 3.980A pdb=" N LYS g 137 " --> pdb=" O ALA g 133 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 4.031A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.526A pdb=" N GLY h 44 " --> pdb=" O LEU h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 Processing helix chain 'i' and resid 34 through 39 Processing helix chain 'i' and resid 41 through 56 removed outlier: 4.084A pdb=" N ILE i 45 " --> pdb=" O SER i 41 " (cutoff:3.500A) Proline residue: i 51 - end of helix removed outlier: 3.857A pdb=" N THR i 55 " --> pdb=" O PRO i 51 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLU i 56 " --> pdb=" O LEU i 52 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 92 removed outlier: 3.549A pdb=" N ASP i 91 " --> pdb=" O LEU i 87 " (cutoff:3.500A) Proline residue: i 92 - end of helix Processing helix chain 'i' and resid 94 through 102 Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.868A pdb=" N ILE j 25 " --> pdb=" O SER j 21 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 91 removed outlier: 3.706A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ASP j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 48 through 53 removed outlier: 3.973A pdb=" N GLY k 53 " --> pdb=" O ALA k 49 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 62 removed outlier: 4.185A pdb=" N THR k 61 " --> pdb=" O SER k 57 " (cutoff:3.500A) Proline residue: k 62 - end of helix No H-bonds generated for 'chain 'k' and resid 57 through 62' Processing helix chain 'k' and resid 63 through 78 removed outlier: 4.577A pdb=" N GLU k 78 " --> pdb=" O LYS k 74 " (cutoff:3.500A) Processing helix chain 'k' and resid 94 through 106 removed outlier: 3.505A pdb=" N GLN k 103 " --> pdb=" O ILE k 99 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY k 106 " --> pdb=" O LEU k 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 21 through 27 removed outlier: 3.772A pdb=" N ASN l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS l 26 " --> pdb=" O PRO l 22 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLY l 27 " --> pdb=" O ALA l 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 21 through 27' Processing helix chain 'l' and resid 126 through 131 removed outlier: 4.976A pdb=" N TYR l 130 " --> pdb=" O GLY l 126 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY l 131 " --> pdb=" O ARG l 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 126 through 131' Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.871A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.731A pdb=" N ALA m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU m 36 " --> pdb=" O GLN m 32 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 64 removed outlier: 3.652A pdb=" N ILE m 56 " --> pdb=" O GLU m 52 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LYS m 64 " --> pdb=" O ILE m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 removed outlier: 4.165A pdb=" N ARG m 70 " --> pdb=" O GLU m 66 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.546A pdb=" N GLY m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 13 removed outlier: 5.122A pdb=" N MET n 6 " --> pdb=" O ALA n 2 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 21 removed outlier: 3.961A pdb=" N GLU n 20 " --> pdb=" O PHE n 16 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N TYR n 21 " --> pdb=" O LYS n 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 16 through 21' Processing helix chain 'n' and resid 40 through 51 Processing helix chain 'o' and resid 4 through 16 removed outlier: 6.018A pdb=" N LYS o 8 " --> pdb=" O THR o 4 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ASN o 9 " --> pdb=" O GLN o 5 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 4.252A pdb=" N GLN o 28 " --> pdb=" O SER o 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 4.137A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 52 through 63 removed outlier: 5.991A pdb=" N ALA p 56 " --> pdb=" O ASP p 52 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU p 57 " --> pdb=" O GLU p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 Processing helix chain 'p' and resid 79 through 89 Processing helix chain 'r' and resid 16 through 22 removed outlier: 3.801A pdb=" N SER r 20 " --> pdb=" O CYS r 16 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 39 removed outlier: 5.578A pdb=" N SER r 39 " --> pdb=" O LYS r 35 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 51 Processing helix chain 'r' and resid 53 through 71 Processing helix chain 's' and resid 12 through 26 removed outlier: 3.972A pdb=" N THR s 25 " --> pdb=" O LYS s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.629A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 6 through 42 removed outlier: 4.740A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN t 42 " --> pdb=" O SER t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 Processing helix chain 't' and resid 68 through 86 removed outlier: 3.691A pdb=" N ALA t 72 " --> pdb=" O HIS t 68 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU t 86 " --> pdb=" O LYS t 82 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.927A pdb=" N MET C 16 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 80 through 83 removed outlier: 6.680A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N THR C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 162 through 165 removed outlier: 5.284A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 91 through 96 removed outlier: 3.675A pdb=" N TYR C 96 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 37 through 41 removed outlier: 4.439A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA D 48 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA D 41 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TYR D 46 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLN D 95 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 166 through 172 removed outlier: 4.987A pdb=" N GLU D 167 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU D 199 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 11.372A pdb=" N LYS D 115 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 13.007A pdb=" N LYS D 197 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER D 198 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL D 27 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 48 through 54 Processing sheet with id= 8, first strand: chain 'E' and resid 2 through 5 Processing sheet with id= 9, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.551A pdb=" N LEU E 192 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS E 191 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 65 through 69 removed outlier: 6.155A pdb=" N VAL F 66 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA F 87 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR F 68 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA F 87 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 16 through 19 removed outlier: 3.501A pdb=" N ALA G 26 " --> pdb=" O THR G 18 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASN G 23 " --> pdb=" O PHE G 38 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 42 through 46 Processing sheet with id= 13, first strand: chain 'G' and resid 96 through 99 Processing sheet with id= 14, first strand: chain 'G' and resid 122 through 126 removed outlier: 5.458A pdb=" N THR G 130 " --> pdb=" O LEU G 90 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 90 " --> pdb=" O THR G 130 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N GLY G 87 " --> pdb=" O GLU G 166 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'J' and resid 16 through 19 Processing sheet with id= 16, first strand: chain 'J' and resid 75 through 79 removed outlier: 6.430A pdb=" N GLY J 84 " --> pdb=" O THR J 79 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'K' and resid 6 through 10 removed outlier: 4.839A pdb=" N THR K 6 " --> pdb=" O THR K 21 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'K' and resid 38 through 42 Processing sheet with id= 19, first strand: chain 'K' and resid 63 through 66 removed outlier: 3.598A pdb=" N ARG K 64 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLU K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.225A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'L' and resid 74 through 77 Processing sheet with id= 22, first strand: chain 'L' and resid 87 through 91 removed outlier: 6.298A pdb=" N LYS L 120 " --> pdb=" O GLU L 87 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR L 89 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 63 through 66 removed outlier: 4.177A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE M 34 " --> pdb=" O LEU M 103 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS M 101 " --> pdb=" O ALA M 36 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 73 through 77 removed outlier: 6.693A pdb=" N TYR M 74 " --> pdb=" O GLU M 91 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA M 89 " --> pdb=" O ALA M 76 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 31 through 37 removed outlier: 8.593A pdb=" N GLU M 31 " --> pdb=" O ARG M 134 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS M 128 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'N' and resid 29 through 33 removed outlier: 5.766A pdb=" N ALA N 112 " --> pdb=" O PRO N 106 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N MET N 114 " --> pdb=" O LEU N 104 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'O' and resid 29 through 36 removed outlier: 3.948A pdb=" N HIS O 39 " --> pdb=" O SER O 36 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA O 54 " --> pdb=" O ILE O 44 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'P' and resid 40 through 45 removed outlier: 3.621A pdb=" N GLY P 45 " --> pdb=" O LEU P 26 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS P 83 " --> pdb=" O HIS P 29 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'P' and resid 49 through 53 removed outlier: 3.740A pdb=" N LYS P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY P 53 " --> pdb=" O SER P 56 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER P 56 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLU P 57 " --> pdb=" O VAL P 76 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 2 through 6 Processing sheet with id= 31, first strand: chain 'R' and resid 18 through 21 removed outlier: 3.945A pdb=" N GLN R 18 " --> pdb=" O ILE R 97 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS R 94 " --> pdb=" O GLU R 63 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLU R 63 " --> pdb=" O LYS R 94 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR R 59 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU R 31 " --> pdb=" O VAL R 62 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'R' and resid 64 through 67 removed outlier: 5.163A pdb=" N LYS R 64 " --> pdb=" O LYS R 94 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 70 through 77 removed outlier: 4.607A pdb=" N VAL R 82 " --> pdb=" O LYS R 77 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'S' and resid 2 through 8 removed outlier: 6.016A pdb=" N ILE S 103 " --> pdb=" O ALA S 7 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 80 through 88 removed outlier: 4.581A pdb=" N THR S 100 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ARG S 88 " --> pdb=" O ARG S 92 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'T' and resid 53 through 66 removed outlier: 3.846A pdb=" N LYS T 53 " --> pdb=" O LYS T 82 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLY T 61 " --> pdb=" O SER T 74 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N SER T 74 " --> pdb=" O GLY T 61 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER T 63 " --> pdb=" O MET T 72 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET T 72 " --> pdb=" O SER T 63 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG T 65 " --> pdb=" O THR T 70 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR T 70 " --> pdb=" O ARG T 65 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'U' and resid 7 through 11 No H-bonds generated for sheet with id= 37 Processing sheet with id= 38, first strand: chain 'U' and resid 24 through 28 removed outlier: 3.533A pdb=" N ALA U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 39 through 45 removed outlier: 4.867A pdb=" N ASN U 39 " --> pdb=" O ALA U 61 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY U 55 " --> pdb=" O SER U 45 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'U' and resid 80 through 85 removed outlier: 5.605A pdb=" N ARG U 80 " --> pdb=" O LYS U 95 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 24 through 27 Processing sheet with id= 42, first strand: chain 'V' and resid 32 through 37 removed outlier: 3.761A pdb=" N ILE V 36 " --> pdb=" O TRP V 171 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR V 177 " --> pdb=" O GLU V 174 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'V' and resid 68 through 72 removed outlier: 3.916A pdb=" N VAL V 156 " --> pdb=" O LEU V 127 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 311 through 315 removed outlier: 7.922A pdb=" N PHE V 291 " --> pdb=" O SER V 350 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'V' and resid 355 through 359 removed outlier: 3.542A pdb=" N ASP V 431 " --> pdb=" O LEU V 358 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU V 318 " --> pdb=" O GLY V 454 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY V 480 " --> pdb=" O SER V 477 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 59 through 62 removed outlier: 6.481A pdb=" N GLY W 60 " --> pdb=" O LEU W 67 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU W 67 " --> pdb=" O GLY W 60 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY W 62 " --> pdb=" O ASP W 65 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'W' and resid 73 through 78 removed outlier: 5.522A pdb=" N LYS W 86 " --> pdb=" O GLU W 78 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'X' and resid 11 through 19 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain 'Z' and resid 34 through 38 removed outlier: 5.133A pdb=" N LYS Z 3 " --> pdb=" O GLN Z 59 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN Z 59 " --> pdb=" O LYS Z 3 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU Z 53 " --> pdb=" O LYS Z 9 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '1' and resid 3 through 7 No H-bonds generated for sheet with id= 50 Processing sheet with id= 51, first strand: chain '1' and resid 30 through 36 removed outlier: 6.046A pdb=" N VAL 1 30 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS 1 41 " --> pdb=" O CYS 1 36 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain '3' and resid 22 through 25 removed outlier: 5.329A pdb=" N LEU 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain '4' and resid 1 through 5 removed outlier: 3.961A pdb=" N GLY 4 37 " --> pdb=" O ARG 4 4 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N HIS 4 32 " --> pdb=" O CYS 4 27 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N CYS 4 27 " --> pdb=" O HIS 4 32 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL 4 23 " --> pdb=" O GLN 4 36 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain '6' and resid 21 through 24 Processing sheet with id= 55, first strand: chain '8' and resid 42 through 47 removed outlier: 3.926A pdb=" N ASN 8 211 " --> pdb=" O ARG 8 47 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL 8 212 " --> pdb=" O VAL 8 224 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain '8' and resid 74 through 79 removed outlier: 3.659A pdb=" N VAL 8 113 " --> pdb=" O ARG 8 74 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL 8 115 " --> pdb=" O LEU 8 76 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR 8 117 " --> pdb=" O PHE 8 78 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'b' and resid 89 through 92 removed outlier: 3.765A pdb=" N LEU b 68 " --> pdb=" O ALA b 160 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU b 161 " --> pdb=" O PRO b 182 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE b 186 " --> pdb=" O ILE b 163 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'c' and resid 52 through 58 removed outlier: 3.825A pdb=" N LYS c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN c 64 " --> pdb=" O GLU c 57 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE c 105 " --> pdb=" O THR c 69 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'c' and resid 163 through 170 removed outlier: 3.710A pdb=" N GLY c 154 " --> pdb=" O ARG c 163 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'd' and resid 165 through 168 removed outlier: 3.617A pdb=" N ASP d 168 " --> pdb=" O GLU d 173 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU d 173 " --> pdb=" O ASP d 168 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'e' and resid 17 through 25 removed outlier: 3.520A pdb=" N THR e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'e' and resid 83 through 88 removed outlier: 7.826A pdb=" N HIS e 83 " --> pdb=" O PRO e 98 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP e 122 " --> pdb=" O ALA e 99 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE e 123 " --> pdb=" O GLY e 104 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'f' and resid 39 through 43 removed outlier: 3.977A pdb=" N GLY f 39 " --> pdb=" O ASN f 64 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LYS f 3 " --> pdb=" O GLU f 93 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'f' and resid 44 through 48 removed outlier: 4.024A pdb=" N GLY f 44 " --> pdb=" O TYR f 60 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG f 56 " --> pdb=" O LEU f 48 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'g' and resid 72 through 79 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain 'h' and resid 23 through 27 removed outlier: 6.104A pdb=" N GLU h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'h' and resid 76 through 80 removed outlier: 4.391A pdb=" N GLY h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE h 80 " --> pdb=" O LEU h 128 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU h 128 " --> pdb=" O ILE h 80 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU h 126 " --> pdb=" O SER h 107 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'i' and resid 5 through 11 removed outlier: 3.527A pdb=" N TYR i 6 " --> pdb=" O LEU i 21 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'j' and resid 42 through 52 removed outlier: 4.921A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS j 11 " --> pdb=" O ASP j 97 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP j 97 " --> pdb=" O LYS j 11 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'k' and resid 32 through 37 removed outlier: 3.539A pdb=" N GLY k 21 " --> pdb=" O THR k 83 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA k 111 " --> pdb=" O LEU k 84 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'l' and resid 42 through 46 removed outlier: 5.194A pdb=" N LEU l 94 " --> pdb=" O VAL l 111 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'l' and resid 64 through 69 removed outlier: 5.321A pdb=" N LYS l 64 " --> pdb=" O ILE l 80 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE l 80 " --> pdb=" O LYS l 64 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'p' and resid 5 through 11 removed outlier: 3.859A pdb=" N ILE p 20 " --> pdb=" O GLY p 38 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY p 38 " --> pdb=" O ILE p 20 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL p 22 " --> pdb=" O THR p 36 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N THR p 36 " --> pdb=" O VAL p 22 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'q' and resid 8 through 13 removed outlier: 5.555A pdb=" N LYS q 8 " --> pdb=" O GLU q 65 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LYS q 62 " --> pdb=" O VAL q 78 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL q 78 " --> pdb=" O LYS q 62 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'q' and resid 21 through 32 No H-bonds generated for sheet with id= 75 Processing sheet with id= 76, first strand: chain 's' and resid 30 through 34 removed outlier: 3.594A pdb=" N VAL s 31 " --> pdb=" O THR s 48 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N HIS s 47 " --> pdb=" O ILE s 62 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE s 62 " --> pdb=" O HIS s 47 " (cutoff:3.500A) 1826 hydrogen bonds defined for protein. 5427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3662 hydrogen bonds 5854 hydrogen bond angles 0 basepair planarities 1460 basepair parallelities 2609 stacking parallelities Total time for adding SS restraints: 258.90 Time building geometry restraints manager: 68.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 17284 1.32 - 1.45: 69369 1.45 - 1.57: 62826 1.57 - 1.70: 9175 1.70 - 1.83: 264 Bond restraints: 158918 Sorted by residual: bond pdb=" C4 ATP V 901 " pdb=" C5 ATP V 901 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.37e+01 bond pdb=" C10 TEL A3001 " pdb=" N6 TEL A3001 " ideal model delta sigma weight residual 1.476 1.319 0.157 2.00e-02 2.50e+03 6.16e+01 bond pdb=" C4 ATP V 900 " pdb=" C5 ATP V 900 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.35e+01 bond pdb=" C5 ATP V 901 " pdb=" C6 ATP V 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" C5 ATP V 900 " pdb=" C6 ATP V 900 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.27e+01 ... (remaining 158913 not shown) Histogram of bond angle deviations from ideal: 89.43 - 99.20: 53 99.20 - 108.98: 58692 108.98 - 118.76: 98370 118.76 - 128.54: 74194 128.54 - 138.32: 6070 Bond angle restraints: 237379 Sorted by residual: angle pdb=" PB ATP V 901 " pdb=" O3B ATP V 901 " pdb=" PG ATP V 901 " ideal model delta sigma weight residual 139.87 111.78 28.09 1.00e+00 1.00e+00 7.89e+02 angle pdb=" PA ATP V 901 " pdb=" O3A ATP V 901 " pdb=" PB ATP V 901 " ideal model delta sigma weight residual 136.83 115.16 21.67 1.00e+00 1.00e+00 4.69e+02 angle pdb=" PA ATP V 900 " pdb=" O3A ATP V 900 " pdb=" PB ATP V 900 " ideal model delta sigma weight residual 136.83 116.72 20.11 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB ATP V 900 " pdb=" O3B ATP V 900 " pdb=" PG ATP V 900 " ideal model delta sigma weight residual 139.87 122.65 17.22 1.00e+00 1.00e+00 2.97e+02 angle pdb=" N GLY k 80 " pdb=" CA GLY k 80 " pdb=" C GLY k 80 " ideal model delta sigma weight residual 112.29 131.23 -18.94 1.12e+00 7.97e-01 2.86e+02 ... (remaining 237374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 88937 35.96 - 71.92: 11583 71.92 - 107.89: 1184 107.89 - 143.85: 52 143.85 - 179.81: 75 Dihedral angle restraints: 101831 sinusoidal: 84574 harmonic: 17257 Sorted by residual: dihedral pdb=" CA ASN R 50 " pdb=" C ASN R 50 " pdb=" N PRO R 51 " pdb=" CA PRO R 51 " ideal model delta harmonic sigma weight residual 180.00 111.74 68.26 0 5.00e+00 4.00e-02 1.86e+02 dihedral pdb=" CA LYS l 57 " pdb=" C LYS l 57 " pdb=" N PRO l 58 " pdb=" CA PRO l 58 " ideal model delta harmonic sigma weight residual -180.00 -117.00 -63.00 0 5.00e+00 4.00e-02 1.59e+02 dihedral pdb=" CA THR S 39 " pdb=" C THR S 39 " pdb=" N PRO S 40 " pdb=" CA PRO S 40 " ideal model delta harmonic sigma weight residual -180.00 -118.69 -61.31 0 5.00e+00 4.00e-02 1.50e+02 ... (remaining 101828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.081: 30296 1.081 - 2.163: 0 2.163 - 3.244: 0 3.244 - 4.325: 0 4.325 - 5.406: 2 Chirality restraints: 30298 Sorted by residual: chirality pdb=" C28 TEL A3001 " pdb=" C24 TEL A3001 " pdb=" C33 TEL A3001 " pdb=" C34 TEL A3001 " both_signs ideal model delta sigma weight residual False -2.76 2.64 -5.41 2.00e-01 2.50e+01 7.31e+02 chirality pdb=" C21 TEL A3001 " pdb=" C15 TEL A3001 " pdb=" C25 TEL A3001 " pdb=" C26 TEL A3001 " both_signs ideal model delta sigma weight residual False 2.76 -2.59 5.35 2.00e-01 2.50e+01 7.15e+02 chirality pdb=" CB VAL R 48 " pdb=" CA VAL R 48 " pdb=" CG1 VAL R 48 " pdb=" CG2 VAL R 48 " both_signs ideal model delta sigma weight residual False -2.63 -1.74 -0.89 2.00e-01 2.50e+01 1.99e+01 ... (remaining 30295 not shown) Planarity restraints: 12898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA d 32 " 0.105 5.00e-02 4.00e+02 1.62e-01 4.18e+01 pdb=" N PRO d 33 " -0.279 5.00e-02 4.00e+02 pdb=" CA PRO d 33 " 0.094 5.00e-02 4.00e+02 pdb=" CD PRO d 33 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 50 " -0.094 5.00e-02 4.00e+02 1.44e-01 3.32e+01 pdb=" N PRO R 51 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO R 51 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO R 51 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP d 9 " 0.032 2.00e-02 2.50e+03 3.23e-02 2.61e+01 pdb=" CG TRP d 9 " -0.087 2.00e-02 2.50e+03 pdb=" CD1 TRP d 9 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP d 9 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP d 9 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP d 9 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP d 9 " 0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP d 9 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP d 9 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP d 9 " -0.002 2.00e-02 2.50e+03 ... (remaining 12895 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.26: 51 2.26 - 2.92: 56829 2.92 - 3.58: 229865 3.58 - 4.24: 454787 4.24 - 4.90: 609677 Nonbonded interactions: 1351209 Sorted by model distance: nonbonded pdb=" OG1 THR V 45 " pdb=" O2A ATP V 901 " model vdw 1.595 2.440 nonbonded pdb=" CD LYS V 43 " pdb=" CG1 VAL V 156 " model vdw 1.782 3.860 nonbonded pdb=" NZ LYS V 43 " pdb=" CG1 VAL V 156 " model vdw 1.826 3.540 nonbonded pdb=" O ILE k 18 " pdb=" O GLY k 80 " model vdw 1.846 3.040 nonbonded pdb=" OG1 THR V 332 " pdb=" O2A ATP V 900 " model vdw 1.910 2.440 ... (remaining 1351204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 15.440 Check model and map are aligned: 1.560 Set scattering table: 1.040 Process input model: 562.160 Find NCS groups from input model: 2.860 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 588.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 0.009 0.157 158918 Z= 0.538 Angle : 1.296 28.094 237379 Z= 0.681 Chirality : 0.078 5.406 30298 Planarity : 0.009 0.162 12898 Dihedral : 24.084 179.811 90716 Min Nonbonded Distance : 1.595 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.15 % Favored : 90.36 % Rotamer: Outliers : 0.87 % Allowed : 5.01 % Favored : 94.12 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % Twisted General : 0.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.09), residues: 5956 helix: -2.75 (0.09), residues: 1883 sheet: -1.88 (0.14), residues: 1072 loop : -2.80 (0.09), residues: 3001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.005 TRP d 9 HIS 0.029 0.004 HIS M 13 PHE 0.051 0.005 PHE Y 30 TYR 0.047 0.005 TYR q 30 ARG 0.019 0.002 ARG P 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1948 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1904 time to evaluate : 6.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 270 ILE cc_start: 0.8742 (mt) cc_final: 0.8366 (pt) REVERT: E 144 LYS cc_start: 0.7823 (ptpt) cc_final: 0.7399 (mmtt) REVERT: F 128 TYR cc_start: 0.6821 (t80) cc_final: 0.6592 (t80) REVERT: K 85 VAL cc_start: 0.8722 (t) cc_final: 0.8388 (p) REVERT: L 81 LYS cc_start: 0.7487 (mttt) cc_final: 0.7234 (mmtt) REVERT: M 44 ASN cc_start: 0.7713 (m-40) cc_final: 0.7173 (m110) REVERT: M 96 VAL cc_start: 0.8952 (t) cc_final: 0.8718 (p) REVERT: N 27 ASN cc_start: 0.8482 (m110) cc_final: 0.7949 (m110) REVERT: N 33 THR cc_start: 0.9063 (p) cc_final: 0.8533 (m) REVERT: N 81 GLN cc_start: 0.7854 (mt0) cc_final: 0.7640 (mt0) REVERT: N 82 LYS cc_start: 0.8407 (tmtp) cc_final: 0.8173 (tttm) REVERT: O 107 LYS cc_start: 0.8016 (tttm) cc_final: 0.7744 (tttp) REVERT: R 2 TYR cc_start: 0.6564 (p90) cc_final: 0.6084 (p90) REVERT: R 81 ASN cc_start: 0.9072 (m-40) cc_final: 0.8868 (m-40) REVERT: T 59 TYR cc_start: 0.7336 (m-80) cc_final: 0.7131 (m-10) REVERT: T 60 LYS cc_start: 0.7642 (mtmt) cc_final: 0.7411 (mtpp) REVERT: U 101 LEU cc_start: 0.7811 (mm) cc_final: 0.7590 (mp) REVERT: V 84 THR cc_start: 0.5784 (t) cc_final: 0.5458 (p) REVERT: V 425 LYS cc_start: 0.6595 (mmpt) cc_final: 0.6375 (mtpt) REVERT: W 37 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7897 (tt0) REVERT: X 37 ARG cc_start: 0.6181 (ttt90) cc_final: 0.5366 (mpt180) REVERT: Y 27 ASN cc_start: 0.7889 (m-40) cc_final: 0.7622 (m110) REVERT: Z 17 GLU cc_start: 0.7548 (tp30) cc_final: 0.6532 (tp30) REVERT: Z 49 LYS cc_start: 0.7702 (tmtp) cc_final: 0.7467 (tttt) REVERT: 1 22 ASN cc_start: 0.8250 (m-40) cc_final: 0.7955 (m110) REVERT: 1 47 GLU cc_start: 0.7536 (tt0) cc_final: 0.7307 (tt0) REVERT: 3 23 LYS cc_start: 0.8718 (tttm) cc_final: 0.8488 (ttpp) REVERT: 4 22 LYS cc_start: 0.8097 (mttt) cc_final: 0.7503 (mtpp) REVERT: 8 54 LYS cc_start: 0.4861 (mttt) cc_final: 0.3991 (ptmt) REVERT: 8 121 MET cc_start: 0.2993 (OUTLIER) cc_final: -0.0991 (tmm) REVERT: b 34 GLU cc_start: 0.4422 (tt0) cc_final: 0.4066 (tp30) REVERT: b 78 ASP cc_start: 0.4625 (m-30) cc_final: 0.3724 (t70) REVERT: b 111 ILE cc_start: 0.5751 (tp) cc_final: 0.5529 (mt) REVERT: b 144 LEU cc_start: 0.7312 (mp) cc_final: 0.6895 (mp) REVERT: c 74 MET cc_start: 0.7269 (tpt) cc_final: 0.6852 (tpp) REVERT: c 165 GLU cc_start: 0.4695 (mt-10) cc_final: 0.4314 (mt-10) REVERT: d 19 LEU cc_start: 0.6172 (pt) cc_final: 0.5844 (pp) REVERT: d 33 PRO cc_start: 0.6510 (Cg_endo) cc_final: 0.5782 (Cg_exo) REVERT: e 23 LYS cc_start: 0.8877 (tmtp) cc_final: 0.8486 (tttp) REVERT: e 45 HIS cc_start: 0.6083 (m90) cc_final: 0.5857 (m-70) REVERT: e 136 MET cc_start: 0.8620 (mtm) cc_final: 0.8406 (mtm) REVERT: e 162 GLU cc_start: 0.4313 (mp0) cc_final: 0.3922 (tp30) REVERT: f 23 ILE cc_start: 0.6063 (mt) cc_final: 0.5439 (pt) REVERT: g 9 LYS cc_start: 0.6241 (pmtt) cc_final: 0.5901 (tptp) REVERT: g 43 LEU cc_start: 0.8200 (tt) cc_final: 0.7876 (tt) REVERT: g 63 GLU cc_start: 0.6845 (mp0) cc_final: 0.6516 (mp0) REVERT: g 125 LEU cc_start: 0.8213 (mt) cc_final: 0.7849 (mt) REVERT: h 18 ASN cc_start: 0.8577 (m-40) cc_final: 0.8362 (m-40) REVERT: h 31 LYS cc_start: 0.6904 (tttt) cc_final: 0.6551 (tppt) REVERT: h 114 THR cc_start: 0.6589 (p) cc_final: 0.5690 (p) REVERT: h 127 VAL cc_start: 0.7912 (t) cc_final: 0.7664 (m) REVERT: i 62 ASP cc_start: 0.5517 (m-30) cc_final: 0.4564 (p0) REVERT: i 100 ARG cc_start: 0.6262 (mtm-85) cc_final: 0.5642 (ttm-80) REVERT: j 72 ARG cc_start: 0.6448 (mtt180) cc_final: 0.5747 (ttm170) REVERT: l 96 ARG cc_start: 0.4803 (ppt-90) cc_final: 0.4571 (ptt90) REVERT: m 83 ILE cc_start: 0.4543 (pt) cc_final: 0.3915 (pt) REVERT: q 32 LYS cc_start: 0.7130 (pptt) cc_final: 0.5933 (mttp) REVERT: r 18 PHE cc_start: 0.6613 (m-80) cc_final: 0.6402 (m-80) REVERT: t 46 LYS cc_start: 0.5910 (tmtt) cc_final: 0.5599 (ptpt) REVERT: t 48 LYS cc_start: 0.7693 (mttm) cc_final: 0.7212 (tptt) outliers start: 44 outliers final: 8 residues processed: 1935 average time/residue: 1.4072 time to fit residues: 4554.2732 Evaluate side-chains 1208 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1199 time to evaluate : 6.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain V residue 365 LEU Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 8 residue 121 MET Chi-restraints excluded: chain b residue 179 LEU Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain f residue 85 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 879 optimal weight: 0.0970 chunk 789 optimal weight: 20.0000 chunk 438 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 532 optimal weight: 9.9990 chunk 421 optimal weight: 0.9980 chunk 816 optimal weight: 10.0000 chunk 316 optimal weight: 4.9990 chunk 496 optimal weight: 0.7980 chunk 607 optimal weight: 2.9990 chunk 946 optimal weight: 10.0000 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN C 177 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN F 135 GLN ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN J 48 HIS L 59 GLN M 13 HIS N 12 GLN N 27 ASN N 68 ASN O 15 HIS Q 29 HIS Q 108 GLN Q 116 GLN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 HIS T 55 ASN ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 64 HIS V 140 GLN V 148 HIS V 207 GLN V 296 ASN V 309 ASN V 335 ASN ** V 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 388 ASN V 461 HIS ** V 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 37 GLN X 17 ASN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 GLN ** Z 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 23 ASN 0 40 HIS ** 0 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 26 ASN 3 35 ASN 4 34 GLN ** 4 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 ASN ** 6 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 67 ASN 8 170 ASN 8 188 ASN b 18 HIS b 24 ASN b 36 ASN b 123 ASN b 180 ASN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN c 175 HIS d 52 GLN d 59 HIS d 82 HIS ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN d 115 ASN d 118 HIS d 147 ASN ** e 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 ASN ** f 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 84 ASN g 106 ASN ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 126 GLN k 120 HIS l 42 GLN l 85 HIS l 90 HIS l 109 HIS n 10 GLN o 10 GLN o 18 HIS ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 51 HIS p 41 ASN q 49 HIS s 47 HIS t 70 ASN t 84 ASN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 158918 Z= 0.191 Angle : 0.715 27.702 237379 Z= 0.366 Chirality : 0.041 2.005 30298 Planarity : 0.006 0.112 12898 Dihedral : 24.932 179.254 78652 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.81 % Favored : 91.81 % Rotamer: Outliers : 4.41 % Allowed : 14.28 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.29 % 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: -2.56 (0.10), residues: 5956 helix: -0.90 (0.11), residues: 1898 sheet: -1.44 (0.15), residues: 1042 loop : -2.35 (0.10), residues: 3016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP d 9 HIS 0.008 0.001 HIS M 13 PHE 0.022 0.002 PHE V 20 TYR 0.029 0.002 TYR V 452 ARG 0.008 0.001 ARG r 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1563 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1341 time to evaluate : 6.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 270 ILE cc_start: 0.8548 (mt) cc_final: 0.8333 (pt) REVERT: D 22 LEU cc_start: 0.8064 (tp) cc_final: 0.7558 (tt) REVERT: E 144 LYS cc_start: 0.7567 (ptpt) cc_final: 0.7313 (mmtt) REVERT: F 112 ARG cc_start: 0.4766 (tpt170) cc_final: 0.4538 (tpt90) REVERT: F 140 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7381 (tm-30) REVERT: G 28 LYS cc_start: 0.5479 (mttt) cc_final: 0.4927 (tttm) REVERT: K 1 MET cc_start: 0.7609 (mmp) cc_final: 0.7380 (mmp) REVERT: K 81 GLU cc_start: 0.7134 (pp20) cc_final: 0.6658 (pp20) REVERT: K 85 VAL cc_start: 0.8698 (t) cc_final: 0.8425 (p) REVERT: L 1 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6700 (tpt) REVERT: L 18 ARG cc_start: 0.7997 (tmm-80) cc_final: 0.7595 (ttp-110) REVERT: L 81 LYS cc_start: 0.7567 (mttt) cc_final: 0.7263 (mmtt) REVERT: N 27 ASN cc_start: 0.8429 (m-40) cc_final: 0.8173 (m110) REVERT: N 33 THR cc_start: 0.9103 (p) cc_final: 0.8801 (m) REVERT: N 114 MET cc_start: 0.8212 (mmm) cc_final: 0.7792 (mmt) REVERT: O 12 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8277 (mp) REVERT: O 107 LYS cc_start: 0.7954 (tttm) cc_final: 0.7740 (tttp) REVERT: Q 106 PHE cc_start: 0.7737 (t80) cc_final: 0.7410 (t80) REVERT: R 95 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8211 (m) REVERT: S 62 TYR cc_start: 0.7683 (m-80) cc_final: 0.7263 (m-10) REVERT: T 56 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8034 (mm) REVERT: U 10 MET cc_start: 0.6854 (tpp) cc_final: 0.6413 (ttm) REVERT: V 96 VAL cc_start: 0.5139 (OUTLIER) cc_final: 0.3786 (t) REVERT: W 80 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.7238 (m-80) REVERT: X 37 ARG cc_start: 0.5999 (ttt90) cc_final: 0.5475 (mpt180) REVERT: Y 24 GLU cc_start: 0.7644 (tp30) cc_final: 0.7053 (tp30) REVERT: Y 52 ARG cc_start: 0.8345 (ptp90) cc_final: 0.7931 (ptp-170) REVERT: Y 58 ARG cc_start: 0.8275 (tpt170) cc_final: 0.8061 (tpp80) REVERT: Z 17 GLU cc_start: 0.7403 (tp30) cc_final: 0.6562 (tp30) REVERT: Z 20 ARG cc_start: 0.8283 (mtp180) cc_final: 0.7500 (mtp180) REVERT: Z 49 LYS cc_start: 0.7507 (tmtp) cc_final: 0.7295 (tttt) REVERT: Z 57 LYS cc_start: 0.7910 (mmtm) cc_final: 0.7653 (mmtp) REVERT: 0 49 TYR cc_start: 0.8808 (t80) cc_final: 0.8569 (t80) REVERT: 1 40 LYS cc_start: 0.8886 (mttt) cc_final: 0.8655 (mttp) REVERT: 3 23 LYS cc_start: 0.8745 (tttm) cc_final: 0.8472 (ttpp) REVERT: 4 22 LYS cc_start: 0.8295 (mttt) cc_final: 0.7622 (mtpp) REVERT: 8 121 MET cc_start: 0.1530 (mmp) cc_final: -0.1497 (mmm) REVERT: b 34 GLU cc_start: 0.3879 (tt0) cc_final: 0.3678 (tp30) REVERT: b 78 ASP cc_start: 0.4845 (m-30) cc_final: 0.3711 (t70) REVERT: b 178 LYS cc_start: 0.5653 (ttmt) cc_final: 0.5432 (tppt) REVERT: c 26 LYS cc_start: 0.6186 (mttt) cc_final: 0.5945 (mmmt) REVERT: c 34 GLU cc_start: 0.6376 (mt-10) cc_final: 0.6074 (mp0) REVERT: c 36 LEU cc_start: 0.7741 (mt) cc_final: 0.7499 (mp) REVERT: c 202 TYR cc_start: 0.8404 (t80) cc_final: 0.8020 (t80) REVERT: d 7 PRO cc_start: 0.4761 (Cg_exo) cc_final: 0.4464 (Cg_endo) REVERT: d 65 GLU cc_start: 0.6701 (tm-30) cc_final: 0.6284 (tm-30) REVERT: d 105 ARG cc_start: 0.4010 (mtt180) cc_final: 0.3783 (mtm180) REVERT: f 23 ILE cc_start: 0.6329 (mt) cc_final: 0.5632 (pt) REVERT: g 9 LYS cc_start: 0.6030 (pmtt) cc_final: 0.5801 (tptp) REVERT: g 43 LEU cc_start: 0.8184 (tt) cc_final: 0.7974 (tt) REVERT: g 97 THR cc_start: 0.7760 (p) cc_final: 0.7350 (p) REVERT: h 18 ASN cc_start: 0.8615 (m-40) cc_final: 0.8128 (m110) REVERT: h 35 GLU cc_start: 0.6883 (tp30) cc_final: 0.6293 (tp30) REVERT: h 78 LYS cc_start: 0.6276 (tttp) cc_final: 0.5562 (tptt) REVERT: i 6 TYR cc_start: 0.6137 (m-80) cc_final: 0.5932 (m-80) REVERT: i 7 TYR cc_start: 0.5724 (t80) cc_final: 0.4993 (t80) REVERT: i 61 TYR cc_start: 0.4146 (m-80) cc_final: 0.2555 (m-80) REVERT: i 100 ARG cc_start: 0.6199 (mtm-85) cc_final: 0.5817 (ttt90) REVERT: i 110 MET cc_start: 0.7755 (mmm) cc_final: 0.7538 (mmp) REVERT: j 24 LYS cc_start: 0.7124 (tppt) cc_final: 0.6423 (ttpt) REVERT: j 62 ARG cc_start: 0.7924 (mtt-85) cc_final: 0.7615 (mtt-85) REVERT: l 79 TYR cc_start: 0.4727 (t80) cc_final: 0.4284 (t80) REVERT: l 89 GLU cc_start: 0.5207 (tt0) cc_final: 0.4910 (mp0) REVERT: l 96 ARG cc_start: 0.5172 (ppt-90) cc_final: 0.4963 (ptt90) REVERT: m 55 LYS cc_start: 0.7088 (mttt) cc_final: 0.6767 (mmmm) REVERT: m 80 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6050 (mt) REVERT: o 37 ASN cc_start: 0.6339 (m-40) cc_final: 0.5927 (m-40) REVERT: q 32 LYS cc_start: 0.7124 (pptt) cc_final: 0.6000 (mttp) REVERT: r 18 PHE cc_start: 0.6651 (m-80) cc_final: 0.6375 (m-80) REVERT: r 33 LEU cc_start: 0.6554 (tp) cc_final: 0.6252 (tp) REVERT: t 48 LYS cc_start: 0.7849 (mttm) cc_final: 0.7303 (tptt) outliers start: 222 outliers final: 106 residues processed: 1466 average time/residue: 1.3638 time to fit residues: 3435.9351 Evaluate side-chains 1261 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1148 time to evaluate : 5.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 37 ASN Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 91 VAL Chi-restraints excluded: chain V residue 96 VAL Chi-restraints excluded: chain V residue 102 HIS Chi-restraints excluded: chain V residue 148 HIS Chi-restraints excluded: chain V residue 175 ASP Chi-restraints excluded: chain V residue 365 LEU Chi-restraints excluded: chain V residue 438 ASP Chi-restraints excluded: chain W residue 80 PHE Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 62 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 24 ARG Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain 0 residue 28 THR Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 6 residue 35 ILE Chi-restraints excluded: chain b residue 127 ASP Chi-restraints excluded: chain b residue 179 LEU Chi-restraints excluded: chain b residue 217 MET Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain d residue 68 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain e residue 97 LYS Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 88 HIS Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 128 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 61 SER Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain n residue 29 ARG Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain s residue 31 VAL Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 525 optimal weight: 3.9990 chunk 293 optimal weight: 9.9990 chunk 787 optimal weight: 10.0000 chunk 644 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 947 optimal weight: 9.9990 chunk 1024 optimal weight: 5.9990 chunk 844 optimal weight: 7.9990 chunk 940 optimal weight: 10.0000 chunk 323 optimal weight: 7.9990 chunk 760 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN G 62 HIS J 59 ASN ** J 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 GLN L 106 ASN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 ASN Q 116 GLN R 65 GLN R 81 ASN ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS V 148 HIS ** V 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 218 ASN V 241 HIS ** V 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 369 GLN ** V 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 444 GLN X 23 ASN Y 27 ASN Z 33 GLN ** Z 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 34 GLN ** 4 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 136 GLN d 50 GLN ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 28 ASN ** g 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN i 126 GLN l 35 HIS l 42 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 13 ASN ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 85 ASN q 54 GLN ** t 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 68 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 158918 Z= 0.454 Angle : 0.889 26.846 237379 Z= 0.449 Chirality : 0.050 2.215 30298 Planarity : 0.007 0.111 12898 Dihedral : 24.871 179.656 78643 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.59 % Favored : 89.94 % Rotamer: Outliers : 6.44 % Allowed : 17.22 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.33 % 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: -2.41 (0.10), residues: 5956 helix: -0.68 (0.11), residues: 1918 sheet: -1.40 (0.15), residues: 1030 loop : -2.32 (0.10), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP b 23 HIS 0.025 0.003 HIS V 148 PHE 0.031 0.003 PHE 0 5 TYR 0.028 0.003 TYR q 30 ARG 0.016 0.001 ARG c 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1546 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 1222 time to evaluate : 6.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 188 CYS cc_start: 0.7691 (m) cc_final: 0.7256 (p) REVERT: E 144 LYS cc_start: 0.8059 (ptpt) cc_final: 0.7790 (mmtt) REVERT: F 103 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7931 (tt) REVERT: F 141 ILE cc_start: 0.7096 (mm) cc_final: 0.6418 (mt) REVERT: G 111 SER cc_start: 0.8366 (p) cc_final: 0.8042 (t) REVERT: G 145 ILE cc_start: 0.8453 (mt) cc_final: 0.8213 (mm) REVERT: K 32 THR cc_start: 0.8362 (p) cc_final: 0.8116 (p) REVERT: L 1 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6684 (tpt) REVERT: L 18 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7352 (ttp-110) REVERT: L 81 LYS cc_start: 0.7760 (mttt) cc_final: 0.7376 (mmtt) REVERT: M 5 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8197 (mmmt) REVERT: M 18 ARG cc_start: 0.7975 (ptm-80) cc_final: 0.7695 (mtm110) REVERT: M 45 ARG cc_start: 0.8297 (mtp85) cc_final: 0.7995 (mmt90) REVERT: P 81 ILE cc_start: 0.8709 (mt) cc_final: 0.8420 (tt) REVERT: R 63 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7641 (tm-30) REVERT: R 95 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8244 (m) REVERT: S 62 TYR cc_start: 0.7925 (m-80) cc_final: 0.7582 (m-10) REVERT: T 56 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8032 (mm) REVERT: U 10 MET cc_start: 0.6985 (tpp) cc_final: 0.6753 (ttm) REVERT: U 101 LEU cc_start: 0.7429 (mt) cc_final: 0.7070 (mp) REVERT: V 196 ARG cc_start: 0.5914 (mtt-85) cc_final: 0.5492 (mmm-85) REVERT: V 452 TYR cc_start: 0.8219 (t80) cc_final: 0.7545 (t80) REVERT: W 19 LYS cc_start: 0.7859 (tppp) cc_final: 0.7630 (mmtm) REVERT: W 80 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: X 7 ILE cc_start: 0.8127 (mt) cc_final: 0.7818 (mt) REVERT: X 37 ARG cc_start: 0.6655 (ttt90) cc_final: 0.5692 (mtt180) REVERT: Z 17 GLU cc_start: 0.7507 (tp30) cc_final: 0.7161 (tp30) REVERT: 0 36 MET cc_start: 0.8337 (mmm) cc_final: 0.8048 (mmp) REVERT: 0 49 TYR cc_start: 0.8815 (t80) cc_final: 0.8568 (t80) REVERT: 2 1 MET cc_start: 0.8629 (mtm) cc_final: 0.8391 (mtm) REVERT: 3 23 LYS cc_start: 0.8908 (tttm) cc_final: 0.8587 (ttpp) REVERT: 3 62 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8417 (pp) REVERT: 4 22 LYS cc_start: 0.8330 (mttt) cc_final: 0.7751 (mtpp) REVERT: 8 121 MET cc_start: 0.0765 (mmp) cc_final: -0.2237 (mmm) REVERT: b 34 GLU cc_start: 0.4707 (tt0) cc_final: 0.4293 (tp30) REVERT: b 78 ASP cc_start: 0.5432 (m-30) cc_final: 0.4171 (t0) REVERT: c 34 GLU cc_start: 0.6510 (mt-10) cc_final: 0.5741 (mp0) REVERT: c 74 MET cc_start: 0.7413 (tpp) cc_final: 0.6771 (ttp) REVERT: d 60 MET cc_start: 0.4873 (tpt) cc_final: 0.4102 (tpt) REVERT: d 139 ILE cc_start: 0.4753 (mm) cc_final: 0.4226 (mm) REVERT: e 138 ARG cc_start: 0.8197 (mmt90) cc_final: 0.7759 (mmt90) REVERT: g 9 LYS cc_start: 0.6398 (pmtt) cc_final: 0.5545 (tptp) REVERT: g 63 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6281 (mt-10) REVERT: g 66 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8091 (mp) REVERT: h 18 ASN cc_start: 0.8689 (m-40) cc_final: 0.8445 (m110) REVERT: h 35 GLU cc_start: 0.6788 (tp30) cc_final: 0.6490 (tp30) REVERT: i 61 TYR cc_start: 0.4780 (m-80) cc_final: 0.2970 (m-80) REVERT: i 100 ARG cc_start: 0.6736 (mtm-85) cc_final: 0.6278 (ttt90) REVERT: j 44 THR cc_start: 0.6973 (OUTLIER) cc_final: 0.6753 (t) REVERT: l 79 TYR cc_start: 0.5092 (t80) cc_final: 0.4620 (t80) REVERT: l 107 ARG cc_start: 0.7194 (mtm-85) cc_final: 0.6885 (ttp-110) REVERT: m 55 LYS cc_start: 0.7024 (mttt) cc_final: 0.6823 (mmmm) REVERT: n 31 HIS cc_start: 0.6126 (m-70) cc_final: 0.5867 (m-70) REVERT: o 37 ASN cc_start: 0.6154 (m-40) cc_final: 0.5758 (t0) REVERT: p 57 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.5943 (mp) REVERT: q 32 LYS cc_start: 0.7466 (pptt) cc_final: 0.6222 (mttp) REVERT: r 18 PHE cc_start: 0.6692 (m-80) cc_final: 0.6291 (m-80) REVERT: s 69 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.6715 (m-70) REVERT: t 48 LYS cc_start: 0.7896 (mttm) cc_final: 0.7296 (tttt) outliers start: 324 outliers final: 210 residues processed: 1428 average time/residue: 1.2938 time to fit residues: 3189.4926 Evaluate side-chains 1310 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1088 time to evaluate : 6.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 37 ASN Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 57 MET Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 91 VAL Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 11 SER Chi-restraints excluded: chain V residue 61 ILE Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 96 VAL Chi-restraints excluded: chain V residue 102 HIS Chi-restraints excluded: chain V residue 123 ASP Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 133 HIS Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 175 ASP Chi-restraints excluded: chain V residue 254 SER Chi-restraints excluded: chain V residue 276 THR Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain V residue 294 VAL Chi-restraints excluded: chain V residue 365 LEU Chi-restraints excluded: chain V residue 377 ASN Chi-restraints excluded: chain V residue 379 THR Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain V residue 438 ASP Chi-restraints excluded: chain V residue 450 SER Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 80 PHE Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Y residue 57 ILE Chi-restraints excluded: chain Y residue 62 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 28 THR Chi-restraints excluded: chain 1 residue 3 VAL Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 21 LYS Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 3 residue 29 THR Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 127 ASP Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 217 MET Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 136 GLN Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain d residue 54 LYS Chi-restraints excluded: chain d residue 68 PHE Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain e residue 4 ILE Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 62 LYS Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 97 LYS Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 88 HIS Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 63 GLU Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 61 SER Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 63 PHE Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 53 LEU Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain n residue 29 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain o residue 68 THR Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 43 VAL Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain r residue 21 ASN Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 936 optimal weight: 7.9990 chunk 712 optimal weight: 20.0000 chunk 491 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 452 optimal weight: 0.0770 chunk 636 optimal weight: 5.9990 chunk 951 optimal weight: 5.9990 chunk 1007 optimal weight: 8.9990 chunk 497 optimal weight: 0.0050 chunk 901 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 overall best weight: 2.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 ASN ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 GLN ** J 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN N 95 GLN P 29 HIS R 81 ASN ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 206 GLN V 216 GLN ** V 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN Z 33 GLN ** Z 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 23 ASN ** 0 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 35 ASN 4 36 GLN ** 6 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN d 52 GLN ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 ASN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 11 GLN ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 85 ASN q 54 GLN ** t 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 158918 Z= 0.209 Angle : 0.678 28.634 237379 Z= 0.348 Chirality : 0.040 2.127 30298 Planarity : 0.005 0.106 12898 Dihedral : 24.722 179.950 78641 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.28 % Favored : 91.37 % Rotamer: Outliers : 5.32 % Allowed : 20.08 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.10), residues: 5956 helix: -0.20 (0.11), residues: 1924 sheet: -1.14 (0.16), residues: 985 loop : -2.13 (0.10), residues: 3047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 200 HIS 0.022 0.001 HIS l 35 PHE 0.025 0.002 PHE f 26 TYR 0.022 0.002 TYR V 275 ARG 0.010 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1479 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1211 time to evaluate : 5.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: C 115 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6428 (tp30) REVERT: C 188 CYS cc_start: 0.7433 (m) cc_final: 0.7142 (p) REVERT: E 144 LYS cc_start: 0.7923 (ptpt) cc_final: 0.7712 (mmtt) REVERT: F 140 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7372 (tm-30) REVERT: F 141 ILE cc_start: 0.6586 (mm) cc_final: 0.6342 (mt) REVERT: G 77 VAL cc_start: 0.7129 (t) cc_final: 0.6910 (m) REVERT: J 107 LYS cc_start: 0.8306 (mtpp) cc_final: 0.8081 (mtpp) REVERT: K 81 GLU cc_start: 0.7323 (pp20) cc_final: 0.7058 (pp20) REVERT: L 18 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7506 (ttp-110) REVERT: L 55 MET cc_start: 0.8310 (mmm) cc_final: 0.8034 (mmm) REVERT: L 81 LYS cc_start: 0.7562 (mttt) cc_final: 0.7259 (mmtt) REVERT: L 126 ASN cc_start: 0.8140 (t0) cc_final: 0.7911 (t0) REVERT: M 45 ARG cc_start: 0.8220 (mtp85) cc_final: 0.7960 (mmt90) REVERT: M 65 TRP cc_start: 0.8382 (m-90) cc_final: 0.7961 (m-90) REVERT: P 81 ILE cc_start: 0.8579 (mt) cc_final: 0.8300 (tt) REVERT: Q 106 PHE cc_start: 0.7952 (t80) cc_final: 0.7373 (t80) REVERT: Q 116 GLN cc_start: 0.8213 (tp40) cc_final: 0.7509 (tm-30) REVERT: R 95 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8303 (m) REVERT: S 62 TYR cc_start: 0.7842 (m-80) cc_final: 0.7495 (m-10) REVERT: T 56 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7992 (mm) REVERT: U 101 LEU cc_start: 0.7277 (mt) cc_final: 0.6991 (mp) REVERT: V 214 GLU cc_start: 0.7863 (mp0) cc_final: 0.7486 (mp0) REVERT: V 396 THR cc_start: 0.5992 (OUTLIER) cc_final: 0.5515 (m) REVERT: V 452 TYR cc_start: 0.7984 (t80) cc_final: 0.7176 (t80) REVERT: W 80 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: Y 24 GLU cc_start: 0.7997 (tp30) cc_final: 0.7450 (tp30) REVERT: Y 53 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7401 (mtt) REVERT: Z 17 GLU cc_start: 0.7351 (tp30) cc_final: 0.6524 (tp30) REVERT: Z 20 ARG cc_start: 0.8353 (mtp180) cc_final: 0.7490 (mtp180) REVERT: 0 36 MET cc_start: 0.8333 (mmm) cc_final: 0.8062 (mmp) REVERT: 0 49 TYR cc_start: 0.8537 (t80) cc_final: 0.8234 (t80) REVERT: 2 1 MET cc_start: 0.8553 (mtm) cc_final: 0.8283 (mtm) REVERT: 4 22 LYS cc_start: 0.8330 (mttt) cc_final: 0.7722 (mtpp) REVERT: 8 120 MET cc_start: 0.0614 (mtm) cc_final: -0.0169 (mtm) REVERT: 8 121 MET cc_start: 0.0261 (mmp) cc_final: -0.1950 (mmm) REVERT: b 34 GLU cc_start: 0.4420 (tt0) cc_final: 0.4195 (tp30) REVERT: b 78 ASP cc_start: 0.5106 (m-30) cc_final: 0.4053 (t70) REVERT: b 129 LEU cc_start: 0.5050 (OUTLIER) cc_final: 0.4306 (tp) REVERT: b 175 GLU cc_start: 0.3200 (OUTLIER) cc_final: 0.2410 (pt0) REVERT: c 34 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6416 (mp0) REVERT: c 74 MET cc_start: 0.7420 (tpp) cc_final: 0.6776 (ttp) REVERT: d 60 MET cc_start: 0.4829 (tpt) cc_final: 0.3943 (tpt) REVERT: d 65 GLU cc_start: 0.6609 (tm-30) cc_final: 0.6258 (tm-30) REVERT: d 87 MET cc_start: 0.7396 (mtm) cc_final: 0.6960 (mtp) REVERT: d 93 ARG cc_start: 0.5947 (tmm-80) cc_final: 0.4868 (ttp-110) REVERT: e 138 ARG cc_start: 0.8153 (mmt90) cc_final: 0.7923 (mmt90) REVERT: g 9 LYS cc_start: 0.6371 (pmtt) cc_final: 0.5368 (tptp) REVERT: g 63 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6041 (mt-10) REVERT: h 57 GLN cc_start: 0.5886 (OUTLIER) cc_final: 0.5338 (tp40) REVERT: i 6 TYR cc_start: 0.6194 (m-80) cc_final: 0.5569 (m-80) REVERT: i 7 TYR cc_start: 0.5516 (t80) cc_final: 0.5291 (t80) REVERT: i 61 TYR cc_start: 0.4729 (m-80) cc_final: 0.3022 (m-80) REVERT: i 100 ARG cc_start: 0.6386 (mtm-85) cc_final: 0.5872 (ttt90) REVERT: j 24 LYS cc_start: 0.6876 (tppt) cc_final: 0.6635 (ttpt) REVERT: l 79 TYR cc_start: 0.5022 (t80) cc_final: 0.4628 (t80) REVERT: l 89 GLU cc_start: 0.5230 (tt0) cc_final: 0.4845 (mp0) REVERT: o 37 ASN cc_start: 0.6127 (m-40) cc_final: 0.5723 (m-40) REVERT: q 32 LYS cc_start: 0.7541 (pptt) cc_final: 0.6362 (mttp) REVERT: t 48 LYS cc_start: 0.7893 (mttm) cc_final: 0.7264 (tttt) outliers start: 268 outliers final: 177 residues processed: 1365 average time/residue: 1.2796 time to fit residues: 3027.4157 Evaluate side-chains 1301 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1113 time to evaluate : 6.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 37 ASN Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 57 MET Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain V residue 11 SER Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 102 HIS Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 133 HIS Chi-restraints excluded: chain V residue 175 ASP Chi-restraints excluded: chain V residue 210 VAL Chi-restraints excluded: chain V residue 216 GLN Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain V residue 365 LEU Chi-restraints excluded: chain V residue 377 ASN Chi-restraints excluded: chain V residue 379 THR Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 396 THR Chi-restraints excluded: chain V residue 426 ASP Chi-restraints excluded: chain V residue 438 ASP Chi-restraints excluded: chain V residue 450 SER Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 80 PHE Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Y residue 62 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 28 THR Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 21 LYS Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 8 residue 110 ASP Chi-restraints excluded: chain 8 residue 209 VAL Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 127 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 175 GLU Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 217 MET Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain d residue 68 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 62 LYS Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 97 LYS Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 141 LEU Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 88 HIS Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 63 GLU Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 118 LEU Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 61 SER Chi-restraints excluded: chain k residue 63 PHE Chi-restraints excluded: chain k residue 95 ARG Chi-restraints excluded: chain k residue 123 CYS Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain n residue 29 ARG Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain o residue 68 THR Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 28 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 838 optimal weight: 6.9990 chunk 571 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 749 optimal weight: 20.0000 chunk 415 optimal weight: 0.0060 chunk 859 optimal weight: 6.9990 chunk 696 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 514 optimal weight: 7.9990 chunk 904 optimal weight: 0.4980 chunk 254 optimal weight: 10.0000 overall best weight: 4.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 HIS C 232 HIS E 10 ASN ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 HIS ** J 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 2 GLN V 158 HIS ** V 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** Z 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 23 ASN ** 0 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 34 GLN 6 60 ASN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 136 GLN d 50 GLN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 HIS q 54 GLN ** t 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 158918 Z= 0.305 Angle : 0.734 28.424 237379 Z= 0.375 Chirality : 0.043 2.123 30298 Planarity : 0.006 0.104 12898 Dihedral : 24.669 179.589 78641 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.54 % Favored : 90.18 % Rotamer: Outliers : 6.81 % Allowed : 20.36 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.10), residues: 5956 helix: -0.15 (0.11), residues: 1922 sheet: -1.20 (0.16), residues: 970 loop : -2.11 (0.10), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 23 HIS 0.011 0.002 HIS M 28 PHE 0.034 0.002 PHE M 29 TYR 0.025 0.002 TYR d 61 ARG 0.009 0.001 ARG b 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 343 poor density : 1135 time to evaluate : 6.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: C 188 CYS cc_start: 0.7640 (m) cc_final: 0.7136 (p) REVERT: C 221 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8433 (mtm-85) REVERT: E 144 LYS cc_start: 0.8118 (ptpt) cc_final: 0.7820 (mmtm) REVERT: F 140 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7400 (tm-30) REVERT: G 145 ILE cc_start: 0.8396 (mt) cc_final: 0.8019 (mm) REVERT: J 107 LYS cc_start: 0.8352 (mtpp) cc_final: 0.8095 (mtpp) REVERT: K 1 MET cc_start: 0.7644 (mmp) cc_final: 0.7402 (mmp) REVERT: K 81 GLU cc_start: 0.7351 (pp20) cc_final: 0.7145 (pp20) REVERT: L 18 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7542 (ttp-110) REVERT: L 55 MET cc_start: 0.8445 (mmm) cc_final: 0.8187 (mmm) REVERT: L 64 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7407 (ttm170) REVERT: L 81 LYS cc_start: 0.7578 (mttt) cc_final: 0.7290 (mmtt) REVERT: L 104 LYS cc_start: 0.8159 (tptm) cc_final: 0.7867 (tptp) REVERT: L 114 ASN cc_start: 0.7392 (OUTLIER) cc_final: 0.7116 (p0) REVERT: M 45 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7941 (mmt90) REVERT: N 102 MET cc_start: 0.8069 (mtp) cc_final: 0.7863 (mtp) REVERT: O 107 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7566 (tttp) REVERT: Q 106 PHE cc_start: 0.8045 (t80) cc_final: 0.7511 (t80) REVERT: R 95 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8316 (m) REVERT: S 62 TYR cc_start: 0.7926 (m-80) cc_final: 0.7471 (m-10) REVERT: T 56 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8029 (mm) REVERT: U 69 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6881 (mtm) REVERT: U 101 LEU cc_start: 0.7386 (mt) cc_final: 0.7124 (mp) REVERT: V 396 THR cc_start: 0.5633 (OUTLIER) cc_final: 0.5380 (m) REVERT: W 80 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: Y 44 ARG cc_start: 0.7777 (ptm-80) cc_final: 0.7498 (ptt-90) REVERT: Z 17 GLU cc_start: 0.7513 (tp30) cc_final: 0.7105 (tp30) REVERT: Z 20 ARG cc_start: 0.8306 (mtp180) cc_final: 0.7559 (mtp180) REVERT: 0 36 MET cc_start: 0.8379 (mmm) cc_final: 0.8122 (mmp) REVERT: 4 22 LYS cc_start: 0.8264 (mttt) cc_final: 0.7724 (mtpp) REVERT: b 34 GLU cc_start: 0.4929 (tt0) cc_final: 0.4438 (tp30) REVERT: b 78 ASP cc_start: 0.5455 (m-30) cc_final: 0.4318 (t70) REVERT: b 103 ASN cc_start: 0.5663 (t0) cc_final: 0.5364 (t0) REVERT: b 129 LEU cc_start: 0.5097 (OUTLIER) cc_final: 0.4244 (tp) REVERT: c 34 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6545 (mp0) REVERT: c 74 MET cc_start: 0.7620 (tpp) cc_final: 0.7036 (ttm) REVERT: d 60 MET cc_start: 0.4707 (tpt) cc_final: 0.3783 (tpt) REVERT: d 65 GLU cc_start: 0.6589 (tm-30) cc_final: 0.6211 (tm-30) REVERT: d 153 GLU cc_start: 0.2935 (mt-10) cc_final: 0.2358 (tp30) REVERT: e 80 THR cc_start: 0.8036 (m) cc_final: 0.7769 (m) REVERT: e 151 GLU cc_start: 0.6833 (pm20) cc_final: 0.6126 (tp30) REVERT: g 9 LYS cc_start: 0.6610 (pmtt) cc_final: 0.5501 (tptp) REVERT: g 27 ILE cc_start: 0.8211 (mm) cc_final: 0.7838 (mt) REVERT: g 31 MET cc_start: 0.5873 (OUTLIER) cc_final: 0.4344 (mtm) REVERT: g 63 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5979 (mt-10) REVERT: i 6 TYR cc_start: 0.6349 (m-80) cc_final: 0.5651 (m-80) REVERT: i 7 TYR cc_start: 0.5559 (t80) cc_final: 0.5345 (t80) REVERT: i 19 VAL cc_start: 0.7716 (t) cc_final: 0.7209 (p) REVERT: i 61 TYR cc_start: 0.4819 (m-80) cc_final: 0.3081 (m-80) REVERT: i 100 ARG cc_start: 0.6560 (mtm-85) cc_final: 0.6128 (ttt90) REVERT: j 24 LYS cc_start: 0.6867 (tppt) cc_final: 0.6625 (ttpt) REVERT: j 98 ILE cc_start: 0.6306 (OUTLIER) cc_final: 0.6077 (tt) REVERT: l 79 TYR cc_start: 0.5089 (t80) cc_final: 0.4667 (t80) REVERT: l 89 GLU cc_start: 0.5031 (tt0) cc_final: 0.4701 (mp0) REVERT: m 80 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6419 (mt) REVERT: n 31 HIS cc_start: 0.5664 (m-70) cc_final: 0.5415 (m-70) REVERT: o 37 ASN cc_start: 0.6297 (m-40) cc_final: 0.5903 (t0) REVERT: q 32 LYS cc_start: 0.7627 (pptt) cc_final: 0.6335 (mttp) REVERT: s 66 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6786 (mtp) REVERT: s 69 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.6603 (m-70) REVERT: t 10 ARG cc_start: 0.4840 (tpt170) cc_final: 0.4386 (mtt-85) REVERT: t 48 LYS cc_start: 0.7844 (mttm) cc_final: 0.7309 (tttt) outliers start: 343 outliers final: 247 residues processed: 1336 average time/residue: 1.2750 time to fit residues: 2969.2743 Evaluate side-chains 1344 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1079 time to evaluate : 6.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain L residue 114 ASN Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 37 ASN Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 107 LYS Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 55 ARG Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 57 MET Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 69 MET Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 11 SER Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 102 HIS Chi-restraints excluded: chain V residue 123 ASP Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 133 HIS Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 142 LEU Chi-restraints excluded: chain V residue 148 HIS Chi-restraints excluded: chain V residue 156 VAL Chi-restraints excluded: chain V residue 175 ASP Chi-restraints excluded: chain V residue 210 VAL Chi-restraints excluded: chain V residue 254 SER Chi-restraints excluded: chain V residue 276 THR Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain V residue 377 ASN Chi-restraints excluded: chain V residue 379 THR Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 396 THR Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 438 ASP Chi-restraints excluded: chain V residue 450 SER Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 80 PHE Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Y residue 57 ILE Chi-restraints excluded: chain Y residue 62 ILE Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 28 THR Chi-restraints excluded: chain 1 residue 3 VAL Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 21 LYS Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 29 THR Chi-restraints excluded: chain 3 residue 35 ASN Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 8 residue 110 ASP Chi-restraints excluded: chain 8 residue 175 ILE Chi-restraints excluded: chain 8 residue 178 VAL Chi-restraints excluded: chain 8 residue 209 VAL Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 127 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain b residue 140 GLU Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 217 MET Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 136 GLN Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 177 LEU Chi-restraints excluded: chain d residue 68 PHE Chi-restraints excluded: chain d residue 114 VAL Chi-restraints excluded: chain d residue 160 PHE Chi-restraints excluded: chain e residue 4 ILE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 62 LYS Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 141 LEU Chi-restraints excluded: chain e residue 149 ARG Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 88 HIS Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 63 GLU Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 118 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 61 SER Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 63 PHE Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain k residue 95 ARG Chi-restraints excluded: chain k residue 123 CYS Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 38 VAL Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 103 LEU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 53 LEU Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain n residue 29 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 68 THR Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 338 optimal weight: 5.9990 chunk 907 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 chunk 591 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 1008 optimal weight: 6.9990 chunk 836 optimal weight: 4.9990 chunk 466 optimal weight: 0.0670 chunk 83 optimal weight: 7.9990 chunk 333 optimal weight: 3.9990 chunk 529 optimal weight: 0.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 HIS ** J 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 95 GLN S 97 ASN V 9 ASN V 216 GLN ** V 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 23 ASN ** 0 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 56 HIS l 29 ASN l 35 HIS ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 HIS q 54 GLN ** t 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 158918 Z= 0.232 Angle : 0.677 28.593 237379 Z= 0.347 Chirality : 0.041 2.120 30298 Planarity : 0.005 0.108 12898 Dihedral : 24.626 179.757 78639 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.70 % Favored : 91.02 % Rotamer: Outliers : 6.46 % Allowed : 21.91 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.10), residues: 5956 helix: 0.07 (0.11), residues: 1907 sheet: -1.13 (0.16), residues: 973 loop : -2.05 (0.10), residues: 3076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP X 29 HIS 0.010 0.001 HIS 6 40 PHE 0.039 0.002 PHE f 26 TYR 0.022 0.002 TYR c 28 ARG 0.007 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1448 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 1123 time to evaluate : 6.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: C 188 CYS cc_start: 0.7516 (m) cc_final: 0.7209 (p) REVERT: E 144 LYS cc_start: 0.8087 (ptpt) cc_final: 0.7808 (mmtm) REVERT: F 140 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7375 (tm-30) REVERT: J 107 LYS cc_start: 0.8360 (mtpp) cc_final: 0.8111 (mtpp) REVERT: K 81 GLU cc_start: 0.7344 (pp20) cc_final: 0.7119 (pp20) REVERT: L 18 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7595 (ttp-110) REVERT: L 29 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8217 (tttp) REVERT: L 64 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7214 (ttm170) REVERT: L 81 LYS cc_start: 0.7585 (mttt) cc_final: 0.7255 (mmtt) REVERT: L 104 LYS cc_start: 0.8100 (tptm) cc_final: 0.7825 (tptp) REVERT: L 114 ASN cc_start: 0.7376 (OUTLIER) cc_final: 0.7103 (p0) REVERT: M 45 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7916 (mmt90) REVERT: N 102 MET cc_start: 0.8108 (mtp) cc_final: 0.7907 (mtp) REVERT: O 107 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7288 (tttp) REVERT: Q 106 PHE cc_start: 0.7961 (t80) cc_final: 0.7448 (t80) REVERT: R 95 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8318 (m) REVERT: S 62 TYR cc_start: 0.7902 (m-80) cc_final: 0.7417 (m-10) REVERT: T 56 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8052 (mm) REVERT: U 69 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6772 (mtm) REVERT: U 101 LEU cc_start: 0.7416 (mt) cc_final: 0.7110 (mp) REVERT: V 360 GLN cc_start: 0.5805 (tp40) cc_final: 0.5516 (tt0) REVERT: V 396 THR cc_start: 0.5757 (OUTLIER) cc_final: 0.5470 (m) REVERT: V 404 ILE cc_start: 0.7667 (mm) cc_final: 0.7431 (mm) REVERT: W 80 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7432 (m-80) REVERT: Y 15 GLU cc_start: 0.7483 (pp20) cc_final: 0.7243 (pm20) REVERT: Y 44 ARG cc_start: 0.7741 (ptm-80) cc_final: 0.7494 (ptt-90) REVERT: Y 53 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7427 (mtt) REVERT: Z 17 GLU cc_start: 0.7430 (tp30) cc_final: 0.7015 (tp30) REVERT: Z 20 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7564 (mtp180) REVERT: 3 4 MET cc_start: 0.8535 (tpp) cc_final: 0.8150 (mmm) REVERT: 4 22 LYS cc_start: 0.8241 (mttt) cc_final: 0.7764 (mtpp) REVERT: b 34 GLU cc_start: 0.4805 (tt0) cc_final: 0.4348 (tp30) REVERT: b 78 ASP cc_start: 0.5406 (m-30) cc_final: 0.4248 (t70) REVERT: b 129 LEU cc_start: 0.4924 (OUTLIER) cc_final: 0.4324 (tp) REVERT: c 74 MET cc_start: 0.7615 (tpp) cc_final: 0.7053 (ttm) REVERT: d 55 GLN cc_start: 0.6338 (mp10) cc_final: 0.6043 (mp10) REVERT: d 60 MET cc_start: 0.4768 (tpt) cc_final: 0.3978 (tpt) REVERT: d 65 GLU cc_start: 0.6538 (tm-30) cc_final: 0.6140 (tm-30) REVERT: d 153 GLU cc_start: 0.3125 (mt-10) cc_final: 0.2569 (tp30) REVERT: e 80 THR cc_start: 0.7999 (m) cc_final: 0.7779 (m) REVERT: e 155 LYS cc_start: 0.7818 (mmmt) cc_final: 0.7133 (mttt) REVERT: f 10 ILE cc_start: 0.4764 (OUTLIER) cc_final: 0.4331 (tt) REVERT: g 9 LYS cc_start: 0.6694 (pmtt) cc_final: 0.5518 (tptp) REVERT: g 27 ILE cc_start: 0.8232 (mm) cc_final: 0.8025 (mm) REVERT: g 31 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.4275 (mtm) REVERT: g 130 ASN cc_start: 0.6797 (OUTLIER) cc_final: 0.6546 (p0) REVERT: i 7 TYR cc_start: 0.5490 (t80) cc_final: 0.5212 (t80) REVERT: i 19 VAL cc_start: 0.7599 (t) cc_final: 0.7131 (p) REVERT: i 61 TYR cc_start: 0.4845 (m-80) cc_final: 0.3190 (m-80) REVERT: i 100 ARG cc_start: 0.6511 (mtm-85) cc_final: 0.6086 (ttt90) REVERT: j 24 LYS cc_start: 0.6842 (tppt) cc_final: 0.6589 (ttpt) REVERT: j 98 ILE cc_start: 0.6151 (OUTLIER) cc_final: 0.5847 (tt) REVERT: l 89 GLU cc_start: 0.5220 (tt0) cc_final: 0.4838 (mp0) REVERT: m 80 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6486 (mt) REVERT: n 31 HIS cc_start: 0.5639 (m-70) cc_final: 0.5388 (m-70) REVERT: o 37 ASN cc_start: 0.5960 (m-40) cc_final: 0.5561 (m-40) REVERT: p 57 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.5911 (mp) REVERT: q 32 LYS cc_start: 0.7596 (pttt) cc_final: 0.6311 (mttp) REVERT: q 79 GLU cc_start: 0.6039 (mp0) cc_final: 0.5748 (mp0) REVERT: s 69 HIS cc_start: 0.7644 (OUTLIER) cc_final: 0.6495 (m-70) REVERT: t 10 ARG cc_start: 0.4851 (tpt170) cc_final: 0.4363 (mtt-85) REVERT: t 48 LYS cc_start: 0.7853 (mttm) cc_final: 0.7304 (tttt) outliers start: 325 outliers final: 241 residues processed: 1317 average time/residue: 1.2708 time to fit residues: 2914.2007 Evaluate side-chains 1335 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1074 time to evaluate : 6.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain L residue 114 ASN Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 37 ASN Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 107 LYS Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 55 ARG Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 57 MET Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 69 MET Chi-restraints excluded: chain U residue 91 VAL Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 102 HIS Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 133 HIS Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 142 LEU Chi-restraints excluded: chain V residue 175 ASP Chi-restraints excluded: chain V residue 210 VAL Chi-restraints excluded: chain V residue 216 GLN Chi-restraints excluded: chain V residue 254 SER Chi-restraints excluded: chain V residue 264 GLU Chi-restraints excluded: chain V residue 276 THR Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain V residue 377 ASN Chi-restraints excluded: chain V residue 379 THR Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 396 THR Chi-restraints excluded: chain V residue 438 ASP Chi-restraints excluded: chain V residue 450 SER Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 80 PHE Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 38 GLU Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Y residue 62 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 28 THR Chi-restraints excluded: chain 1 residue 3 VAL Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 21 LYS Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 35 ASN Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 8 residue 110 ASP Chi-restraints excluded: chain 8 residue 209 VAL Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain b residue 95 ARG Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 127 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 217 MET Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 177 LEU Chi-restraints excluded: chain d residue 68 PHE Chi-restraints excluded: chain d residue 114 VAL Chi-restraints excluded: chain d residue 160 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 141 LEU Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 88 HIS Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 130 ASN Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 118 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 61 SER Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 63 PHE Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain k residue 95 ARG Chi-restraints excluded: chain k residue 123 CYS Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 38 VAL Chi-restraints excluded: chain l residue 44 ARG Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain n residue 29 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 70 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 972 optimal weight: 30.0000 chunk 113 optimal weight: 20.0000 chunk 574 optimal weight: 10.0000 chunk 736 optimal weight: 20.0000 chunk 570 optimal weight: 6.9990 chunk 848 optimal weight: 10.0000 chunk 562 optimal weight: 1.9990 chunk 1004 optimal weight: 10.0000 chunk 628 optimal weight: 10.0000 chunk 612 optimal weight: 4.9990 chunk 463 optimal weight: 8.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN E 8 ASN E 10 ASN ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 116 GLN S 95 GLN ** V 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** 0 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 26 HIS 8 188 ASN ** b 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 ASN c 136 GLN d 50 GLN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 38 HIS i 75 GLN l 29 ASN ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 85 ASN q 54 GLN ** t 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 158918 Z= 0.420 Angle : 0.842 28.596 237379 Z= 0.425 Chirality : 0.048 2.121 30298 Planarity : 0.006 0.103 12898 Dihedral : 24.752 179.797 78639 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.49 % Favored : 89.20 % Rotamer: Outliers : 7.39 % Allowed : 22.09 % Favored : 70.52 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.29 % 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: -2.18 (0.10), residues: 5956 helix: -0.32 (0.11), residues: 1921 sheet: -1.44 (0.16), residues: 941 loop : -2.23 (0.10), residues: 3094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 23 HIS 0.035 0.002 HIS l 35 PHE 0.030 0.003 PHE f 26 TYR 0.025 0.003 TYR V 420 ARG 0.011 0.001 ARG V 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1465 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 372 poor density : 1093 time to evaluate : 6.428 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: C 61 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: C 221 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8505 (mtm-85) REVERT: E 144 LYS cc_start: 0.8338 (ptpt) cc_final: 0.8033 (mmtt) REVERT: F 128 TYR cc_start: 0.7379 (t80) cc_final: 0.7058 (t80) REVERT: F 141 ILE cc_start: 0.6987 (mm) cc_final: 0.6681 (mt) REVERT: F 156 ILE cc_start: 0.8415 (mm) cc_final: 0.8146 (pt) REVERT: L 18 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7748 (ttp-110) REVERT: L 29 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.6199 (mmtt) REVERT: L 64 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7512 (tpm170) REVERT: L 71 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6446 (ttt-90) REVERT: L 81 LYS cc_start: 0.7655 (mttt) cc_final: 0.7373 (mmtt) REVERT: L 114 ASN cc_start: 0.7327 (OUTLIER) cc_final: 0.7120 (p0) REVERT: N 114 MET cc_start: 0.8633 (mmm) cc_final: 0.8063 (mmm) REVERT: O 107 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7725 (tttp) REVERT: P 49 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8710 (ttmt) REVERT: R 80 LYS cc_start: 0.8958 (mmtt) cc_final: 0.8700 (mmtt) REVERT: R 95 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8423 (m) REVERT: S 18 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.6810 (mpt-90) REVERT: T 56 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8022 (mm) REVERT: U 101 LEU cc_start: 0.7577 (mt) cc_final: 0.7264 (mp) REVERT: V 20 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.5927 (t80) REVERT: V 93 LYS cc_start: 0.6222 (mmtt) cc_final: 0.5935 (mttt) REVERT: W 80 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: Y 24 GLU cc_start: 0.7833 (tp30) cc_final: 0.7603 (tp30) REVERT: Y 28 LEU cc_start: 0.7939 (mm) cc_final: 0.7667 (mm) REVERT: Z 17 GLU cc_start: 0.7461 (tp30) cc_final: 0.7119 (tp30) REVERT: 2 1 MET cc_start: 0.8431 (mtm) cc_final: 0.8091 (mtp) REVERT: 4 22 LYS cc_start: 0.8281 (mttt) cc_final: 0.7823 (mtpp) REVERT: b 34 GLU cc_start: 0.5085 (tt0) cc_final: 0.4638 (tp30) REVERT: b 78 ASP cc_start: 0.5398 (m-30) cc_final: 0.4311 (t0) REVERT: b 129 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.4370 (tp) REVERT: c 31 PHE cc_start: 0.5483 (m-10) cc_final: 0.5240 (m-10) REVERT: c 74 MET cc_start: 0.7640 (tpp) cc_final: 0.7194 (ttm) REVERT: d 60 MET cc_start: 0.4842 (tpt) cc_final: 0.4178 (tpt) REVERT: d 65 GLU cc_start: 0.6517 (tm-30) cc_final: 0.6115 (tm-30) REVERT: d 153 GLU cc_start: 0.3052 (mt-10) cc_final: 0.2420 (tp30) REVERT: e 23 LYS cc_start: 0.8930 (tmtp) cc_final: 0.8611 (tttp) REVERT: e 54 GLN cc_start: 0.6885 (mt0) cc_final: 0.6679 (tp-100) REVERT: e 80 THR cc_start: 0.8041 (m) cc_final: 0.7828 (m) REVERT: e 155 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7207 (mttt) REVERT: g 27 ILE cc_start: 0.8523 (mm) cc_final: 0.8031 (mt) REVERT: g 31 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.4787 (mtm) REVERT: g 43 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8154 (tp) REVERT: g 59 MET cc_start: 0.7003 (mmt) cc_final: 0.6608 (mmt) REVERT: g 130 ASN cc_start: 0.6912 (OUTLIER) cc_final: 0.6625 (p0) REVERT: h 114 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.7823 (p) REVERT: i 7 TYR cc_start: 0.5593 (t80) cc_final: 0.5339 (t80) REVERT: i 61 TYR cc_start: 0.4849 (m-80) cc_final: 0.3059 (m-80) REVERT: j 24 LYS cc_start: 0.6872 (tppt) cc_final: 0.6607 (ttpt) REVERT: j 98 ILE cc_start: 0.6270 (OUTLIER) cc_final: 0.6051 (tt) REVERT: l 89 GLU cc_start: 0.5019 (tt0) cc_final: 0.4645 (mp0) REVERT: n 31 HIS cc_start: 0.5811 (m-70) cc_final: 0.5557 (m-70) REVERT: p 57 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.5883 (mp) REVERT: q 56 LYS cc_start: 0.3495 (pttm) cc_final: 0.3213 (pttm) REVERT: q 79 GLU cc_start: 0.6070 (mp0) cc_final: 0.5870 (mp0) REVERT: r 70 MET cc_start: 0.3259 (mmt) cc_final: 0.2919 (mmp) REVERT: s 66 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7124 (mtp) REVERT: s 69 HIS cc_start: 0.7660 (OUTLIER) cc_final: 0.6942 (m-70) REVERT: t 10 ARG cc_start: 0.5063 (tpt170) cc_final: 0.4487 (mtt-85) REVERT: t 48 LYS cc_start: 0.7850 (mttm) cc_final: 0.7340 (tttt) outliers start: 372 outliers final: 288 residues processed: 1336 average time/residue: 1.3891 time to fit residues: 3252.1541 Evaluate side-chains 1347 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1036 time to evaluate : 6.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 131 HIS Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain L residue 114 ASN Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 37 ASN Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 107 LYS Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 49 LYS Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 55 ARG Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 22 ASP Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 57 MET Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 91 VAL Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 11 SER Chi-restraints excluded: chain V residue 20 PHE Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 80 PHE Chi-restraints excluded: chain V residue 102 HIS Chi-restraints excluded: chain V residue 123 ASP Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 133 HIS Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 142 LEU Chi-restraints excluded: chain V residue 156 VAL Chi-restraints excluded: chain V residue 162 PHE Chi-restraints excluded: chain V residue 175 ASP Chi-restraints excluded: chain V residue 210 VAL Chi-restraints excluded: chain V residue 254 SER Chi-restraints excluded: chain V residue 264 GLU Chi-restraints excluded: chain V residue 276 THR Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain V residue 314 ILE Chi-restraints excluded: chain V residue 359 THR Chi-restraints excluded: chain V residue 377 ASN Chi-restraints excluded: chain V residue 379 THR Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 396 THR Chi-restraints excluded: chain V residue 438 ASP Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 80 PHE Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain Y residue 36 GLN Chi-restraints excluded: chain Y residue 38 GLU Chi-restraints excluded: chain Y residue 57 ILE Chi-restraints excluded: chain Y residue 62 ILE Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 28 THR Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 21 LYS Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 35 ASN Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 110 ASP Chi-restraints excluded: chain 8 residue 175 ILE Chi-restraints excluded: chain 8 residue 178 VAL Chi-restraints excluded: chain 8 residue 209 VAL Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 127 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 217 MET Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 177 LEU Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 114 VAL Chi-restraints excluded: chain d residue 160 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 141 LEU Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 55 PHE Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain f residue 83 ASP Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 88 HIS Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 130 ASN Chi-restraints excluded: chain h residue 32 LEU Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 118 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 61 SER Chi-restraints excluded: chain j residue 70 HIS Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 63 PHE Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 95 ARG Chi-restraints excluded: chain k residue 123 CYS Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 44 ARG Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 103 LEU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 53 LEU Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain n residue 29 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain o residue 68 THR Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain q residue 35 LEU Chi-restraints excluded: chain q residue 61 VAL Chi-restraints excluded: chain r residue 21 ASN Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 70 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 621 optimal weight: 3.9990 chunk 401 optimal weight: 0.7980 chunk 599 optimal weight: 0.0000 chunk 302 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 638 optimal weight: 6.9990 chunk 684 optimal weight: 20.0000 chunk 496 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 789 optimal weight: 20.0000 overall best weight: 3.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 40 GLN ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 HIS ** Q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 28 GLN V 216 GLN ** V 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 180 ASN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 136 GLN c 146 GLN d 50 GLN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 158918 Z= 0.233 Angle : 0.691 28.702 237379 Z= 0.353 Chirality : 0.041 2.125 30298 Planarity : 0.005 0.103 12898 Dihedral : 24.669 179.511 78639 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.95 % Favored : 90.77 % Rotamer: Outliers : 6.06 % Allowed : 24.06 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.10), residues: 5956 helix: 0.02 (0.11), residues: 1924 sheet: -1.30 (0.16), residues: 961 loop : -2.12 (0.10), residues: 3071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP b 23 HIS 0.013 0.001 HIS l 35 PHE 0.042 0.002 PHE f 26 TYR 0.027 0.002 TYR q 30 ARG 0.008 0.001 ARG i 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1390 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1085 time to evaluate : 6.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: E 144 LYS cc_start: 0.8224 (ptpt) cc_final: 0.8005 (mmtt) REVERT: F 52 SER cc_start: 0.7626 (m) cc_final: 0.6904 (p) REVERT: F 141 ILE cc_start: 0.7082 (mm) cc_final: 0.6642 (mt) REVERT: J 107 LYS cc_start: 0.8381 (mtpp) cc_final: 0.8115 (mtpp) REVERT: L 17 ASN cc_start: 0.6905 (t0) cc_final: 0.6243 (m110) REVERT: L 18 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7404 (ttp-110) REVERT: L 29 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8137 (tttp) REVERT: L 64 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7292 (ttm170) REVERT: L 71 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6277 (ttt-90) REVERT: L 81 LYS cc_start: 0.7620 (mttt) cc_final: 0.7330 (mmtt) REVERT: O 107 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7578 (tttp) REVERT: Q 97 ASP cc_start: 0.6890 (OUTLIER) cc_final: 0.6665 (t70) REVERT: Q 106 PHE cc_start: 0.7951 (t80) cc_final: 0.7433 (t80) REVERT: T 56 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8023 (mm) REVERT: U 92 ARG cc_start: 0.8444 (mtm180) cc_final: 0.8180 (mtm180) REVERT: U 101 LEU cc_start: 0.7745 (mt) cc_final: 0.7319 (mt) REVERT: V 20 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.5890 (t80) REVERT: V 93 LYS cc_start: 0.6240 (mmtt) cc_final: 0.6034 (mttt) REVERT: W 80 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: Y 24 GLU cc_start: 0.7798 (tp30) cc_final: 0.7491 (tp30) REVERT: Y 28 LEU cc_start: 0.7858 (mm) cc_final: 0.7495 (mm) REVERT: Z 17 GLU cc_start: 0.7382 (tp30) cc_final: 0.6964 (tp30) REVERT: 1 33 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8017 (mtpt) REVERT: 3 4 MET cc_start: 0.8594 (tpp) cc_final: 0.8272 (mmm) REVERT: 4 22 LYS cc_start: 0.8236 (mttt) cc_final: 0.7797 (mtpp) REVERT: b 34 GLU cc_start: 0.5006 (tt0) cc_final: 0.4621 (tp30) REVERT: b 78 ASP cc_start: 0.5518 (m-30) cc_final: 0.4222 (t0) REVERT: b 129 LEU cc_start: 0.5170 (OUTLIER) cc_final: 0.4575 (tp) REVERT: b 178 LYS cc_start: 0.6509 (tppt) cc_final: 0.6125 (tppt) REVERT: c 55 GLU cc_start: 0.6199 (mp0) cc_final: 0.5947 (mp0) REVERT: c 74 MET cc_start: 0.7665 (tpp) cc_final: 0.7283 (ttm) REVERT: d 60 MET cc_start: 0.5208 (tpt) cc_final: 0.4541 (tpt) REVERT: d 65 GLU cc_start: 0.6453 (tm-30) cc_final: 0.6053 (tm-30) REVERT: d 153 GLU cc_start: 0.3317 (mt-10) cc_final: 0.2707 (tp30) REVERT: e 80 THR cc_start: 0.8058 (m) cc_final: 0.7857 (m) REVERT: e 155 LYS cc_start: 0.7826 (mmmt) cc_final: 0.7169 (mttt) REVERT: f 10 ILE cc_start: 0.4789 (OUTLIER) cc_final: 0.4364 (tt) REVERT: g 27 ILE cc_start: 0.8280 (mm) cc_final: 0.7850 (mt) REVERT: g 31 MET cc_start: 0.6171 (OUTLIER) cc_final: 0.4437 (mtm) REVERT: g 43 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8035 (tp) REVERT: g 59 MET cc_start: 0.7021 (mmt) cc_final: 0.6734 (mmt) REVERT: g 130 ASN cc_start: 0.6802 (OUTLIER) cc_final: 0.6559 (p0) REVERT: h 10 MET cc_start: 0.7312 (ppp) cc_final: 0.7082 (ppp) REVERT: h 57 GLN cc_start: 0.5689 (OUTLIER) cc_final: 0.4961 (tp40) REVERT: i 7 TYR cc_start: 0.5587 (t80) cc_final: 0.5262 (t80) REVERT: i 61 TYR cc_start: 0.4767 (m-80) cc_final: 0.3133 (m-80) REVERT: i 110 MET cc_start: 0.7903 (mmm) cc_final: 0.7462 (mtt) REVERT: i 116 TYR cc_start: 0.6135 (p90) cc_final: 0.5914 (p90) REVERT: j 24 LYS cc_start: 0.6877 (tppt) cc_final: 0.6626 (ttpt) REVERT: j 98 ILE cc_start: 0.6043 (OUTLIER) cc_final: 0.5771 (tt) REVERT: n 31 HIS cc_start: 0.5776 (m-70) cc_final: 0.5528 (m-70) REVERT: q 56 LYS cc_start: 0.3376 (pttm) cc_final: 0.3159 (pttm) REVERT: q 79 GLU cc_start: 0.6043 (mp0) cc_final: 0.5702 (mp0) REVERT: s 56 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.6097 (pptt) REVERT: s 69 HIS cc_start: 0.7666 (OUTLIER) cc_final: 0.6539 (m-70) REVERT: t 10 ARG cc_start: 0.4931 (tpt170) cc_final: 0.4337 (mtt-85) REVERT: t 48 LYS cc_start: 0.7842 (mttm) cc_final: 0.7329 (tttt) outliers start: 305 outliers final: 239 residues processed: 1279 average time/residue: 1.3772 time to fit residues: 3100.9671 Evaluate side-chains 1295 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1036 time to evaluate : 6.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 37 ASN Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 107 LYS Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 55 ARG Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 57 MET Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 91 VAL Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 11 SER Chi-restraints excluded: chain V residue 20 PHE Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 80 PHE Chi-restraints excluded: chain V residue 102 HIS Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 133 HIS Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 142 LEU Chi-restraints excluded: chain V residue 162 PHE Chi-restraints excluded: chain V residue 175 ASP Chi-restraints excluded: chain V residue 210 VAL Chi-restraints excluded: chain V residue 254 SER Chi-restraints excluded: chain V residue 264 GLU Chi-restraints excluded: chain V residue 276 THR Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain V residue 359 THR Chi-restraints excluded: chain V residue 377 ASN Chi-restraints excluded: chain V residue 379 THR Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 396 THR Chi-restraints excluded: chain V residue 438 ASP Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 80 PHE Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain Y residue 62 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 28 THR Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 21 LYS Chi-restraints excluded: chain 1 residue 33 LYS Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 6 residue 2 LYS Chi-restraints excluded: chain 8 residue 110 ASP Chi-restraints excluded: chain 8 residue 175 ILE Chi-restraints excluded: chain 8 residue 209 VAL Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 127 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 140 GLU Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 177 LEU Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 63 VAL Chi-restraints excluded: chain d residue 114 VAL Chi-restraints excluded: chain d residue 160 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 141 LEU Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 55 PHE Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 88 HIS Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain g residue 130 ASN Chi-restraints excluded: chain g residue 138 ARG Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 93 GLU Chi-restraints excluded: chain i residue 111 LYS Chi-restraints excluded: chain i residue 118 LEU Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 70 HIS Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 63 PHE Chi-restraints excluded: chain k residue 95 ARG Chi-restraints excluded: chain k residue 123 CYS Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 38 VAL Chi-restraints excluded: chain l residue 44 ARG Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain n residue 29 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain o residue 68 THR Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 35 LEU Chi-restraints excluded: chain q residue 61 VAL Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 56 LYS Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 70 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 913 optimal weight: 0.9990 chunk 962 optimal weight: 0.0020 chunk 877 optimal weight: 7.9990 chunk 935 optimal weight: 1.9990 chunk 961 optimal weight: 6.9990 chunk 563 optimal weight: 4.9990 chunk 407 optimal weight: 2.9990 chunk 734 optimal weight: 20.0000 chunk 287 optimal weight: 10.0000 chunk 845 optimal weight: 0.2980 chunk 885 optimal weight: 9.9990 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 ASN ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 326 ASN ** V 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 444 GLN ** V 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** 0 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 60 GLN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 146 GLN d 50 GLN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 40 GLN ** g 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 35 HIS ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 54 GLN ** t 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 158918 Z= 0.154 Angle : 0.625 28.577 237379 Z= 0.318 Chirality : 0.037 2.096 30298 Planarity : 0.005 0.104 12898 Dihedral : 24.484 179.739 78639 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.68 % Favored : 91.07 % Rotamer: Outliers : 4.55 % Allowed : 25.69 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.11), residues: 5956 helix: 0.36 (0.12), residues: 1918 sheet: -1.05 (0.16), residues: 997 loop : -2.02 (0.11), residues: 3041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 200 HIS 0.009 0.001 HIS q 49 PHE 0.038 0.002 PHE f 26 TYR 0.028 0.002 TYR q 30 ARG 0.011 0.001 ARG V 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1357 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1128 time to evaluate : 6.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 ARG cc_start: 0.8785 (mpp80) cc_final: 0.8318 (mtp-110) REVERT: E 144 LYS cc_start: 0.7972 (ptpt) cc_final: 0.7708 (mmtt) REVERT: F 106 VAL cc_start: 0.8233 (t) cc_final: 0.8000 (m) REVERT: F 125 ARG cc_start: 0.7196 (mmm-85) cc_final: 0.6618 (mmt-90) REVERT: F 134 GLU cc_start: 0.7927 (tp30) cc_final: 0.7562 (tt0) REVERT: F 141 ILE cc_start: 0.7075 (mm) cc_final: 0.6813 (mt) REVERT: G 28 LYS cc_start: 0.5661 (mttt) cc_final: 0.5031 (tttm) REVERT: L 81 LYS cc_start: 0.7313 (mttt) cc_final: 0.7093 (mttm) REVERT: N 33 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8544 (m) REVERT: N 102 MET cc_start: 0.8001 (mtp) cc_final: 0.7744 (mtp) REVERT: N 114 MET cc_start: 0.8471 (mmm) cc_final: 0.7624 (mmm) REVERT: O 107 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7457 (tttp) REVERT: Q 55 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8299 (mtm180) REVERT: Q 71 MET cc_start: 0.8168 (mmm) cc_final: 0.7965 (mtt) REVERT: Q 85 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6699 (tt) REVERT: Q 106 PHE cc_start: 0.7850 (t80) cc_final: 0.7532 (t80) REVERT: Q 116 GLN cc_start: 0.8233 (tp40) cc_final: 0.7576 (tm-30) REVERT: S 59 GLU cc_start: 0.6868 (mm-30) cc_final: 0.5991 (mp0) REVERT: S 64 MET cc_start: 0.8346 (mtm) cc_final: 0.7792 (mtt) REVERT: T 56 ILE cc_start: 0.8230 (mt) cc_final: 0.7875 (mm) REVERT: T 60 LYS cc_start: 0.7327 (mtpp) cc_final: 0.7026 (mtpp) REVERT: U 43 LYS cc_start: 0.7546 (tttt) cc_final: 0.7086 (ptmm) REVERT: U 101 LEU cc_start: 0.7652 (mt) cc_final: 0.7386 (mp) REVERT: V 20 PHE cc_start: 0.6219 (OUTLIER) cc_final: 0.5843 (t80) REVERT: V 253 LYS cc_start: 0.8375 (mmtt) cc_final: 0.8143 (mttm) REVERT: V 396 THR cc_start: 0.5812 (OUTLIER) cc_final: 0.5489 (m) REVERT: V 407 MET cc_start: 0.6446 (ttm) cc_final: 0.6244 (mtp) REVERT: Y 24 GLU cc_start: 0.7375 (tp30) cc_final: 0.7145 (tp30) REVERT: Y 28 LEU cc_start: 0.7561 (mm) cc_final: 0.7126 (mm) REVERT: Y 52 ARG cc_start: 0.8182 (ptp90) cc_final: 0.7879 (ptp-170) REVERT: Z 17 GLU cc_start: 0.7092 (tp30) cc_final: 0.6788 (tp30) REVERT: 3 4 MET cc_start: 0.8561 (tpp) cc_final: 0.8206 (mmm) REVERT: 4 22 LYS cc_start: 0.8209 (mttt) cc_final: 0.7759 (mtpp) REVERT: 8 198 LYS cc_start: 0.3161 (pptt) cc_final: 0.2345 (tptt) REVERT: b 34 GLU cc_start: 0.5092 (tt0) cc_final: 0.4554 (tp30) REVERT: b 78 ASP cc_start: 0.5622 (m-30) cc_final: 0.4198 (t0) REVERT: b 178 LYS cc_start: 0.6308 (tppt) cc_final: 0.6048 (tppt) REVERT: c 18 TRP cc_start: 0.8071 (m-90) cc_final: 0.7290 (m-90) REVERT: c 26 LYS cc_start: 0.6921 (mttt) cc_final: 0.6455 (mmmt) REVERT: c 74 MET cc_start: 0.7603 (tpp) cc_final: 0.7208 (ttm) REVERT: d 60 MET cc_start: 0.5374 (tpt) cc_final: 0.4626 (tpt) REVERT: d 153 GLU cc_start: 0.2939 (mt-10) cc_final: 0.2438 (tp30) REVERT: e 76 MET cc_start: 0.6310 (mmm) cc_final: 0.6091 (mmm) REVERT: e 80 THR cc_start: 0.8099 (m) cc_final: 0.7884 (m) REVERT: e 151 GLU cc_start: 0.6772 (pm20) cc_final: 0.5859 (tp30) REVERT: e 155 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7168 (mttt) REVERT: g 27 ILE cc_start: 0.8014 (mm) cc_final: 0.7546 (mt) REVERT: g 31 MET cc_start: 0.5699 (OUTLIER) cc_final: 0.4259 (mtm) REVERT: g 43 LEU cc_start: 0.8206 (tt) cc_final: 0.7704 (tp) REVERT: g 66 LEU cc_start: 0.8232 (tp) cc_final: 0.7965 (tp) REVERT: g 78 ARG cc_start: 0.5537 (mmt90) cc_final: 0.5001 (mmt180) REVERT: h 35 GLU cc_start: 0.6354 (tp30) cc_final: 0.5634 (tp30) REVERT: h 57 GLN cc_start: 0.5963 (OUTLIER) cc_final: 0.5490 (tp40) REVERT: i 100 ARG cc_start: 0.5716 (OUTLIER) cc_final: 0.5188 (ttt90) REVERT: i 110 MET cc_start: 0.7957 (mmm) cc_final: 0.7542 (mtt) REVERT: i 116 TYR cc_start: 0.5894 (p90) cc_final: 0.5680 (p90) REVERT: j 24 LYS cc_start: 0.6919 (tppt) cc_final: 0.6709 (ttpt) REVERT: j 60 ASP cc_start: 0.8114 (m-30) cc_final: 0.7839 (m-30) REVERT: j 72 ARG cc_start: 0.6332 (mtt90) cc_final: 0.5849 (mtt90) REVERT: j 98 ILE cc_start: 0.5889 (OUTLIER) cc_final: 0.5624 (tt) REVERT: m 53 LEU cc_start: 0.8553 (tp) cc_final: 0.8268 (pp) REVERT: n 31 HIS cc_start: 0.5665 (m-70) cc_final: 0.5410 (m-70) REVERT: q 79 GLU cc_start: 0.6187 (mp0) cc_final: 0.5811 (mp0) REVERT: t 48 LYS cc_start: 0.7866 (mttm) cc_final: 0.7335 (tttt) REVERT: t 82 LYS cc_start: 0.6893 (mmtm) cc_final: 0.5686 (ptmt) outliers start: 229 outliers final: 158 residues processed: 1263 average time/residue: 1.2841 time to fit residues: 2818.3999 Evaluate side-chains 1209 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1040 time to evaluate : 6.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 37 ASN Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 107 LYS Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain Q residue 55 ARG Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 57 MET Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 67 ASN Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 20 PHE Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 102 HIS Chi-restraints excluded: chain V residue 133 HIS Chi-restraints excluded: chain V residue 175 ASP Chi-restraints excluded: chain V residue 276 THR Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain V residue 377 ASN Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 396 THR Chi-restraints excluded: chain V residue 438 ASP Chi-restraints excluded: chain V residue 450 SER Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain Y residue 62 ILE Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 28 THR Chi-restraints excluded: chain 1 residue 21 LYS Chi-restraints excluded: chain 3 residue 60 GLN Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 6 residue 2 LYS Chi-restraints excluded: chain 8 residue 209 VAL Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 127 ASP Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 217 MET Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 160 PHE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 55 PHE Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 88 HIS Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain g residue 138 ARG Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 100 ARG Chi-restraints excluded: chain j residue 70 HIS Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 63 PHE Chi-restraints excluded: chain k residue 95 ARG Chi-restraints excluded: chain k residue 123 CYS Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 38 VAL Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain n residue 29 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 35 LEU Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 70 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 932 optimal weight: 8.9990 chunk 614 optimal weight: 0.7980 chunk 989 optimal weight: 10.0000 chunk 604 optimal weight: 5.9990 chunk 469 optimal weight: 0.0270 chunk 687 optimal weight: 20.0000 chunk 1038 optimal weight: 10.0000 chunk 955 optimal weight: 9.9990 chunk 826 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 638 optimal weight: 0.2980 overall best weight: 3.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN L 106 ASN M 28 HIS ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 216 GLN V 326 ASN ** V 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 136 GLN d 50 GLN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 54 GLN ** t 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 158918 Z= 0.233 Angle : 0.671 28.433 237379 Z= 0.340 Chirality : 0.040 2.111 30298 Planarity : 0.005 0.101 12898 Dihedral : 24.457 179.451 78639 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.27 % Favored : 90.46 % Rotamer: Outliers : 3.95 % Allowed : 26.66 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.11), residues: 5956 helix: 0.33 (0.12), residues: 1923 sheet: -1.10 (0.16), residues: 1005 loop : -2.02 (0.11), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 23 HIS 0.012 0.001 HIS 3 7 PHE 0.042 0.002 PHE g 47 TYR 0.025 0.002 TYR q 30 ARG 0.016 0.001 ARG r 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11912 Ramachandran restraints generated. 5956 Oldfield, 0 Emsley, 5956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1058 time to evaluate : 6.457 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: E 144 LYS cc_start: 0.8128 (ptpt) cc_final: 0.7830 (mmtm) REVERT: F 141 ILE cc_start: 0.6914 (mm) cc_final: 0.6658 (mt) REVERT: G 28 LYS cc_start: 0.5679 (mttt) cc_final: 0.5081 (tttm) REVERT: G 42 MET cc_start: 0.4345 (ttm) cc_final: 0.4007 (ttp) REVERT: L 64 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7309 (ttm170) REVERT: L 81 LYS cc_start: 0.7396 (mttt) cc_final: 0.7149 (mttm) REVERT: N 102 MET cc_start: 0.8065 (mtp) cc_final: 0.7853 (mtp) REVERT: N 114 MET cc_start: 0.8527 (mmm) cc_final: 0.7686 (mmm) REVERT: O 107 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7659 (tttp) REVERT: Q 106 PHE cc_start: 0.7922 (t80) cc_final: 0.7606 (t80) REVERT: T 56 ILE cc_start: 0.8291 (mt) cc_final: 0.7921 (mm) REVERT: U 101 LEU cc_start: 0.7784 (mt) cc_final: 0.7510 (mp) REVERT: V 20 PHE cc_start: 0.6342 (OUTLIER) cc_final: 0.5824 (t80) REVERT: Y 24 GLU cc_start: 0.7568 (tp30) cc_final: 0.7207 (tp30) REVERT: Y 28 LEU cc_start: 0.7691 (mm) cc_final: 0.7205 (mm) REVERT: Z 17 GLU cc_start: 0.7140 (tp30) cc_final: 0.6818 (tp30) REVERT: 3 4 MET cc_start: 0.8384 (tpp) cc_final: 0.8003 (mmm) REVERT: 4 22 LYS cc_start: 0.8232 (mttt) cc_final: 0.7782 (mtpp) REVERT: 8 120 MET cc_start: 0.0273 (mtt) cc_final: -0.0554 (ptp) REVERT: 8 198 LYS cc_start: 0.3010 (pptt) cc_final: 0.2099 (tptt) REVERT: b 34 GLU cc_start: 0.5422 (tt0) cc_final: 0.4782 (tp30) REVERT: b 78 ASP cc_start: 0.5504 (m-30) cc_final: 0.4253 (t0) REVERT: c 18 TRP cc_start: 0.8185 (m-90) cc_final: 0.7381 (m-90) REVERT: c 26 LYS cc_start: 0.6759 (mttt) cc_final: 0.6223 (mmmt) REVERT: c 74 MET cc_start: 0.7609 (tpp) cc_final: 0.7190 (ttm) REVERT: d 60 MET cc_start: 0.5521 (tpt) cc_final: 0.4753 (tpt) REVERT: d 87 MET cc_start: 0.7361 (mtm) cc_final: 0.7094 (mtm) REVERT: d 146 ARG cc_start: 0.5736 (tpt170) cc_final: 0.5482 (tpt90) REVERT: d 153 GLU cc_start: 0.2767 (mt-10) cc_final: 0.2307 (tp30) REVERT: e 151 GLU cc_start: 0.6802 (pm20) cc_final: 0.6082 (tp30) REVERT: e 155 LYS cc_start: 0.7822 (mmmt) cc_final: 0.7347 (tmtt) REVERT: g 27 ILE cc_start: 0.8120 (mm) cc_final: 0.7636 (mt) REVERT: g 31 MET cc_start: 0.5867 (OUTLIER) cc_final: 0.4389 (mtm) REVERT: h 57 GLN cc_start: 0.5995 (OUTLIER) cc_final: 0.5474 (tp40) REVERT: i 7 TYR cc_start: 0.5722 (t80) cc_final: 0.5521 (t80) REVERT: i 110 MET cc_start: 0.7905 (mmm) cc_final: 0.7471 (mtt) REVERT: i 116 TYR cc_start: 0.6039 (p90) cc_final: 0.5644 (p90) REVERT: j 10 LEU cc_start: 0.6253 (mt) cc_final: 0.5287 (mp) REVERT: j 24 LYS cc_start: 0.6930 (tppt) cc_final: 0.6693 (ttpt) REVERT: j 72 ARG cc_start: 0.6395 (mtt90) cc_final: 0.6035 (mtt90) REVERT: j 98 ILE cc_start: 0.5724 (OUTLIER) cc_final: 0.5448 (tt) REVERT: l 89 GLU cc_start: 0.4970 (tt0) cc_final: 0.4618 (mp0) REVERT: n 31 HIS cc_start: 0.5685 (m-70) cc_final: 0.5445 (m-70) REVERT: p 14 LYS cc_start: 0.6098 (mmtp) cc_final: 0.5741 (mmmt) REVERT: p 57 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.5892 (mp) REVERT: q 79 GLU cc_start: 0.6142 (mp0) cc_final: 0.5737 (mp0) REVERT: t 48 LYS cc_start: 0.7891 (mttm) cc_final: 0.7357 (tttt) outliers start: 199 outliers final: 172 residues processed: 1186 average time/residue: 1.3030 time to fit residues: 2694.9473 Evaluate side-chains 1213 residues out of total 5034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1034 time to evaluate : 6.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 37 ASN Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 107 LYS Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain Q residue 55 ARG Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 57 MET Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 20 PHE Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 102 HIS Chi-restraints excluded: chain V residue 133 HIS Chi-restraints excluded: chain V residue 162 PHE Chi-restraints excluded: chain V residue 175 ASP Chi-restraints excluded: chain V residue 216 GLN Chi-restraints excluded: chain V residue 254 SER Chi-restraints excluded: chain V residue 276 THR Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain V residue 326 ASN Chi-restraints excluded: chain V residue 359 THR Chi-restraints excluded: chain V residue 365 LEU Chi-restraints excluded: chain V residue 377 ASN Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 396 THR Chi-restraints excluded: chain V residue 438 ASP Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain Y residue 38 GLU Chi-restraints excluded: chain Y residue 62 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 28 THR Chi-restraints excluded: chain 1 residue 21 LYS Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 8 residue 209 VAL Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain b residue 127 ASP Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 63 VAL Chi-restraints excluded: chain d residue 160 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain f residue 55 PHE Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 88 HIS Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain g residue 138 ARG Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 70 HIS Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 63 PHE Chi-restraints excluded: chain k residue 95 ARG Chi-restraints excluded: chain k residue 123 CYS Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 38 VAL Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain n residue 29 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain q residue 35 LEU Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 70 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 506 optimal weight: 2.9990 chunk 656 optimal weight: 0.7980 chunk 880 optimal weight: 0.9980 chunk 253 optimal weight: 10.0000 chunk 762 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 chunk 827 optimal weight: 5.9990 chunk 346 optimal weight: 8.9990 chunk 850 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN N 12 GLN ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 60 GLN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 ASN ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.154096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.126536 restraints weight = 300271.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128484 restraints weight = 105931.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.129606 restraints weight = 57777.390| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 158918 Z= 0.229 Angle : 0.670 28.577 237379 Z= 0.340 Chirality : 0.040 2.112 30298 Planarity : 0.005 0.101 12898 Dihedral : 24.474 178.096 78639 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.54 % Favored : 90.23 % Rotamer: Outliers : 3.99 % Allowed : 26.66 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.11), residues: 5956 helix: 0.32 (0.12), residues: 1926 sheet: -1.05 (0.16), residues: 982 loop : -2.03 (0.11), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 23 HIS 0.010 0.001 HIS G 39 PHE 0.051 0.002 PHE g 47 TYR 0.026 0.002 TYR q 30 ARG 0.014 0.001 ARG V 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42046.86 seconds wall clock time: 734 minutes 22.60 seconds (44062.60 seconds total)